;; Bioinformatics module
(define-module (gn packages bioinformatics)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix utils)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix hg-download)
#:use-module (guix build-system ant)
#:use-module (guix build-system cargo)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (guix build-system meson)
#:use-module (guix build-system perl)
#:use-module (guix build-system python)
#:use-module (guix build-system trivial)
#:use-module (guix build-system waf)
#:use-module (gnu packages)
#:use-module (gn packages crates-io)
#:use-module (gn packages databases)
#:use-module (gn packages java)
#:use-module (gn packages perl)
#:use-module (gn packages python)
#:use-module (gn packages twint)
#:use-module (gnu packages algebra)
#:use-module (gnu packages autotools)
#:use-module (gnu packages base)
#:use-module (gnu packages bash)
#:use-module (gnu packages bioconductor)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages cmake)
#:use-module (gnu packages compression)
#:use-module (gnu packages cran)
#:use-module (gnu packages crates-io)
#:use-module (gnu packages curl)
#:use-module (gnu packages databases)
#:use-module (gnu packages datastructures)
#:use-module (gnu packages elf)
#:use-module (gnu packages fontutils)
#:use-module (gnu packages gcc)
#:use-module (gnu packages ghostscript)
#:use-module (gnu packages gtk)
#:use-module (gnu packages guile)
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages java)
#:use-module (gnu packages jemalloc)
#:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages python-science)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages rdf)
#:use-module (gnu packages readline)
#:use-module (gnu packages rsync)
#:use-module (gnu packages ruby)
#:use-module (gnu packages rust)
#:use-module (gnu packages serialization)
#:use-module (gnu packages shells)
#:use-module (gnu packages statistics)
#:use-module (gnu packages sqlite)
#:use-module (gnu packages tcl)
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
#:use-module (gnu packages vim)
#:use-module (gnu packages web))
(define-public contra
(package
(name "contra")
(version "2.0.6")
(source (origin
(method url-fetch)
(uri (string-append
"mirror://sourceforge/contra-cnv/CONTRA.V"
(version-major+minor version) "/CONTRA.v" version ".tar.gz"))
(sha256
(base32
"0agpcm2xh5f0i9n9sx1kvln6mzdksddmh11bvzj6bh76yw5pnw91"))
(modules '((guix build utils)))
(snippet
'(begin
(delete-file "BEDTools.v2.11.2.tar.gz") #t))))
(build-system gnu-build-system)
(propagated-inputs
`(("python" ,python-2)
("r" ,r)
;; ("r-dnacopy" ,r-dnacopy) <-- missing in Pjotr's tree
("bedtools" ,bedtools)
("samtools" ,samtools)))
(arguments
`(#:tests? #f ; There are no tests.
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build) ; We can use Guix's BEDtools instead.
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(doc (string-append out "/share/doc/contra")))
(copy-recursively "scripts" (string-append bin "/scripts"))
(install-file "contra.py" bin)
(install-file "baseline.py" bin)
;; There's only a pre-built PDF available.
(install-file "CONTRA_User_Guide.2.0.pdf" doc))
#t)))))
(home-page "http://contra-cnv.sourceforge.net/")
(synopsis "Tool for copy number variation (CNV) detection for targeted
resequencing data")
(description "CONTRA is a tool for copy number variation (CNV) detection
for targeted resequencing data such as those from whole-exome capture data.
CONTRA calls copy number gains and losses for each target region with key
strategies including the use of base-level log-ratios to remove GC-content
bias, correction for an imbalanced library size effect on log-ratios, and the
estimation of log-ratio variations via binning and interpolation. It takes
standard alignment formats (BAM/SAM) and outputs in variant call format
(VCF 4.0) for easy integration with other next generation sequencing analysis
package.")
(license license:gpl3+)))
(define boost-delly
(package (inherit boost)
(name "boost-delly")
(version "1.57.0")
(source (origin
(method url-fetch)
(uri (string-append
"mirror://sourceforge/boost/boost_"
(string-map (lambda (x) (if (eq? x #\.) #\_ x)) version)
".tar.bz2"))
(sha256
(base32
"0rs94vdmg34bwwj23fllva6mhrml2i7mvmlb11zyrk1k5818q34i"))))))
(define-public delly
(package
(name "delly")
(version "0.7.2")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/tobiasrausch/delly/archive/v"
version ".tar.gz"))
(sha256
(base32 "173mmg43dbxqkyq0kiffz63xbmggr2kzd55mwxci9yfh5md1zprn"))
(patches (list (search-patch "delly-use-system-libraries.patch")))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)))
(inputs
`(("boost" ,boost-delly) ; Use version 1.57.0 instead.
("htslib" ,htslib)
("zlib" ,zlib)
("bzip2" ,bzip2)))
(arguments
`(#:tests? #f ; There are no tests to run.
#:phases
(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase.
(replace 'install
(lambda _
(let ((bin (string-append (assoc-ref %outputs "out") "/bin")))
(install-file "src/cov" bin)
(install-file "src/delly" bin)
(install-file "src/extract" bin)
(install-file "src/iover" bin)
(install-file "src/stats" bin)))))))
(home-page "https://github.com/tobiasrausch/delly")
(synopsis "Integrated structural variant prediction method")
(description "Delly is an integrated structural variant prediction method
that can discover and genotype deletions, tandem duplications, inversions and
translocations at single-nucleotide resolution in short-read massively parallel
sequencing data. It uses paired-ends and split-reads to sensitively and
accurately delineate genomic rearrangements throughout the genome. Structural
variants can be visualized using Delly-maze and Delly-suave.")
(license license:gpl3)))
(define-public freec
(package
(name "control-freec")
(version "8.7")
(source (origin
(method url-fetch)
(uri "http://bioinfo-out.curie.fr/projects/freec/src/FREEC_Linux64.tar.gz")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "12sl7gxbklhvv0687qjhml1z4lwpcn159zcyxvawvclsrzqjmv0h"))))
(build-system gnu-build-system)
;; The source code's filename indicates only a 64-bit Linux build.
;; We need to investigate whether this is true.
(supported-systems '("x86_64-linux"))
(arguments
`(#:phases
(modify-phases %standard-phases
;; There's no configure phase because there are no external
;; dependencies.
(delete 'configure)
;; There are no tests.
(delete 'check)
(replace
'unpack
(lambda* (#:key source #:allow-other-keys)
(and
(zero? (system* "mkdir" "source"))
(with-directory-excursion "source"
(zero? (system* "tar" "xvf" source))))))
(replace
'build
(lambda* (#:key inputs #:allow-other-keys)
(with-directory-excursion "source"
(zero? (system* "make")))))
(replace
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "source/freec" bin)))))))
(home-page "http://bioinfo-out.curie.fr/projects/freec/")
(synopsis "Tool for detection of copy-number changes and allelic imbalances
(including LOH) using deep-sequencing data")
(description "Control-FREEC automatically computes, normalizes, segments
copy number and beta allele frequency (BAF) profiles, then calls copy number
alterations and LOH. The control (matched normal) sample is optional for whole
genome sequencing data but mandatory for whole exome or targeted sequencing
data. For whole genome sequencing data analysis, the program can also use
mappability data (files created by GEM). ")
(license license:gpl2+)))
(define-public plink2
(package
(name "plink2")
(version "1.90b3")
(source
(origin
(method url-fetch)
;; https://github.com/chrchang/plink-ng/archive/v1.90b3.tar.gz
(uri (string-append
"https://github.com/chrchang/plink-ng/archive/v"
version ".tar.gz"))
(sha256
(base32 "03fzib1al5qkr9vxv63wxmv6y2pfb1rmir0h8jpi72r87hczqjig"))
(patches (list (search-patch "plink-ng-Makefile-zlib.patch")))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'build
(lambda _
(zero? (system* "make" "-f" "Makefile.std"))
))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out")
"/bin/")))
(install-file "plink2" bin)
#t))))))
(inputs
`(("zlib" ,zlib)
("openblas" ,openblas)
;; ("atlas" ,atlas)
;; ("lapack" ,lapack)
("gfortran" ,gfortran)
))
(native-inputs
`(("unzip" ,unzip)))
(home-page "https://www.cog-genomics.org/plink2")
(synopsis "Whole genome association analysis toolset")
(description
"PLINK is a whole genome association analysis toolset, designed to
perform a range of basic, large-scale analyses in a computationally efficient
manner. The focus of PLINK is purely on analysis of genotype/phenotype data,
so there is no support for steps prior to this (e.g. study design and
planning, generating genotype or CNV calls from raw data). Through
integration with gPLINK and Haploview, there is some support for the
subsequent visualization, annotation and storage of results.")
;; Code is released under GPLv2, except for fisher.h, which is under
;; LGPLv2.1+
(license (list license:gpl2 license:lgpl2.1+))))
(define-public plink-ng-gn
(let ((commit "5d1db4313ba0cc976562da233db4aced78975d10"))
(package
(name "plink-ng-gn")
(version (string-append "1.90b3-" commit )) ; Aug 11, 2016
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/genenetwork/plink-ng.git")
(commit commit)))
(file-name (string-append name "-" commit))
(sha256
(base32
"1366li3ks9076bblvd1rpzkjq4j8f8f08lhga4c1ckrkil3xww4m"))))
;; no longer (patches (list (search-patch "plink-ng-Makefile-zlib-git.patch")))))
(inputs
`(("zlib" ,zlib)
("openblas" ,openblas)
;; ("atlas" ,atlas) ; openblas replaces atlas
("lapack" ,lapack) ; lapack is disabled in GUIX openblas
;; ("gfortran" ,gfortran)
;; ("python" ,python-2) ;; for tests - currently disabled
))
(native-inputs
`(("unzip" ,unzip)))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target. Some of the python-based tests fail
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'build
(lambda _
(zero? (system* "make" "-f" "Makefile.guix"))
))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out")
"/bin/")))
(install-file "plink2" bin)
#t))))))
(home-page "https://www.cog-genomics.org/plink2")
(synopsis "Whole genome association analysis toolset")
(description
"PLINK is a whole genome association analysis toolset, designed to
perform a range of basic, large-scale analyses in a computationally efficient
manner. The focus of PLINK is purely on analysis of genotype/phenotype data,
so there is no support for steps prior to this (e.g. study design and
planning, generating genotype or CNV calls from raw data). Through
integration with gPLINK and Haploview, there is some support for the
subsequent visualization, annotation and storage of results.")
(license license:gpl3+))))
(define-public pindel
(package
(name "pindel")
(version "0.2.5b8")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/genome/pindel.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "16a32fbgv1n58nfcxa1nyphrdrad80sgpinfa9p028n6plwycpww"))))
(build-system gnu-build-system)
(inputs
`(("samtools" ,samtools)
("htslib" ,htslib)
("zlib" ,zlib)))
(native-inputs
`(("cppcheck" ,cppcheck)
("python" ,python-2)
("perl" ,perl)))
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase.
;; The build phase needs to run 'make' twice for the reasons described
;; below.
(replace 'build
(lambda* (#:key inputs #:allow-other-keys)
;; The first run creates a Makefile.local file. Make will report
;; the failure to find Makefile.local, but we can ignore this error.
(system* "make" (string-append "SAMTOOLS=" (assoc-ref inputs "samtools")))
;; The second run actually compiles the program. Now Makefile.local
;; is available, and we should treat an exiting make with an error as
;; a true error.
(invoke "make")))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "src/pindel" bin)
(install-file "src/pindel2vcf" bin)
(install-file "src/pindel2vcf4tcga" bin)
(install-file "src/sam2pindel" bin))))
;; There are multiple test targets, so in order to run all
;; tests, we must run the separate make targets.
(replace 'check
(lambda _
(for-each (lambda (target)
(invoke "make" target))
'("acceptance-tests" "coverage-tests" "cppcheck"
"functional-tests" "regression-tests")))))))
(home-page "https://github.com/genome/pindel")
(synopsis "Structural variants detector for next-gen sequencing data")
(description "Pindel can detect breakpoints of large deletions, medium sized
insertions, inversions, tandem duplications and other structural variants at
single-based resolution from next-gen sequence data. It uses a pattern growth
approach to identify the breakpoints of these variants from paired-end short
reads.")
(license license:gpl3+)))
(define-public varscan
(package
(name "varscan")
(version "2.4.1")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/dkoboldt/varscan/releases/download/v"
version "/VarScan.v" version ".source.jar"))
(sha256
(base32 "0y45ympkza7qwcbcisg006286pwjbr5978n03hx5nvl09f0mapk8"))))
(build-system ant-build-system)
(arguments
`(#:tests? #f ; build.xml does not exist
#:phases
(modify-phases %standard-phases
(replace 'unpack
(lambda _
(mkdir "source")
(chdir "source")
;; Unpack the Java archive containing the source files.
(invoke "jar" "xf" (assoc-ref %build-inputs "source"))
;; Remove existing compiled output.
(with-directory-excursion "net/sf/varscan/"
(for-each (lambda (file)
(delete-file file))
(find-files "." "^.java$" #:directories? #f)))
#t))
(replace 'build
(lambda _
;; Compile the source files.
(with-directory-excursion "net/sf/varscan/"
(for-each (lambda (file)
(invoke "javac" file))
(find-files "." ".java$" #:directories? #f)))
;; Construct the new Java archive.
(apply invoke "jar" "cfm"
(string-append "varscan-" ,version ".jar")
"META-INF/MANIFEST.MF"
(find-files "net/sf/varscan" ".java$"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (string-append (assoc-ref outputs "out")
"/share/java/varscan/")))
(install-file (string-append "varscan-" ,version ".jar") out))
#t)))))
(home-page "https://dkoboldt.github.io/varscan/")
(synopsis "Variant detection in massively parallel sequencing data")
(description "Variant detection in massively parallel sequencing data.")
;; Free for non-commercial use by academic, government, and
;; non-profit/not-for-profit institutions
(license license:non-copyleft)))
(define-public edirect-gn
(deprecated-package "edirect-gn" edirect))
(define-public gfaffix
(package
(name "gfaffix")
(version "0.1.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/marschall-lab/GFAffix")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0xpzi0zvaa4pajs4vbp3vkwj2ha8pi62ly7bd8cpf3fi6r32pgdz"))
(modules '((guix build utils)))
(snippet
'(begin
(substitute* "Cargo.toml"
(("^handlegraph.*") "handlegraph = \"0.7\"\n"))))))
(build-system cargo-build-system)
(arguments
`(#:rust ,(if (> (string->number (version-major+minor (package-version rust-1.49)))
(string->number (version-major+minor (package-version rust))))
rust-1.49
rust)
#:cargo-inputs
(("rust-clap" ,rust-clap-3)
("rust-rustc-hash" ,rust-rustc-hash-1)
("rust-regex" ,rust-regex-1)
("rust-handlegraph" ,rust-handlegraph-0.7)
("rust-gfa" ,rust-gfa-0.10)
("rust-quick-csv", rust-quick-csv-0.1)
("rust-log" ,rust-log-0.4)
("rust-env-logger" ,rust-env-logger-0.7))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'adjust-dependency-version
(lambda* (#:key inputs #:allow-other-keys)
(let ((handlebar-version ,(package-version rust-handlegraph-0.7)))
(substitute* "Cargo.toml"
(("\"0.7\"")
(string-append "{ version = \"" handlebar-version "\" }")))
#t))))))
(home-page "https://github.com/marschall-lab/GFAffix")
(synopsis "Identify walk-preserving shared affixes in variation graphs")
(description
"GFAffix identifies walk-preserving shared affixes in variation graphs and
collapses them into a non-redundant graph structure.")
(license license:expat)))
(define-public pangenie
(let ((commit "e779076827022d1416ab9fabf99a03d8f4725956") ; September 2, 2021 from phasing-tests branch
(revision "2"))
(package
(name "pangenie")
(version (git-version "0.0.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://bitbucket.org/jana_ebler/pangenie.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1mphrvidaz328kcwrjgz8q5i4iwnz6ygl6279lm2acv4zgqhmp5i"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags (list (string-append "-DCMAKE_BUILD_RPATH="
(assoc-ref %outputs "out") "/lib"))
#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "make" "-C" "tests"))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(with-directory-excursion "src"
(install-file "PanGenie" (string-append out "/bin"))
(install-file "PanGenie-graph" (string-append out "/bin"))
(install-file "libPanGenieLib.so" (string-append out "/lib"))
)
#t))))))
(native-inputs
`(("pkg-config" ,pkg-config)))
(inputs
`(("jellyfish" ,jellyfish)))
(home-page "https://bitbucket.org/jana_ebler")
(synopsis "Genotyping based on k-mers and pangenome graphs")
(description
"This package provides a genotyper for various types of genetic variants
(such as SNPs, indels and structural variants). Genotypes are computed based on
read k-mer counts and a panel of known haplotypes. A description of the method
can be found @url{https://www.biorxiv.org/content/10.1101/2020.11.11.378133v1,
here}.")
(license license:expat))))
(define-public pbsim2
(let ((commit "e71f7892aea0bd3c963b4f1f5628db4f830ee475") ; Dec 2, 2020
(revision "1"))
(package
(name "pbsim2")
(version (git-version "0.0.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/yukiteruono/pbsim2")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "13d3mhdp3rs58w14j9a5sbda4q8k9vzic7rgfa8223m7cm5ih6y7"))))
(build-system gnu-build-system)
(home-page "https://github.com/yukiteruono/pbsim2")
(synopsis "Simulator for long read sequencers")
(description "PBSIM simulates @acronym{Continuous Long Reads, CLRs} of
PacBio, and Nanopore reads. In it sampling-based and model-based simulations
are implemented.")
(license license:gpl2))))
(define-public pirs
(let ((commit "bee9b594f4d0e10580aae77ec411cecec4a77219") ; Sept 7, 2017
(revision "1"))
(package
(name "pirs")
(version (git-version "2.0.2" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/galaxy001/pirs")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0pn74h98cqcr5qayp4riss982n4272p35y5dp472cmqpwjjil9cd"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags (list "--enable-pirs-diploid"
;; TODO: Enable after core-updates merge, late 2021.
;,@(if (not (or (target-x86-64?)
; (target-x86-32?)))
; `("--disable-sse2")
; '())
)
#:phases
(modify-phases %standard-phases
(add-before 'bootstrap 'chdir
(lambda _
(chdir "src")))
(add-after 'unpack 'patch-source
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(substitute* "src/configure.ac"
(("ssse2") "sse2"))
(substitute* "src/stator/gcContCvgBias/Makefile"
(("gzstream.o ") "")
(("-lz")"-lgzstream -lz")
(("-static") "")
(("-mtune=generic") ""))
(substitute* "src/pirs/gccMakefile"
(("/usr/local") out)))))
(replace 'check
(lambda* (#:key tests? test-target #:allow-other-keys #:rest args)
(when tests?
(apply (assoc-ref %standard-phases 'check) args)
(with-directory-excursion "stator/gcContCvgBias"
; ((assoc-ref %standard-phases 'check)
; #:test-target "test" args))
(invoke "make" "test")))))
(add-after 'build 'build-more
(lambda* (#:key #:allow-other-keys #:rest args)
(with-directory-excursion "stator/gcContCvgBias"
(apply (assoc-ref %standard-phases 'build) args))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys #:rest args)
(let ((out (assoc-ref outputs "out")))
(apply (assoc-ref %standard-phases 'install) args)
(with-directory-excursion "stator/gcContCvgBias"
;(apply (assoc-ref %standard-phases 'install) args)
(install-file "gc_coverage_bias" (string-append out "/bin")))))))))
(inputs
`(("gnuplot" ,gnuplot)
("perl" ,perl)
("zlib" ,zlib)))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("boost" ,boost)
("gzstream" ,gzstream)
("libtool" ,libtool)))
(home-page "https://github.com/galaxy001/pirs")
(synopsis "Profile based Illumina pair-end Reads Simulator")
(description "@code{pIRS} is a program for simulating paired-end reads
from a reference genome. It is optimized for simulating reads similar to those
generated from the Illumina platform.")
(license license:gpl2))))
;; TODO: Unbundle zlib, bamtools, tclap
(define-public sniffles
(package
(name "sniffles")
(version "1.0.11")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/fritzsedlazeck/Sniffles.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32 "0rkwqn1ycckfzrg2wdid4cqahq8q2jmmgi7vvl8qxgpsihqfbq0j"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(install-file (string-append "../source/bin/sniffles-core-"
,version "/sniffles")
(string-append out "/bin")))
#t))
(replace 'check
(lambda _
(with-directory-excursion "../source/test_set"
(for-each make-file-writable (find-files "."))
(invoke (string-append "../bin/sniffles-core-" ,version "/sniffles")
"-m" "reads_region.bam" "-v" "test.vcf")))))))
(native-inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/fritzsedlazeck/Sniffles")
(synopsis "Structural variation caller using third generation sequencing")
(description
"Sniffles is a structural variation caller using third generation sequencing
(PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence
from split-read alignments, high-mismatch regions, and coverage analysis.")
(license license:expat)))
;; TODO: Unbundle Complete-Striped-Smith-Waterman-Library
(define-public ngmlr
(package
(name "ngmlr")
(version "0.2.7")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/philres/ngmlr.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0lmsy8w0kxbyfnrln7lxgmnx3d82sv2b20n2yw5742rvfhq1v31n"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'patch-source-shebangs 'patch-more-tools
(lambda* (#:key inputs #:allow-other-keys)
(let ((bed (assoc-ref inputs "bedtools"))
(sam (assoc-ref inputs "samtools")))
(substitute* (find-files "test" "\\.sh$")
(("bedtools") (string-append bed "/bin/bedtools"))
(("samtools") (string-append sam "/bin/samtools")))
#t)))
(replace 'check
(lambda _
(with-directory-excursion "../source"
(invoke "sh" "test/test_travis.sh")))))))
(native-inputs
`(("bedtools" ,bedtools)
("samtools" ,samtools)))
(inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/philres/ngmlr")
(synopsis "Long-read mapper designed to align PacBio or Oxford Nanopore")
(description
"NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore
(standard and ultra-long) to a reference genome with a focus on reads that span
structural variations.")
(license license:expat)))
(define-public svim
(package
(name "svim")
(version "1.2.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/eldariont/svim.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "08j02in9jbq41b67dna1apnc3y30i37v44d1khml1xlx0iga720s"))))
(build-system python-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
(invoke "python3" "-m" "unittest" "discover" "-s" "src/"))))))
(propagated-inputs
`(("python-matplotlib" ,python-matplotlib)
("python-numpy" ,python-numpy)
("python-pysam" ,python-pysam)
("python-scipy" ,python-scipy)
("minimap2" ,minimap2)
("ngmlr" ,ngmlr)
("samtools" ,samtools)))
(home-page "https://github.com/eldariont/svim")
(synopsis "Structural Variant Identification Method using Long Reads")
(description
"SVIM (pronounced SWIM) is a structural variant caller for long reads. It
is able to detect, classify and genotype five different classes of structural
variants. Unlike existing methods, SVIM integrates information from across the
genome to precisely distinguish similar events, such as tandem and interspersed
duplications and novel element insertions.")
(license license:gpl3)))
(define-public bamaddrg
(let ((commit "3fccbf057eef21f6304fade6c306c5bb64158865") ; May 26, 2012
(revision "1"))
(package
(name "bamaddrg")
(version (git-version "0.0.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ekg/bamaddrg.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "14hq66cc7f4cssagb6079fmd2i6hfr9vmpcw5vi5kzsqr3ifc5yk"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no tests
#:phases
(modify-phases %standard-phases
(delete 'configure)
;; The Makefile wants to vendor bamtools' source so we mimic it.
(replace 'build
(lambda* (#:key inputs #:allow-other-keys)
(let ((bam (assoc-ref inputs "bamtools")))
(apply invoke
`("g++" "-O3"
,(string-append "-I" bam "/include/bamtools")
,(string-append "-L" bam "/lib/libbamtools.a")
"bamaddrg.cpp" "-o" "bamaddrg" "-lbamtools" "-lz")))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "bamaddrg" bin)
#t))))))
(native-inputs
`(("bamtools" ,bamtools)))
(inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/ekg/bamaddrg")
(synopsis "Adds read groups to input BAM files, streams BAM output on stdout")
(description
"This is intended for use \"fixing up\" RG tags on the fly so that they
reflect the source file from which the aligment originated from. This allows
the \"safe\" merging of many files from many individuals into one stream,
suitable for input into downstream processing systems such as freebayes (
population variant detector).")
(license #f)))) ; no license listed
(define-public qctool
(let ((changeset "73662f5f6e1e6efe75796bc64e342fb5d5d35e54") ; May 30, 2019
(revision "1"))
(package
(name "qctool")
(version (string-append "2.0.5-" revision "." (string-take changeset 7)))
(source
(origin
(method hg-fetch)
(uri (hg-reference
(url "https://bitbucket.org/gavinband/qctool")
(changeset changeset)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32 "0lcir6jdw1gsi1l0yrsyqgrb8dryxxw3gyncfx5bx34qbhd6f5dv"))))
(build-system waf-build-system)
(arguments
`(#:python ,python-2
#:tests? #f ; no check command
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'rename-waf
(lambda _
(rename-file "waf-1.5.18" "waf")
#t)))))
(native-inputs
`(("readline" ,readline)
("zlib" ,zlib)))
(inputs
`(("lapack" ,lapack)
("openblas" ,openblas)))
(home-page "https://www.well.ox.ac.uk/~gav/qctool_v2/")
(synopsis "Quality control and analysis of gwas datasets")
(description
"QCTOOL is a command-line utility program for manipulation and quality
control of gwas datasets and other genome-wide data. QCTOOL can be used
@enumerate
@item To compute per-variant and per-sample QC metrics.
@item To filter out samples or variants.
@item To merge datasets in various ways.
@item To convert dataset between file formats. (In particular QCTOOL can read
and write BGEN files, including full support for the BGEN v1.2 format that has
been used for the UK Biobank imputed data full release).
@item To manipulate datasets in various ways - e.g. by updating data fields or
aligning alleles to a reference sequence based on information in a strand file.
@item To annotate variants with information from BED files, sequence from FASTA
files, or with genetic map positions.
@item To compute LD metrics between variants.
@item To compare genotypes for individuals typed or imputed or phased in
different datasets.
@item To compute between-sample relatedness and principal components.
@item To compute 'genetic risk predictor' scores.
@end enumerate")
(license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt")))))
(define-public rn6-assembly-error-app
(package
(name "rn6-assembly-error-app")
(version "0.12")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/chen42/rn6_assembly_error_app.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0ilmn6w0l17041dlizf4dy4pqn26k7956k7fjx4fvssb525g4gi6"))))
(build-system trivial-build-system)
(arguments
`(#:modules ((guix build utils))
#:builder
(begin
(use-modules (guix build utils))
(let* ((out (assoc-ref %outputs "out"))
(targetdir (string-append out "/share/" ,name))
(app (string-append out "/bin/" ,name))
(Rbin (string-append (assoc-ref %build-inputs "r-min")
"/bin/Rscript"))
(convert (string-append (assoc-ref %build-inputs "imagemagick")
"/bin/convert"))
(cp (string-append (assoc-ref %build-inputs "coreutils")
"/bin/cp"))
(source (assoc-ref %build-inputs "source")))
(copy-recursively source targetdir)
(substitute* (string-append targetdir "/server.r")
;; This version is ideal for deploying with the included PNGs.
;; But we want all of them, so we use a local copy in shepherd's $HOME.
;;(("./pngs") (string-append targetdir "/pngs"))
(("./pngs") "/home/shepherd/rn6app/pngs")
(("cp") cp)
(("convert") convert))
(mkdir-p (string-append out "/bin"))
(call-with-output-file app
(lambda (port)
(format port
"#!~a
library(shiny)
setwd(\"~a\")
runApp(launch.browser=0, port=4202)~%\n"
Rbin targetdir)))
(chmod app #o555)
#t))))
(native-inputs `(("source" ,source)))
(inputs
`(("coreutils" ,coreutils-minimal)
("imagemagick" ,imagemagick)
("r-min" ,r-minimal)))
(propagated-inputs
`(("freetype" ,freetype)
("r" ,r)
("r-ggplot2" ,r-ggplot2)
("r-shiny" ,r-shiny)))
(home-page "http://rn6err.opar.io/")
(synopsis "Display potential assembly errors in rn6")
(description
"Display potential assembly errors in rn6.")
(license license:expat)))
(define-public bxd-power-calculator-app
(let ((commit "7cdd73daa9a7aa79af1de04dc314c325f9706fb8")
(revision "1"))
(package
(name "bxd-power-calculator-app")
(version (git-version "0.7" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Dashbrook/BXD_power_calculator_app/")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0vdfilzy78jalkh9w9xxvarnzgnlaz943crmhlds8bcrvwbmf6yh"))))
(build-system trivial-build-system)
(arguments
`(#:modules ((guix build utils))
#:builder
(begin
(use-modules (guix build utils))
(let* ((out (assoc-ref %outputs "out"))
(targetdir (string-append out "/share/" ,name))
(app (string-append out "/bin/" ,name))
(Rbin (string-append (assoc-ref %build-inputs "r-min")
"/bin/Rscript"))
(datasets (assoc-ref %build-inputs "datasets"))
(source (assoc-ref %build-inputs "source")))
(copy-recursively source targetdir)
(mkdir-p (string-append out "/bin"))
(call-with-output-file app
(lambda (port)
(format port
"#!~a
library(shiny)
setwd(\"~a\")
runApp(launch.browser=0, port=3978)~%\n"
Rbin targetdir)))
(chmod app #o555)
(substitute* (string-append targetdir "/server.R")
(("read.csv.*")
(string-append "read.csv(url(\"file://" datasets "\"), header = TRUE)\n")))
#t))))
(native-inputs `(("source" ,source)))
(propagated-inputs
`(("r" ,r)
("r-data-table" ,r-data-table)
("r-dt" ,r-dt)
("r-dplyr" ,r-dplyr)
("r-ggplot2" ,r-ggplot2)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-shiny" ,r-shiny)))
(inputs
`(("r-min" ,r-minimal)
;; Also available from ipfs
;; ipfs get Qma3LWJBoks77btTmp6rn6jGSBcuBoPgcPCmofY2RRKEKf
("datasets" ,(origin
(method url-fetch)
(uri "https://web.archive.org/web/20191016132922/http://individual.utoronto.ca/D_Ashbrook/Effect_size_analysis_heritability_28th_Nov_2018_recalc.csv")
(sha256
(base32
"1ldr9infavd0vak8n8ry9smcnrir3xgs1bahmmx7n2csx4n6qx2x"))))))
(home-page "https://dashbrook1.shinyapps.io/bxd_power_calculator_app/")
(synopsis "Visualize probability (beta) of detecting a QTL")
(description
"The BXD power app seeks to provide a quick and easy graphical interface
for users to calculate the theortical power to detect an effect in a two parent
recombinant inbred population. A power calculator such as this is needed as all
grants require a calculation of the applications power to detect the effect of
interest, and this app can provide values and figures for applicants to use.")
(license license:gpl3))))
(define-public singlecellrshiny
(let ((commit "bdca74f4819d11e8fe7b15d9ab91b853f6542f7a")
(revision "3"))
(package
(name "singlecellrshiny")
(version (git-version "0.0.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/genenetwork/singleCellRshiny")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1rxj933s9p9r7358vnp15f7ag6c0j65r4hgr8kyirfhmp1i8xdlw"))))
(build-system trivial-build-system)
(arguments
`(#:modules ((guix build utils))
#:builder
(begin
(use-modules (guix build utils))
(let* ((out (assoc-ref %outputs "out"))
(targetdir (string-append out "/share/" ,name))
(app (string-append out "/bin/" ,name))
(Rbin (string-append (assoc-ref %build-inputs "r-min")
"/bin/Rscript"))
(top1001 (assoc-ref %build-inputs "RobTop1001.csv"))
(celltypes (assoc-ref %build-inputs "CellTypes_RGC_Master_08Dec2018.csv"))
(800-H1 (assoc-ref %build-inputs "800-H1-H20-RNA-Seq.csv"))
(source (assoc-ref %build-inputs "source")))
(copy-recursively source targetdir)
(substitute* (string-append targetdir "/app.R")
;; As seen in https://github.com/genenetwork/singleCellRshiny/commit/6b2a344dd0d02f65228ad8c350bac0ced5850d05.patch
(("library\\(DT\\)") "library(DT)\nlibrary(multtest)"))
(substitute* (string-append targetdir "/global.R")
(("800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv") 800-H1)
(("CellTypes_RGC_Master_08Dec2018.csv") celltypes)
(("RobTop1001.csv") top1001)
;; As seen in https://github.com/genenetwork/singleCellRshiny/commit/6b2a344dd0d02f65228ad8c350bac0ced5850d05.patch
(("dim\\(sc.object.1") "dim(sc.object"))
(mkdir-p (string-append out "/bin"))
(call-with-output-file app
(lambda (port)
(format port
"#!~a
library(shiny)
setwd(\"~a\")
runApp(launch.browser=0, port=4208)~%\n"
Rbin targetdir)))
(chmod app #o555)
#t))))
(inputs
`(("r-min" ,r-minimal)
("RobTop1001.csv"
,(origin
(method url-fetch)
(uri "https://archive.org/download/celltypesrgcmaster08dec2018/RobTop1001.csv")
(file-name "RobTop1001.csv")
(sha256
(base32 "0pa73kc1p8417sjvvvhp9xsbh2h8g7h85pnmm16mnv4wjalhq0gn"))))
("CellTypes_RGC_Master_08Dec2018.csv"
,(origin
(method url-fetch)
(uri "https://archive.org/download/celltypesrgcmaster08dec2018/CellTypes_RGC_Master_08Dec2018.csv")
(file-name "CellTypes_RGC_Master_08Dec2018.csv")
(sha256
(base32 "0y411968np1f5g21iym9xc9yj5c1jsn94rpkwkxh9pw2z43gvghn"))))
("800-H1-H20-RNA-Seq.csv"
,(origin
(method url-fetch)
(uri "https://archive.org/download/celltypesrgcmaster08dec2018/800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv")
(file-name "800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv")
(sha256
(base32 "1b1y4lfs8drypm04i1rypbmk67rdqgs27nfh05pwnv3sja2nanam"))))))
(propagated-inputs
`(("r" ,r)
("r-dt" ,r-dt)
("r-multtest" ,r-multtest)
("r-seurat" ,r-seurat)
("r-shiny" ,r-shiny)))
(home-page "http://singlecell.opar.io/")
(synopsis "RNA sequencing data analysis")
(description
"This is the R-Shiny programs to run some basic single cell RNA sequencing
(scRNA-seq) data analysis.")
(license license:agpl3))))
(define-public seqwish-0.1
(package
(name "seqwish")
(version "0.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ekg/seqwish.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1gp72cmi13hbkmwwhgckmxkbx8w644jc5l6dvvvxdbl6sk8xsi5r"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'build
(lambda* (#:key inputs #:allow-other-keys)
(let ((sdsl-lite (assoc-ref inputs "sdsl-lite"))
(sufsort (assoc-ref inputs "sufsort"))
(bsort (assoc-ref inputs "bsort"))
(mmap_allocator (assoc-ref inputs "mmap-allocator"))
(tayweeargs (assoc-ref inputs "tayweeargs-source"))
(gzipreader (assoc-ref inputs "gzipreader-source"))
(mmmultimap (assoc-ref inputs "mmmultimap-source"))
(iitii (assoc-ref inputs "iitii-source"))
(ips4o (assoc-ref inputs "ips4o-source")))
(apply invoke "g++" "-o" "seqwish"
"-O3" "-g" "-std=c++14" "-fopenmp"
"-latomic" "-lz"
(string-append "-I" sdsl-lite "/include")
(string-append "-I" sdsl-lite "/include/sdsl")
(string-append "-I" bsort "/include")
(string-append "-I" tayweeargs)
(string-append "-I" gzipreader)
(string-append "-I" mmmultimap "/src")
(string-append "-I" iitii "/src")
(string-append "-I" mmap_allocator "/include")
(string-append "-I" ips4o)
(append
(find-files "src" ".")
(list
(string-append sdsl-lite "/lib/libsdsl.so")
(string-append sufsort "/lib/libdivsufsort.so")
(string-append sufsort "/lib/libdivsufsort64.so")
(string-append mmap_allocator "/lib/libmmap_allocator.a")
(string-append bsort "/lib/libbsort.a")))))))
(replace 'check
(lambda _
;; Add seqwish to the PATH for the tests.
(setenv "PATH" (string-append (getcwd) ":" (getenv "PATH")))
(with-directory-excursion "test"
(invoke "make"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(install-file "seqwish" (string-append out "/bin")))
#t)))))
(inputs
`(("bsort" ,ekg-bsort)
("mmap-allocator" ,ekg-mmap-allocator)
("openmpi" ,openmpi)
("sdsl-lite" ,sdsl-lite)
("sufsort" ,libdivsufsort)
("zlib" ,zlib)))
(native-inputs
`(("prove" ,perl)
("tayweeargs-source" ,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Taywee/args.git")
(commit "3de44ec671db452cc0c4ef86399b108939768abb")))
(file-name "tayweeargs-source-for-seqwish")
(sha256
(base32
"1v8kq1gvl5waysrfp0s58881rx39mnf3ifdsl6pb3y3c4zaki2xh"))))
("gzipreader-source" ,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gatoravi/gzip_reader.git")
(commit "0ef26c0399e926087f9d6c4a56067a7bf1fc4f5e")))
(file-name "gzipreader-source-for-seqwish")
(sha256
(base32
"1wy84ksx900840c06w0f1mgzvr7zsfsgxq1b0jdjh8qka26z1r17"))))
("mmmultimap-source" ,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ekg/mmmultimap.git")
(commit "88c734c36563048b0f3acc04dd8856f19e02b75f")))
(file-name "mmmultimap-source-for-seqwish")
(sha256
(base32
"06mnf3bd32s3ngxkl573ylg2qsvlw80r1ksdwamx3fzxa1a5yls0"))))
("iitii-source" ,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ekg/iitii.git")
(commit "85209e07a3ee403fb6557387a7f897cd76be4406")))
(file-name "iitii-source-for-seqwish")
(sha256
(base32
"0sszvffkswf89nkbjmjg3wjwqvy2w0d3wgy3ngy33ma4sy4s025s"))))
("ips4o-source" ,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/SaschaWitt/ips4o.git")
(commit "bff3ccf0bf349497f2bb10f825d160b792236367")))
(file-name "ips4o-source-for-seqwish")
(sha256
(base32
"0yjfvrkiwgmy5cn0a7b9j8jwc3zp0l8j4dl5n0jgz68pdnhlp96h"))))))
(home-page "https://github.com/ekg/seqwish")
(synopsis "Alignment to variation graph inducer")
(description "Seqwish implements a lossless conversion from pairwise
alignments between sequences to a variation graph encoding the sequences and
their alignments. As input we typically take all-versus-all alignments, but the
exact structure of the alignment set may be defined in an application specific
way. This algorithm uses a series of disk-backed sorts and passes over the
alignment and sequence inputs to allow the graph to be constructed from very
large inputs that are commonly encountered when working with large numbers of
noisy input sequences. Memory usage during construction and traversal is
limited by the use of sorted disk-backed arrays and succinct rank/select
dictionaries to record a queryable version of the graph.")
(license license:expat)))
(define ekg-bsort
(let ((commit "c3ab0d3308424030e0a000645a26d2c10a59a124")
(revision "1"))
(package
(name "bsort")
(version (git-version "0.0.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ekg/bsort.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0dgpflzcp3vdhbjwbjw347czi86gyk73hxcwjdqnaqh5vg61bdb6"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no test target
#:out-of-source? #f
#:phases
(modify-phases %standard-phases
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(install-file "bin/bsort" (string-append out "/bin"))
(install-file "src/bsort.hpp" (string-append out "/include"))
(install-file "lib/libbsort.a" (string-append out "/lib")))
#t)))))
(home-page "")
(synopsis "")
(description "")
(license license:gpl2))))
(define ekg-mmap-allocator
(let ((commit "ed61daf094de1c2e1adbe8306287ad52da5f0264")
(revision "1"))
(package
(name "mmap-allocator")
(version (git-version "0.10.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ekg/mmap_allocator.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1f30b2kpwwzh6333s0qi5samk458ghbnvyycf6rwx6n6j7xswhbw"))))
(build-system gnu-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(delete 'configure) ; no configure script
(add-before 'install 'pre-install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(substitute* "Makefile"
(("HEADERS=") "HEADERS=mmappable_vector.h ")
(("/usr") out))
(mkdir-p (string-append out "/lib"))
(mkdir (string-append out "/include"))
#t))))
#:test-target "test"))
(home-page "")
(synopsis "")
(description "")
(license license:lgpl2.0+)))) ; README just says "lpgl".
;; TODO: Unbundle BBHash, concurrentqueue, parallel-hashmap zstr
(define-public graphaligner
(package
(name "graphaligner")
(version "1.0.10")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/maickrau/GraphAligner/files/"
"3879798/GraphAligner.tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "0sk0cfjw44wslmlgplzwcqi0w4862vhf75p4x6syalvyi34pw3ck"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no tests
#:make-flags '("all")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-source
(lambda* (#:key inputs #:allow-other-keys)
(let ((sdsl (assoc-ref inputs "sdsl-lite")))
(substitute* "makefile"
(("VERSION .*") (string-append "VERSION = " ,version "\n"))))
#t))
(delete 'configure) ; no configure phase
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(for-each
(lambda (program)
(install-file program (string-append out "/bin")))
(find-files "bin" "."))
(for-each
(lambda (header)
(install-file header (string-append out "/include")))
(find-files "src" "\\.h(pp)?$")))
#t)))))
(native-inputs
`(("pkg-config" ,pkg-config)
("protobuf" ,protobuf "static")
("sdsl-lite" ,sdsl-lite)
("sparsehash" ,sparsehash)
("zlib" ,zlib "static")))
(inputs
`(("boost" ,boost-static)
("jemalloc" ,jemalloc)
("libdivsufsort" ,libdivsufsort)
("mummer" ,mummer)
("protobuf" ,protobuf)
("zlib" ,zlib)))
(home-page "https://github.com/maickrau/GraphAligner")
(synopsis "Seed-and-extend program for aligning genome graphs")
(description "Seed-and-extend program for aligning long error-prone reads to
genome graphs. For a description of the bitvector alignment extension
algorithm, see
@url{https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz162/5372677
here}.")
(license license:expat)))
(define-public mummer
(package
(name "mummer")
(version "4.0.0beta2")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/mummer4/mummer/releases/"
"download/v" version "/mummer-" version ".tar.gz"))
(sha256
(base32
"14qvrmf0gkl4alnh8zgxlzmvwc027arfawl96i7jk75z33j7dknf"))))
(build-system gnu-build-system)
(inputs
`(("gnuplot" ,gnuplot)
("perl" ,perl)))
(home-page "http://mummer.sourceforge.net/")
(synopsis "Efficient sequence alignment of full genomes")
(description "MUMmer is a versatil alignment tool for DNA and protein sequences.")
(license license:artistic2.0)))
(define-public diagnostic-slider
(let ((commit "514d65d4982133e4869e578c5553fced4c6d506c")
(revision "1"))
(package
(name "diagnostic-slider")
(version (git-version "0.0.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/sens/diagnostic-slider")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "04g8if32g8syg6v0bd3jjn05i3d394nx8i3ccl0883p8mlmdvlmx"))))
(build-system trivial-build-system)
(arguments
`(#:modules ((guix build utils))
#:builder
(begin
(use-modules (guix build utils))
(let* ((out (assoc-ref %outputs "out"))
(targetdir (string-append out "/share/" ,name))
(app (string-append out "/bin/" ,name))
(Rbin (string-append (assoc-ref %build-inputs "r-min")
"/bin/Rscript"))
(source (assoc-ref %build-inputs "source")))
(copy-recursively source targetdir)
(mkdir-p (string-append out "/bin"))
(call-with-output-file app
(lambda (port)
(format port
"#!~a
library(shiny)
setwd(\"~a\")
runApp(launch.browser=0, port=4206)~%\n"
Rbin targetdir)))
(chmod app #o555)
#t))))
(native-inputs
`(("source" ,source)))
(inputs
`(("r-min" ,r-minimal)))
(propagated-inputs
`(("r" ,r)
("r-shiny" ,r-shiny)))
(home-page "https://github.com/sens/diagnostic-slider")
(synopsis "")
(description
"")
(license #f))))
(define-public clustalw
(package
(name "clustalw")
(version "2.1")
(source (origin
(method url-fetch)
(uri "http://www.clustal.org/download/current/clustalw-2.1.tar.gz")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "11llyj08liq0bg6vqan8728qjrbam3xhna2wd6g8rzdbhydhalp0"))))
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after
'install 'post-install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")))
(rename-file (string-append out "/bin/clustalw2")
(string-append out "/bin/clustalw"))
))))))
(build-system gnu-build-system)
(home-page "http://www.clustal.org/")
(synopsis "")
(description
"")
(license #f)))
(define-public python-whatshap
(package
(name "python-whatshap")
(version "1.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "whatshap" version))
(sha256
(base32 "0vxv6y8sg25yii106j6k55vc5z7n1l1y1nax49dgbarbrvk8cr2f"))))
(build-system python-build-system)
(inputs
`(("python-biopython" ,python-biopython)
("python-networkx" ,python-networkx)
("python-pyfaidx" ,python-pyfaidx)
("python-pysam" ,python-pysam)
("python-scipy" ,python-scipy)
("python-xopen" ,python-xopen)))
(native-inputs
`(("python-cython" ,python-cython)
("python-setuptools-scm" ,python-setuptools-scm)))
(home-page "https://github.com/whatshap/whatshap/")
(synopsis "Read-based phasing of genomic variants")
(description
"WhatsHap is a software for phasing genomic variants using DNA sequencing
reads, also called read-based phasing or haplotype assembly. It is especially
suitable for long reads, but works also well with short reads.")
(license license:expat)))
(define-public bh20-seq-resource
(let ((commit "ae4cb3c2cf7103bbc84f52618bb755d7ce25775b")
(revision "3"))
(package
(name "bh20-seq-resource")
(version (git-version "1.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/arvados/bh20-seq-resource")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "1k0gsz4yc8l5znanzd094g2jp40ksbpa9667zr31ayrjx6labz02"))
(modules '((guix build utils)))
(snippet
'(begin
(substitute* "setup.py"
(("py-dateutil") "python-dateutil"))
#t))))
(build-system python-build-system)
(propagated-inputs
`(("python-arvados-python-client" ,python-arvados-python-client)
("python-dateutil" ,python-dateutil)
("python-flask" ,python-flask)
("python-magic" ,python-magic)
("python-pyyaml" ,python-pyyaml)
("python-pycurl" ,python-pycurl)
("python-pyshex" ,python-pyshex)
("python-redis" ,python-redis)
("python-ruaml.yaml" ,python38-ruaml.yaml-0.15.76)
("clustalw" ,clustalw)
("python-schema-salad" ,python-schema-salad)
("python-twint" ,python-twint)
;; and for the service
("python" ,python)
("gunicorn" ,gunicorn)))
(native-inputs
`(("git" ,(@ (gnu packages version-control) git))
("python-oauth2client" ,python-oauth2client)
("python-pytest" ,python-pytest-4)
("python-pytest-runner" ,python-pytest-runner-2)
("python-uritemplate" ,python-uritemplate)))
(home-page "https://github.com/arvados/bh20-seq-resource")
(synopsis
"Tool to upload SARS-CoV-19 sequences and service to kick off analysis")
(description "This repository provides a sequence uploader for the
COVID-19 Virtual Biohackathon's Public Sequence Resource project. You can use
it to upload the genomes of SARS-CoV-2 samples to make them publicly and freely
available to other researchers.")
(license license:asl2.0))))
(define-public python-scanpy-git
(let ((commit "590d42309f9ed6550d7b887039990edfc1ac7648") ; April 22, 2020
(revision "1"))
(package
(inherit python-scanpy)
(name "python-scanpy-git")
(version (git-version "1.4.6" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/theislab/scanpy")
(commit commit)))
(file-name (git-file-name "python-scanpy" version))
(sha256
(base32 "0z3pk9vh4b7fqq7fs262i6z0pm1dnn6bf49a4r7r73k6gjj6namd"))))
(arguments
(substitute-keyword-arguments (package-arguments python-scanpy)
((#:phases phases)
`(modify-phases ,phases
(add-before 'build 'fix-build
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(pyv (python-version (assoc-ref inputs "python"))))
(substitute* "setup.py"
(("use_scm_version=True") "use_scm_version=False"))
(substitute* "scanpy/__init__.py"
(("__version__.*")
(string-append "__version__ = '" ,version "'\n")))
(mkdir-p
(string-append out "/lib/python" pyv "/site-packages"))
(setenv "PYTHONPATH"
(string-append out
"/lib/python" pyv "/site-packages/:"
(getenv "PYTHONPATH"))))
;; These tests fail on this git revision
(delete-file "scanpy/tests/test_neighbors_key_added.py")
(delete-file "scanpy/tests/test_pca.py")
#t)))))))))
(define-public vg
(package
(name "vg")
(version "1.33.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/vgteam/vg/releases/download/v"
version "/vg-v" version ".tar.gz"))
(sha256
(base32
"1pd4gdqb3ar0r1igzhf730kh9x0wj5l4shmjxz0j2mj78wy8y2sg"))
(modules '((guix build utils)))
(snippet
'(begin
;; List all the options, makes it easier to try to remove them.
;(delete-file-recursively "deps/BBHash")
;(delete-file-recursively "deps/DYNAMIC")
;(delete-file-recursively "deps/FlameGraph")
;(delete-file-recursively "deps/atomic_queue")
;(delete-file-recursively "deps/backward-cpp")
(delete-file-recursively "deps/bash-tap")
;(delete-file-recursively "deps/dozeu")
(delete-file-recursively "deps/elfutils")
;(delete-file-recursively "deps/fastahack") ; Fasta.o
;(delete-file-recursively "deps/fermi-lite")
;(delete-file-recursively "deps/gbwt")
(delete-file-recursively "deps/gbwt/deps")
;(delete-file-recursively "deps/gbwtgraph")
(delete-file-recursively "deps/gbwtgraph/deps")
;(delete-file-recursively "deps/gcsa2")
;(delete-file-recursively "deps/gfakluge")
;(delete-file-recursively "deps/gssw")
(delete-file-recursively "deps/htslib")
;(delete-file-recursively "deps/ips4o")
(delete-file-recursively "deps/jemalloc")
;(delete-file-recursively "deps/libVCFH")
;(delete-file-recursively "deps/libbdsg")
;(delete-file-recursively "deps/libbdsg/bdsg/deps")
(delete-file-recursively "deps/libbdsg/bdsg/deps/BBHash")
(delete-file-recursively "deps/libbdsg/bdsg/deps/DYNAMIC")
;(delete-file-recursively "deps/libbdsg/bdsg/deps/hopscotch-map")
(delete-file-recursively "deps/libbdsg/bdsg/deps/libhandlegraph")
(delete-file-recursively "deps/libbdsg/bdsg/deps/pybind11")
(delete-file-recursively "deps/libbdsg/bdsg/deps/sdsl-lite")
(delete-file-recursively "deps/libbdsg/bdsg/deps/sparsepp")
;(delete-file-recursively "deps/libdeflate")
;(delete-file-recursively "deps/libhandlegraph")
;(delete-file-recursively "deps/libvgio")
;(delete-file-recursively "deps/libvgio/deps") ; libhandlegraph
;(delete-file-recursively "deps/lru_cache")
;(delete-file-recursively "deps/mio")
;(delete-file-recursively "deps/mmmultimap")
(delete-file-recursively "deps/mmmultimap/deps/DYNAMIC")
(delete-file-recursively "deps/mmmultimap/deps/args")
(delete-file-recursively "deps/mmmultimap/deps/atomic_queue")
;(delete-file-recursively "deps/mmmultimap/deps/hopscotch-map")
(delete-file-recursively "deps/mmmultimap/deps/ips4o")
(delete-file-recursively "deps/mmmultimap/deps/mio")
;(delete-file-recursively "deps/mmmultimap/deps/paryfor")
(delete-file-recursively "deps/mmmultimap/deps/sdsl-lite")
;(delete-file-recursively "deps/pinchesAndCacti")
;(delete-file-recursively "deps/progress_bar")
(delete-file-recursively "deps/raptor")
;(delete-file-recursively "deps/sdsl-lite")
(delete-file-recursively "deps/snappy")
;(delete-file-recursively "deps/sonLib")
(delete-file-recursively "deps/sparsehash")
;(delete-file-recursively "deps/sparsepp")
;(delete-file-recursively "deps/ssw")
;(delete-file-recursively "deps/structures")
;(delete-file-recursively "deps/sublinear-Li-Stephens")
(delete-file-recursively "deps/sublinear-Li-Stephens/deps")
(delete-file-recursively "deps/tabixpp")
(delete-file-recursively "deps/vcflib")
;(delete-file-recursively "deps/xg")
(delete-file-recursively "deps/xg/deps")
;; libvgio doesn't search the correct include directory.
(copy-recursively "deps/libhandlegraph/src/include/handlegraph"
"deps/libvgio/include/handlegraph")
#t))))
(build-system gnu-build-system)
(arguments
'(#:phases
(modify-phases %standard-phases
(delete 'configure) ; no configure script
(add-after 'unpack 'patch-source
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "Makefile"
;; PKG_CONFIG_DEPS needs to be substituted to actually link to everything.
(("cairo jansson")
"cairo htslib jansson libdw libelf protobuf raptor2 sdsl-lite tabixpp vcflib")
;; Skip the part where we link static libraries special. It doesn't like the changes we make
(("-Wl,-B.*") "\n")
(("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libtabixpp\\.a") "$(LIB_DIR)/libtabixpp.a")
((" \\$\\(LIB_DIR\\)/libtabixpp\\.a")
(string-append " " (assoc-ref inputs "tabixpp") "/lib/libtabixpp.so"))
(("\\$\\(LIB_DIR\\)/pkgconfig/tabixpp\\.pc")
(string-append " " (assoc-ref inputs "tabixpp") "/lib/pkgconfig/tabixpp.pc"))
(("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libhts\\.a") "$(LIB_DIR)/libhts.a")
((" \\$\\(LIB_DIR\\)/libhts\\.a")
(string-append " " (assoc-ref inputs "htslib") "/lib/libhts.so"))
(("\\$\\(LIB_DIR\\)/pkgconfig/htslib\\.pc")
(string-append " " (assoc-ref inputs "htslib") "/lib/pkgconfig/htslib.pc"))
((" \\$\\(LIB_DIR\\)/libvcflib.a")
(string-append " " (assoc-ref inputs "vcflib") "/lib/libvcflib.so"))
((" \\$\\(BIN_DIR\\)/vcf2tsv")
(string-append " " (assoc-ref inputs "vcflib") "/bin/vcf2tsv"))
((" \\$\\(VCFLIB_DIR\\)/bin/vcf2tsv")
(string-append " " (assoc-ref inputs "vcflib") "/bin/vcf2tsv"))
((" \\$\\(FASTAHACK_DIR\\)/fastahack")
(string-append " " (assoc-ref inputs "fastahack") "/bin/fastahack"))
((" \\$\\(FASTAHACK_DIR\\)/bin/fastahack")
(string-append " " (assoc-ref inputs "fastahack") "/bin/fastahack"))
((" \\$\\(LIB_DIR\\)/libsnappy.a")
(string-append " " (assoc-ref inputs "snappy") "/lib/libsnappy.so"))
;; Only link against the libraries in the elfutils package.
(("-ldwfl -ldw -ldwelf -lelf -lebl") "-ldw -lelf")
((" \\$\\(LIB_DIR\\)/libelf.a")
(string-append " " (assoc-ref inputs "elfutils") "/lib/libelf.so"))
((" \\$\\(LIB_DIR\\)/libdw.a")
(string-append " " (assoc-ref inputs "elfutils") "/lib/libdw.so"))
;; We need the Make.helper file in SDSL_DIR for gcsa2
;((" \\$\\(LIB_DIR\\)/libsdsl.a")
; (string-append " " (assoc-ref inputs "sdsl-lite") "/lib/libsdsl.so"))
((" \\$\\(LIB_DIR\\)/libdivsufsort.a")
(string-append " " (assoc-ref inputs "libdivsufsort") "/lib/libdivsufsort.so"))
((" \\$\\(LIB_DIR\\)/libdivsufsort64.a")
(string-append " " (assoc-ref inputs "libdivsufsort") "/lib/libdivsufsort64.so"))
((" \\$\\(LIB_DIR\\)/libjemalloc.a")
(string-append " " (assoc-ref inputs "jemalloc") "/lib/libjemalloc.so"))
((" \\$\\(INC_DIR\\)/sparsehash")
(string-append " " (assoc-ref inputs "sparsehash") "/include/sparsehash"))
((" \\$\\(INC_DIR\\)/raptor2")
(string-append " " (assoc-ref inputs "raptor2") "/include/raptor2"))
((" \\$\\(LIB_DIR\\)/libraptor2.a")
(string-append " " (assoc-ref inputs "raptor2") "/lib/libraptor2.so"))
((" \\$\\(BIN_DIR\\)/rapper")
(string-append " " (assoc-ref inputs "raptor2") "/bin/rapper")))
;; vcf2tsv shows up in a couple of other places
(substitute* "test/t/02_vg_construct.t"
(("../deps/vcflib/bin/vcf2tsv") (which "vcf2tsv")))
#t))
(add-after 'unpack 'fix-fastahack-dependency
(lambda _
(substitute* "src/aligner.hpp"
(("Fasta.h") "fastahack/Fasta.h"))
#t))
(add-after 'unpack 'fix-hopscotch-dependency
(lambda _
(substitute* "Makefile"
;; The build directory for hopscotch_map-prefix.
(("rm -Rf build && ") ""))
;; Don't try to download hopscotch_map from the internet.
(substitute* "deps/DYNAMIC/CMakeLists.txt"
((".*GIT_REPOSITORY.*")
"SOURCE_DIR \"../../libbdsg/bdsg/deps/hopscotch-map\"\n")
((".*BUILD_IN_SOURCE.*") ""))
;; We still need to copy it to the expected location.
(copy-recursively
"deps/libbdsg/bdsg/deps/hopscotch-map"
"deps/DYNAMIC/build/hopscotch_map-prefix/src/hopscotch_map")
#t))
(add-after 'unpack 'adjust-tests
(lambda* (#:key inputs #:allow-other-keys)
(let ((bash-tap (assoc-ref inputs "bash-tap")))
(substitute* (find-files "test/t")
(("BASH_TAP_ROOT.*")
(string-append "BASH_TAP_ROOT=" bash-tap "/bin\n"))
((".*bash-tap-bootstrap")
(string-append ". " bash-tap "/bin/bash-tap-bootstrap")))
;; Lets skip the 4 failing tests for now. They fail with our
;; bash-tap and the bundled one.
(substitute* "test/t/02_vg_construct.t"
((".*the graph contains.*") "is $(true) \"\" \"\"\n"))
(substitute* '("test/t/07_vg_map.t"
"test/t/33_vg_mpmap.t")
((".*node id.*") "is $(true) \"\" \"\"\n"))
;; Don't test the docs, we're not providing npm
(substitute* "Makefile"
((".*test-docs.*") ""))
#t)))
(add-after 'build 'build-manpages
(lambda _
(invoke "make" "man")))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(install-file "bin/vg" (string-append out "/bin"))
(install-file "lib/libvg.a" (string-append out "/lib"))
(for-each
(lambda (file)
(install-file file (string-append out "/share/man/man1")))
(find-files "doc/man" "\\.1$"))
#t))))
#:test-target "test"))
(native-inputs
`(("asciidoctor" ,ruby-asciidoctor)
("bash-tap" ,bash-tap)
("bc" ,bc)
("cmake" ,cmake-minimal)
("jq" ,jq)
("perl" ,perl)
("pkg-config" ,pkg-config)
("samtools" ,samtools)
("util-linux" ,util-linux)
("which" ,which)
("xxd" ,xxd)))
(inputs
`(("boost" ,boost)
("cairo" ,cairo)
("curl" ,curl-minimal)
("elfutils" ,elfutils)
("fastahack" ,fastahack)
("htslib" ,htslib)
("jansson" ,jansson)
("jemalloc" ,jemalloc)
("libdivsufsort" ,libdivsufsort)
("ncurses" ,ncurses)
("protobuf" ,protobuf)
("raptor2" ,raptor2)
("sdsl-lite" ,sdsl-lite)
("smithwaterman" ,smithwaterman)
("snappy" ,snappy)
("sparsehash" ,sparsehash)
("tabixpp" ,tabixpp)
("vcflib" ,vcflib)
("zlib" ,zlib)))
(home-page "https://www.biostars.org/t/vg/")
(synopsis "Tools for working with genome variation graphs")
(description "Variation graphs provide a succinct encoding of the sequences
of many genomes. A variation graph (in particular as implemented in vg) is
composed of:
@enumerate
@item nodes, which are labeled by sequences and ids
@item edges, which connect two nodes via either of their respective ends
@item paths, describe genomes, sequence alignments, and annotations (such as
gene models and transcripts) as walks through nodes connected by edges
@end enumerate
This model is similar to sequence graphs that have been used in assembly and
multiple sequence alignment.")
(license
(list
license:expat ; main program
license:bsd-2 ; deps/xg/deps/ips4o
license:bsd-3 ; deps/sparsepp, deps/sonLib/C/{impl,inc}
license:asl2.0 ; deps/sonLib/externalTools/quicktree_1.1, deps/structures
license:gpl3+ ; all sdsl-lite copies
license:zlib ; deps/sonLib/externalTools/cutest
license:boost1.0)))) ; catch.hpp
(define-public ucsc-genome-browser
(package
(name "ucsc-genome-browser")
(version "413")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://genome-source.gi.ucsc.edu/kent.git/")
(commit (string-append "v" version "_base"))))
(file-name (git-file-name name version))
(sha256
(base32 "1qcjhd4wcajik71z5347fw2sfhfkv0p6y7yldrrkmycw2qhqmpzn"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
#:parallel-tests? #f ; not supported
#:phases
(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase.
(add-before 'build 'pre-build
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
;; Start by setting some variables.
(chdir "src")
(setenv "CC" ,(cc-for-target))
(setenv "HOME" (getcwd))
;; And here we set the output directories
(setenv "CGI_BIN" (string-append out "/cgi-bin"))
(setenv "CGI_BIN_USER" (string-append out "/cgi-bin"))
(setenv "DOCUMENTROOT" (string-append out "/html"))
(setenv "DOCUMENTROOT_USER" (string-append out "/html"))
(setenv "BINDIR" (string-append out "/bin"))
;; Now let's fix some errors:
(mkdir-p (string-append out "/cgi-bin"))
(substitute* "inc/cgi_build_rules.mk"
(("rm -f.*") ""))
(substitute* (cons* "inc/cgi_build_rules.mk"
(find-files "." "makefile"))
(("CGI_BIN\\}-\\$\\{USER") "CGI_BIN_USER"))
;; Force linking with freetype.
(substitute* "inc/common.mk"
(("libpng-config --ldflags") "pkg-config --libs libpng freetype2")
(("libpng-config --I_opts") "pkg-config --cflags-only-I libpng freetype2")
(("\\$\\{HG_INC\\}" hg_inc) (string-append hg_inc " -DUSE_FREETYPE")))
;; Force the trash location.
(substitute* (cons*
"utils/qa/showTracks"
"webBlat/webBlat.cfg"
"hg/js/hgTracks.js"
(find-files "." "\\.c$"))
;; This line is specifically needed as-is.
(("\\.\\./trash") "/var/cache/genome"))
#t)))
(add-before 'check 'pre-check
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(triplet ,(gnu-triplet->nix-system (%current-system))))
(setenv "PATH" (string-append (getenv "PATH")
":" out "/bin"))
(setenv "MACHTYPE"
(string-take triplet (string-index triplet #\-)))
(for-each make-file-writable
(find-files "utils/bedJoinTabOffset/tests"))
(substitute* '("utils/bamToPsl/tests/makefile"
"utils/trackDbIndexBb/tests/makefile")
(("/cluster/bin/bedtools/bedtools") (which "bedtools")))
;; These tests fail intermittently:
(substitute* "utils/vcfFilter/tests/makefile"
((" testRenameNoGt ") " ")
((" testMinAc1NoGt ") " "))
;; These tests can't find their database:
(substitute* "hg/lib/tests/makefile"
((" spDbTest ") " ")
((" hdbTest ") " "))
(substitute* "hg/lib/tests/genePredTests.mk"
((" tableTests ") " ")
((" compatTblTests ") " "))
(substitute* "hg/lib/tests/pslReaderTests.mk"
((" tableTests") " "))
(substitute* "hg/lib/tests/makefile"
((" annoGratorTest ") " ")
((" customTrackTest ") " ")
((" hgvsTest") " "))
(substitute* "hg/autoSql/tests/makefile"
((" dbLinkTest ") " ")
((" symColsTest ") " "))
(delete-file "hg/checkTableCoords/tests/makefile")
(delete-file "hg/hgGetAnn/tests/makefile")
(substitute* "hg/sqlToXml/makefile"
((".*doTest.*") ""))
(substitute* "hg/utils/genePredFilter/tests/makefile"
((" gencodeHackDbTest") " "))
(substitute* "hg/utils/refSeqGet/tests/makefile"
(("^test::.*") "test:: mkout\n"))
(delete-file "hg/utils/vcfToHgvs/tests/makefile")
(substitute* "hg/bedItemOverlapCount/tests/makefile"
((".*RunTest.*") ""))
;; Depends on /cluster
(substitute* "hg/liftOver/tests/makefile"
(("^test:.*") "test: mkdirs scaffoldEndBug\n"))
(delete-file "hg/mouseStuff/netToAxt/tests/makefile")
(substitute* "hg/pslToChain/tests/makefile"
((" example1 ") " "))
;; Depends on /gbdb
(delete-file "hg/mouseStuff/chainBridge/tests/makefile")
;; Depends on /hive
(delete-file "hg/utils/genePredToProt/tests/makefile")
;; Unclear why this fails
(delete-file "hg/utils/hgvsToVcf/tests/makefile")
;; Wants network
(substitute* "hg/utils/hubCheck/tests/makefile"
(("^test::.*") "test:: one two\n"))
#t)))
;; Install happens during the 'build phase.
;; Install the website files too
(replace 'install
(lambda _
(invoke "make" "doc-install")
#t))
(add-after 'install 'create-hg-conf
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(with-output-to-file (string-append out "/cgi-bin/hg.conf")
(lambda ()
(display
"include /var/lib/genome/hg.conf\n")))
#t)))
(add-after 'install 'create-symlink
(lambda* (#:key inputs #:allow-other-keys)
(mkdir-p "htdocs")
;; Fallback location for fonts.
(symlink (string-append (assoc-ref inputs "gs-fonts")
"/share/fonts/type1/ghostscript")
"htdocs/urw-fonts")
#t)))))
(inputs
`(("freetype" ,freetype)
("libpng" ,libpng)
("mysql:dev" ,mariadb "dev")
("mysql:lib" ,mariadb "lib")
("openssl" ,openssl)
("perl" ,perl)
("python2" ,python-2)
("zlib" ,zlib)))
(native-inputs
`(("bedtools" ,bedtools)
("gs-fonts" ,gs-fonts)
("pkg-config" ,pkg-config)
("python" ,python)
("rsync" ,rsync) ; For installing js files from the source checkout
("tcl" ,tcl)
("tcsh" ,tcsh)
("util-linux:lib" ,util-linux "lib")
("which" ,(@ (gnu packages base) which))))
(home-page "https://www.genome.ucsc.edu/")
(synopsis "Structural variants detector for next-gen sequencing data")
(description
"The UCSC Genome Browser provides a rapid and reliable display of any
requested portion of genomes at any scale, together with dozens of aligned
annotation tracks (known genes, predicted genes, ESTs, mRNAs, CpG islands,
assembly gaps and coverage, chromosomal bands, mouse homologies, and more).
Half of the annotation tracks are computed at UCSC from publicly available
sequence data. The remaining tracks are provided by collaborators worldwide.
Users can also add their own custom tracks to the browser for educational or
research purposes.
The Genome Browser stacks annotation tracks beneath genome coordinate positions,
allowing rapid visual correlation of different types of information. The user
can look at a whole chromosome to get a feel for gene density, open a specific
cytogenetic band to see a positionally mapped disease gene candidate, or zoom in
to a particular gene to view its spliced ESTs and possible alternative splicing.
The Genome Browser itself does not draw conclusions; rather, it collates all
relevant information in one location, leaving the exploration and interpretation
to the user.")
(license (list
license:bsd-0 ; kent/src/{utils,lib,inc,tabStorm,parasol,hg/ausoSql,hg/autoXml}
license:bsd-3 ; these two for bundled htslib-1.3
license:expat
(license:non-copyleft
"https://www.genome.ucsc.edu/license/"
"Free for academic/non-profit/personal use only.")
(license:non-copyleft ; Blat, In-Silico PCR
"http://www.kentinformatics.com/index.html"
"Free for universities and non-profit institutions.")))))
(define-public bam2fastx
(package
(name "bam2fastx")
(version "1.3.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/PacificBiosciences/bam2fastx")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0pyfmvh874w29kaq6gbb1bd86135qs2jc4f8giw98kxw1b2gjdh0"))))
(build-system meson-build-system)
(arguments
`(#:configure-flags '("-Dtests=true")))
(inputs
`(("boost" ,boost)
;("htslib" ,htslib)
("pbbam" ,pbbam)
("pbcopper" ,pbcopper)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)
("python-cram" ,python-cram)
("python-wrapper" ,python-wrapper)))
(home-page "https://github.com/PacificBiosciences/bam2fastx")
(synopsis "Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files")
(description "Conversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded data.")
(license license:bsd-3)))
(define-public pbbam-1
(package
(name "pbbam")
(version "1.6.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/PacificBiosciences/pbbam")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1z3sh9cmrap37ijrm0cv85j92r1xkq6kba2j10mrr4fv7fc9zzfb"))))
(build-system meson-build-system)
;; These libraries are listed as "Required" in the pkg-config file.
(propagated-inputs
`(("htslib" ,htslib)
("pbcopper" ,pbcopper)
("zlib" ,zlib)))
(inputs
`(("boost" ,boost)
("samtools" ,samtools)))
(native-inputs
`(("cram" ,python-cram)
("googletest" ,googletest)
("pkg-config" ,pkg-config)
("python" ,python-wrapper))) ; for tests
(home-page "https://github.com/PacificBiosciences/pbbam")
(synopsis "Work with PacBio BAM files")
(description
"The pbbam software package provides components to create, query, and
edit PacBio BAM files and associated indices. These components include a core
C++ library, bindings for additional languages, and command-line utilities.
This library is not intended to be used as a general-purpose BAM utility - all
input and output BAMs must adhere to the PacBio BAM format specification.
Non-PacBio BAMs will cause exceptions to be thrown.")
(license license:bsd-3)))
(define-public pbcopper
(package
(name "pbcopper")
(version "1.9.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/PacificBiosciences/pbcopper")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1pphklil5kn1ds796ch41bgvdf7yq03z6w5rgi572s8xg8k5b0xn"))))
(build-system meson-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-source
(lambda _
(substitute* "meson.build"
;; uncomment when upstreaming
;(("sse4\\.1") "nosse4.1")
(("v8\\.2-a") "v8-a"))
#t)))))
(inputs
`(("boost" ,boost)))
(native-inputs
`(("googletest" ,googletest)))
(home-page "https://github.com/PacificBiosciences/pbcopper")
(synopsis "Data structures, algorithms, and utilities for C++ applications")
(description "The pbcopper library provides a suite of data structures,
algorithms, and utilities for PacBio C++ applications.")
(license license:bsd-3)))
(define-public pbmm2
(package
(name "pbmm2")
(version "1.4.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/PacificBiosciences/pbmm2")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0c01c647c7wvq5jzkf68xsf0bn8mlyw0hbz2fiyirxg7hj05jyac"))))
(build-system meson-build-system)
(arguments
`(#:tests? #f)) ; TODO: Fix later.
(inputs
`(("boost" ,boost)
("htslib" ,htslib)
("minimap2" ,minimap2-for-pbmm2)
("pbbam" ,pbbam-1)
("pbcopper" ,pbcopper)))
(native-inputs
`(("cram" ,python-cram)
("googletest" ,googletest)
("pkg-config" ,pkg-config)
("samtools" ,samtools)
("util-linux" ,util-linux)
("zlib" ,zlib)))
(home-page "https://github.com/PacificBiosciences/pbmm2")
(synopsis "minimap2 frontend for PacBio native data formats")
(description "pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR.")
(license license:bsd-3)))
(define minimap2-for-pbmm2
(package
(name "minimap2")
(version "2.17")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pacificbiosciences/minimap2")
(commit (string-append version "-meson"))))
(file-name (git-file-name "minimap2-for-pbmm2" version))
(sha256
(base32
"1833y6xdcblz7k4fyclryd6lwibsisp4svp2mk9w6ivk64icl6jq"))))
(build-system meson-build-system)
(inputs
`(("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "https://lh3.github.io/minimap2/")
(synopsis "Pairwise aligner for genomic and spliced nucleotide sequences")
(description "Minimap2 is a versatile sequence alignment program that
aligns DNA or mRNA sequences against a large reference database. Typical use
cases include:
@enumerate
@item mapping PacBio or Oxford Nanopore genomic reads to the human genome;
@item finding overlaps between long reads with error rate up to ~15%;
@item splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA
reads against a reference genome;
@item aligning Illumina single- or paired-end reads;
@item assembly-to-assembly alignment;
@item full-genome alignment between two closely related species with
divergence below ~15%.
@end enumerate\n")
(license license:expat)))
(define-public hap.py
(package
(name "hap.py")
(version "0.3.14")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Illumina/hap.py")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1bnm7s86651p3zf6wahz5pic7n8416fx677kj47lwckr3syp2x1h"))
(modules '((guix build utils)))
(snippet
'(begin
(delete-file-recursively "external/bcftools.tar.gz")
(delete-file-recursively "external/boost_subset_1_58_0.tar.bz2")
(delete-file-recursively "external/htslib.tar.gz")
;; TODO: Unbundle jsoncpp.
;(delete-file-recursively "external/jsoncpp")
;(delete-file-recursively "external/klib")
(delete-file-recursively "external/samtools.tar.gz")
(delete-file-recursively "external/virtualenv-12.0.7.tar.gz")
(delete-file-recursively "external/zlib-1.2.8.tar.gz")
#t))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags (list "-DBUILD_VCFEVAL=ON")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'set-package-version
(lambda _
(substitute* "CMakeLists.txt"
(("git describe --tags --always")
(string-append "echo " ,version)))
#t))
;; A shared library conflicts with boost-static.
;; Not using boost-static causes linking errors.
;(add-after 'unpack 'build-dynamic-library
; (lambda _
; (substitute* "src/c++/lib/CMakeLists.txt"
; (("STATIC") "SHARED"))
; #t))
(add-after 'unpack 'fix-build
(lambda* (#:key inputs #:allow-other-keys)
(let ((zlib (assoc-ref inputs "zlib"))
(bcftools (assoc-ref inputs "bcftools"))
(boost (assoc-ref inputs "boost"))
(htslib (assoc-ref inputs "htslib"))
(samtools (assoc-ref inputs "samtools")))
(mkdir-p "external/bin")
(mkdir-p "external/lib")
(mkdir-p "external/include")
(mkdir-p "external/scratch/lib")
(substitute* "external/make_dependencies.sh"
(("zlib-1\\.2\\.8/libz\\.a") "lib/libz.so"))
(substitute* "src/cmake/FindHTSLib.cmake"
(("libhts\\.a") "libhts.so"))
(substitute* "CMakeLists.txt"
(("ZLIB_LIBRARIES .*\\)")
(string-append "ZLIB_LIBRARIES \"" zlib "/lib/libz.so\")")))
(setenv "BOOST_ROOT" boost)
(setenv "LDFLAGS"
(string-append "-L" (assoc-ref %build-inputs "htslib") "/lib"))
(symlink (string-append zlib "/lib/libz.so")
"external/scratch/lib/libz.so")
(symlink (string-append htslib "/include/htslib")
"external/include/htslib")
(symlink (string-append htslib "/lib/libhts.so")
"external/lib/libhts.so")
(symlink (string-append htslib "/lib/libhts.so")
"external/lib/libhts.so.3")
(symlink (string-append bcftools "/bin/bcftools")
"external/bin/bcftools")
(symlink (string-append samtools "/bin/samtools")
"external/bin/samtools")
#t)))
(add-after 'fix-build 'insert-rtg-tools
(lambda* (#:key inputs #:allow-other-keys)
(let ((rtg-tools (assoc-ref inputs "rtg-tools"))
(dest "external/libexec/rtg-tools-install"))
(mkdir-p (dirname dest))
(symlink rtg-tools dest)
#t)))
(replace 'configure
(lambda* (#:key outputs (configure-flags '()) (out-of-source? #t)
build-type target
#:allow-other-keys)
"Configure the given package."
(let* ((out (assoc-ref outputs "out"))
(abs-srcdir (getcwd))
(srcdir (if out-of-source?
(string-append "../" (basename abs-srcdir))
".")))
(format #t "source directory: ~s (relative from build: ~s)~%"
abs-srcdir srcdir)
(when out-of-source?
(mkdir "../build")
;; Extra code added here!!
(copy-recursively "external/scratch" "../build/scratch")
(copy-recursively "external/libexec" "../build/libexec")
(copy-recursively "external/lib" "../build/lib")
(copy-recursively "external/bin" "../build/bin")
(copy-recursively "external/include" "../build/include")
(chdir "../build"))
(format #t "build directory: ~s~%" (getcwd))
(let ((args `(,srcdir
,@(if build-type
(list (string-append "-DCMAKE_BUILD_TYPE="
build-type))
'())
,(string-append "-DCMAKE_INSTALL_PREFIX=" out)
;; ensure that the libraries are installed into /lib
"-DCMAKE_INSTALL_LIBDIR=lib"
;; add input libraries to rpath
"-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE"
;; add (other) libraries of the project itself to rpath
,(string-append "-DCMAKE_INSTALL_RPATH=" out "/lib")
;; enable verbose output from builds
"-DCMAKE_VERBOSE_MAKEFILE=ON"
;; Cross-build
,@(if target
(list (string-append "-DCMAKE_C_COMPILER="
target "-gcc")
(string-append "-DCMAKE_CXX_COMPILER="
target "-g++")
(if (string-contains target "mingw")
"-DCMAKE_SYSTEM_NAME=Windows"
"-DCMAKE_SYSTEM_NAME=Linux"))
'())
,@configure-flags)))
(format #t "running 'cmake' with arguments ~s~%" args)
(apply invoke "cmake" args)))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "./bin/test_haplotypes"))
#t))
(add-before 'install 'remove-extra-files
(lambda _
(delete-file "bin/bcftools")
(delete-file "bin/samtools")
(delete-file "bin/test_haplotypes")
(delete-file "lib/libhts.so")
(delete-file "lib/libhts.so.3")
#t))
(add-after 'install 'wrap-programs
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(bcftools (assoc-ref inputs "bcftools"))
(samtools (assoc-ref inputs "samtools")))
(for-each
(lambda (file)
(wrap-script file
`("PYTHONPATH" ":" prefix (,(getenv "PYTHONPATH")))
`("PATH" ":" prefix (,(string-append bcftools "/bin")
,(string-append samtools "/bin")))))
(find-files (string-append out "/bin") "\\.py$"))
#t))))))
(inputs
`(("bcftools" ,bcftools)
("boost" ,boost-static) ; has to be boost-static
("guile" ,guile-3.0) ; for wrap-script
("htslib" ,htslib)
;; The software specifically states python-2.
("python" ,python-2)
("python2-bx-python" ,python2-bx-python)
("python2-numpy" ,python2-numpy)
("python2-pandas" ,python2-pandas)
("python2-pysam" ,python2-pysam)
("python2-scipy" ,python2-scipy)
("rtg-tools" ,rtg-tools)
("samtools" ,samtools)
("zlib" ,zlib)))
(home-page "https://github.com/Illumina/hap.py")
(synopsis "Haplotype VCF comparison tools")
(description
"This is a set of programs based on htslib to benchmark variant calls
against gold standard truth datasets.
The main two tools are @code{hap.py} (diploid precision/recall evaluation) and
@code{som.py} (somatic precision/recall evaluation -- this ignores the GT and
just checks for presence of alleles). Other tools are @code{qfy.py} (which just
executes the quantification step of the analysis pipeline, this requires a
GA4GH-intermediate VCF file), and @code{pre.py}, which is @code{hap.py}'s input
cleaning and variant normalisation step.
To run the bundled rtg-tools software you will also need java. The
@code{icedtea:jdk} output should work nicely.")
(license (list license:expat ; bundled jsoncpp, klib
license:bsd-2))))
(define-public braker
(package
(name "braker")
(version "2.1.6")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Gaius-Augustus/BRAKER")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0jx9ycyh8s42yb4va84mcjyh7m95wzvf42skc3p4pvc5r7c5ns41"))))
(build-system perl-build-system)
(arguments
`(#:modules ((srfi srfi-26)
,@%perl-build-system-modules)
#:phases
(modify-phases %standard-phases
(delete 'configure) ; No configure script.
(delete 'build)
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "prove" "--verbose" "--lib" "t"))))
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(for-each
(cut install-file <> bin)
(find-files "scripts" "\\.(py|pl|pm)$"))
(for-each
(cut wrap-script <>
`("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")
,bin)))
;; braker.pl is the entry point so wrap it separately.
(delete (string-append bin "/braker.pl")
(find-files bin "\\.pl$")))
(wrap-script (string-append bin "/braker.pl")
`("PERL5LIB" ":" prefix (,(getenv "PERL5LIB")
,bin))
`("PATH" ":" prefix (,(assoc-ref inputs "augustus")
;,(assoc-ref inputs "genemark")
,(assoc-ref inputs "bamtools")
,(assoc-ref inputs "samtools")
,(assoc-ref inputs "prothint")
;,(assoc-ref inputs "genomethreader")
,(assoc-ref inputs "spaln")
,(assoc-ref inputs "exonerate")
,(assoc-ref inputs "ncbi-blast")
,(assoc-ref inputs "diamond")
,(assoc-ref inputs "cdbfasta")
,(assoc-ref inputs "gushr")
,(assoc-ref inputs "ucsc")))
;`("GENEMARK_PATH" "=" (,(string-append (assoc-ref inputs "genemark") "/bin")))
`("AUGUSTUS_BIN_PATH" "=" (,(string-append (assoc-ref inputs "augustus") "/bin")))
`("AUGUSTUS_AUGUSTUS_SCRIPTS_PATH" "=" (,(string-append (assoc-ref inputs "augustus") "/share/augustus")))
`("PYTHON3_PATH" "=" (,(string-append (assoc-ref inputs "python") "/bin")))
`("BAMTOOLS_PATH" "=" (,(string-append (assoc-ref inputs "bamtools") "/bin")))
`("DIAMOND_PATH" "=" (,(string-append (assoc-ref inputs "diamond") "/bin")))
`("BLAST_PATH" "=" (,(string-append (assoc-ref inputs "blast+") "/bin")))
`("PROTHINT_PATH" "=" (,(string-append (assoc-ref inputs "prothint") "/bin")))
`("SAMTOOLS_PATH" "=" (,(string-append (assoc-ref inputs "samtools") "/bin")))
`("CDBTOOLS_PATH" "=" (,(string-append (assoc-ref inputs "cdbfasta") "/bin")))
`("ALIGNMENT_TOOL_PATH" "=" (,(string-append (assoc-ref inputs "spaln") "/bin/spaln")
,(string-append (assoc-ref inputs "exonerate") "/bin/exonerate")))
;`("MAKEHUB_PATH" "=" (,(string-append (assoc-ref inputs "makehub") "/bin")))
)))))))
(inputs
`(("guile" ,guile-3.0) ; for wrap-script
("augustus" ,augustus-bio)
;("genemark" ,genemark)
("bamtools" ,bamtools)
("samtools" ,samtools)
("prothint" ,prothint)
;("genometracker" ,genometracker)
("spaln" ,spaln)
("exonerate" ,exonerate)
("ncbi-blast" ,blast+)
("diamond" ,diamond)
("cdbfasta" ,cdbfasta) ; provides cdbfasta and cdbyank
("gushr" ,gushr)
;("makehub" ,makehub)
("ucsc" ,ucsc-genome-browser) ; provides bin/twoBitInfo and bin/faToTwoBit
("perl" ,perl)
("perl-hash-merge" ,perl-hash-merge)
("perl-math-utils" ,perl-math-utils)
("perl-mce" ,perl-mce)
("perl-module-load-conditional" ,perl-module-load-conditional)
("perl-parallel-forkmanager" ,perl-parallel-forkmanager)
("perl-yaml" ,perl-yaml)
("python" ,python)))
(home-page "https://github.com/Gaius-Augustus/BRAKER")
(synopsis
"Pipeline for fully automated prediction of protein coding gene structures")
(description "The rapidly growing number of sequenced genomes requires
fully automated methods for accurate gene structure annotation. With this goal
in mind, we have developed BRAKER1, a combination of GeneMark-ET and AUGUSTUS
that uses genomic and RNA-Seq data to automatically generate full gene structure
annotations in novel genome.
However, the quality of RNA-Seq data that is available for annotating a novel
genome is variable, and in some cases, RNA-Seq data is not available, at all.
BRAKER2 is an extension of BRAKER1 which allows for fully automated training of
the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein
homology information, and that integrates the extrinsic evidence from RNA-Seq
and protein homology information into the prediction.
In contrast to other available methods that rely on protein homology
information, BRAKER2 reaches high gene prediction accuracy even in the absence
of the annotation of very closely related species and in the absence of
RNA-Seq data.")
(license license:artistic2.0)))
(define-public prothint
(package
(name "prothint")
(version "2.6.0")
(source
(origin
;; Tests not included in release.
(method git-fetch)
(uri (git-reference
(url "https://github.com/gatech-genemark/ProtHint")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0fwz8rxlmfxn5im2ck0jnqi3qaps1rnpkbh0l8k0waw2di5982zf"))
(modules '((guix build utils)))
(snippet
'(begin
;; Lets at least remove the executables ...
(delete-file "dependencies/diamond")
(delete-file "dependencies/probuild")
(delete-file "dependencies/spaln")
(delete-file "dependencies/spaln_boundary_scorer")))))
(build-system perl-build-system)
(arguments
`(#:modules ((srfi srfi-26)
(guix build perl-build-system)
(guix build utils))
#:tests? #f ; TODO: Test suite fails, or packaging is wrong?
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'adjust-source
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "bin/spalnBatch.sh"
(("\\$binDir/\\.\\./dependencies/spaln\\\"")
(string-append (assoc-ref inputs "spaln") "/bin/spaln\""))
(("\\$binDir/\\.\\./dependencies/spaln_boundary_scorer\\\"")
(string-append (assoc-ref inputs "spaln-boundary-scorer")
"/bin/spaln_boundary_scorer\""))
(("\\$binDir/\\.\\./dependencies/spaln_table\\\"")
(string-append (assoc-ref inputs "spaln")
"/share/spaln/table\"")))))
(delete 'configure)
(delete 'build)
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(substitute* "tests/common.py"
(("/bin/bash") (which "bash")))
(invoke "./tests/test_ProtHint.py")
(invoke "./tests/test_Spaln.py")
(invoke "./tests/test_iter.py"))))
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(for-each (cut install-file <> bin)
(find-files "bin" "\\.(pl|py|sh)$"))
(for-each
(cut wrap-script <>
`("PERL5LIB" ":" prefix (,(getenv "PERL5LIB"))))
(find-files bin "\\.pl$"))
(for-each
(cut wrap-script <>
`("PATH" ":" prefix (,(assoc-ref inputs "coreutils")
,(assoc-ref inputs "diamond")
;,(assoc-ref inputs "genemark")
,(assoc-ref inputs "grep")
,(assoc-ref inputs "spaln"))))
(find-files bin "\\.py$"))))))))
(inputs
`(("guile" ,guile-3.0) ; for wrap-script
;("genemark" ,genemark)
("spaln" ,spaln)
("spaln-boundary-scorer" ,spaln-boundary-scorer)
("diamond" ,diamond)
("grep" ,grep)
("perl" ,perl)
("perl-mce" ,perl-mce)
("perl-math-utils" ,perl-math-utils)
("perl-yaml" ,perl-yaml)
("python" ,python)))
(home-page "https://github.com/gatech-genemark/ProtHint")
(synopsis
"Protein hint generation pipeline for gene finding in eukaryotic genomes")
(description "ProtHint is a pipeline for predicting and scoring hints (in
the form of introns, start and stop codons) in the genome of interest by mapping
and spliced aligning predicted genes to a database of reference protein
sequences.")
;; Licensee may use the Product solely for Licensee's own internal research purposes.
(license license:non-copyleft)))
(define-public cdbfasta
(let ((commit "014498c66eebdd59b6f1b97e8aad0fcedbdd20b1") ; Oct 5, 2018
(revision "4"))
(package
(name "cdbfasta")
(version (git-version "0.0.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gpertea/cdbfasta")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1gqgv3q9qwdq6lqnxd9xnfc7bzkxkiz4crr0vmywafsvwvg6nghk"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ; TODO: run test suite.
#:phases
(modify-phases %standard-phases
(delete 'configure) ; No configure script.
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "perl" "perltest.pl" "<fasta.cidx>" "<key>"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out")
"/bin/")))
(install-file "cdbfasta" bin)
(install-file "cdbyank" bin)
#t))))))
(inputs
`(("zlib" ,zlib)))
(native-inputs
`(("perl" ,perl)))
(home-page "https://github.com/gpertea/cdbfasta")
(synopsis "CDB (Constant DataBase) indexing and retrieval tools for FASTA files")
(description
"This package provides platform independent file-based hashing tools
(cdbfasta and cdbyank) that can be used for creating indices for quick retrieval
of any particular sequences from large multi-FASTA files.")
(license license:artistic2.0))))
(define-public spaln
(package
(name "spaln")
(version "2.4.11")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ogotoh/spaln")
(commit (string-append "ver." version))))
(file-name (git-file-name name version))
(sha256
(base32
"049jmaf06v8h8b7fxnwf713dg1hkpb1nf3v4glkvxmq9jwv3d90y"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
(let ((out (assoc-ref %outputs "out")))
(list "--use_zlib=1"
(string-append "--exec_prefix=" out "/bin")
(string-append "--table_dir=" out "/share/spaln/table")
(string-append "--alndbs_dir=" out "/share/spaln/seqdb")))
#:test-target "test"
#:tests? #f ; test.sh not included in source
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "src")))
(add-before 'configure 'adjust-source
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "Makefile.in"
(("CFLAGS =") "CFLAGS +=")
(("(\\s+)\\./makmdm.*" all space)
(string-append space "chmod +w $(table_dir)/mdm_*\n" all
space "chmod -w $(table_dir)/mdm_*\n")))))
(replace 'configure
(lambda* (#:key configure-flags #:allow-other-keys)
;; The custom configure script doesn't recognize some common flags.
(apply invoke "./configure" configure-flags)))
;; Move 'check phase to after 'install.
(delete 'check)
(add-after 'install 'check
(assoc-ref %standard-phases 'check))
(add-after 'install 'make-tarballs-writable
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(for-each make-file-writable (find-files out "\\.gz$")))))
(add-after 'install 'install-manpages
(lambda* (#:key outputs #:allow-other-keys)
(let ((man1 (string-append (assoc-ref outputs "out")
"/share/man/man1")))
(mkdir-p man1)
(install-file "../spaln.1" man1)
(install-file "../sortgrcd.1" man1))))
(add-before 'install-license-files 'chdir
(lambda _
(chdir "../"))))))
(inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/ogotoh/spaln")
(synopsis
"Genome mapping and spliced alignment of cDNA or amino acid sequences")
(description "@acronym{Spaln, space-efficient spliced alignment} is a
stand-alone program that maps and aligns a set of cDNA or protein sequences onto
a whole genomic sequence in a single job. Spaln also performs spliced or
ordinary alignment after rapid similarity search against a protein sequence
database, if a genomic segment or an amino acid sequence is given as a query.")
(license license:gpl2+)))
(define-public spaln-boundary-scorer
(let ((commit "b48977154a75a8559ff0398b8858dc2a51768632")
(revision "1"))
(package
(name "spaln-boundary-scorer")
(version "0.0.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gatech-genemark/spaln-boundary-scorer")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"1f2q37kgw1vk0g3xqq7dkq2wvl6vsfbc58g9g487mq7prjb7nkqc"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'check
(lambda* (#:key tests? test-target #:allow-other-keys)
(when tests?
(invoke "make" test-target)
(invoke "./test/t_spaln_boundary_scorer"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "spaln_boundary_scorer" bin)))))))
(home-page "https://github.com/gatech-genemark/spaln-boundary-scorer")
(synopsis
"Parse introns, starts, stops and exons from Spaln's alignment output and scores them")
(description "Spaln boundary scorer parses introns, starts, stops and
exons from Spaln's alignment output and scores them. Introns, starts and stops
are scored based on local alignment quality around their boundaries.")
;; https://github.com/gatech-genemark/spaln-boundary-scorer/issues/1
(license license:non-copyleft))))
;; Not currently working
(define-public genemark
(package
(name "genemark")
(version "4.68")
(source
(origin
(method url-fetch)
(uri "file:///gnu/store/1xjfwgqz6kif8a9dy0hlc3a67vjrpipx-gmes_linux_64.tar.gz")
(file-name "gmes_linux_64.tar.gz")
(sha256
(base32
"11j7fr3jmammicvdphq69sh8wmi56aipxiimb6vdfc9z3lafz308"))
(modules '((guix build utils)))
(snippet
'(begin
(delete-file-recursively "ProtHint")))))
(build-system gnu-build-system)
(arguments
`(
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(add-after 'unpack 'add-license-key
(lambda _
(setenv "HOME" (getcwd))
;; Provided key good until ~ 2022-09-04
(with-output-to-file ".gm_key"
(lambda _
(format #t
"AACCCACTCACGGGCCAGGGTTTGAGCACTCGAGCTAGTGCAGCATGTTTTTTTTTTTTTTTTCATATGAGCGCCAGTGG~@
454168340~%")))))
;; This doesn't work, it's statically linked
;(add-after 'unpack 'set-interpreter
; (lambda* (#:key inputs #:allow-other-keys)
; (invoke "patchelf" "--set-interpreter" (car (find-files (assoc-ref inputs "libc") "ld-linux.*\\.so")) "gmhmme3")))
(replace 'check
(lambda _
(invoke "bash" "check_install.bash")))
)))
(inputs
`(("perl" ,perl)
("perl-hash-merge" ,perl-hash-merge)
("perl-mce" ,perl-mce)
("perl-math-utils" ,perl-math-utils)
("perl-parallel-forkmanager" ,perl-parallel-forkmanager)
("perl-yaml" ,perl-yaml)
("python" ,python)))
(native-inputs
`(
;("patchelf" ,patchelf)
))
(home-page "http://exon.gatech.edu/GeneMark/license_download.cgi")
(synopsis "")
(description "")
;; Precompiled binary
(supported-systems '("x86_64-linux"))
;; Licensee may use the Product solely for Licensee's own internal research purposes.
(license license:non-copyleft)))
;; Name collision with augustus in games.
(define-public augustus-bio
(package
(name "augustus-bio")
(version "3.4.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/Gaius-Augustus/Augustus"
"/releases/download/v" version
"/augustus-" version ".tar.gz"))
(sha256
(base32
"1j0ny6v8v3hsk76w4f4vvcqzpjjn8qfvp5q1mdanglb2g1rp4rr4"))
(modules '((guix build utils)))
(snippet
'(begin
(for-each delete-file
(append
'("auxprogs/aln2wig/aln2wig"
"auxprogs/bam2hints/bam2hints"
"auxprogs/bam2wig/bam2wig"
"auxprogs/compileSpliceCands/compileSpliceCands"
"auxprogs/filterBam/data/BAMseek2011July24.jar"
"auxprogs/homGeneMapping/src/homGeneMapping"
"auxprogs/joingenes/joingenes"
"auxprogs/utrrnaseq/Debug/utrrnaseq")
(find-files "." "\\.pdf$")
(find-files "mansrc" "\\.1$")))
(for-each delete-file-recursively
'("bin"
"tests/__pycache__"
"tests/examples/__pycache__"
"tests/examples_test/__pycache__"
"tests/utils/__pycache__"))))))
(build-system gnu-build-system)
(arguments
`(#:test-target "unit_test"
#:make-flags (list (string-append "CC = " ,(cc-for-target)))
#:phases
(modify-phases %standard-phases
(delete 'configure) ; No configure script.
(add-after 'unpack 'adjust-sources
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "common.mk"
(("AUGVERSION =.*")
(string-append "AUGVERSION = ",version "\n")))
(substitute* '("src/Makefile"
"src/unittests/Makefile")
(("/usr/include/mysql ")
(string-append (assoc-ref inputs "mariadb:dev") "/include/mysql "))
(("/usr/include/mysql\\+\\+")
(string-append (assoc-ref inputs "mysql++") "/include/mysql++ "))
(("/usr/include/lpsolve")
(string-append (assoc-ref inputs "lpsolve") "/include/lpsolve")))
(substitute* '("auxprogs/bam2hints/Makefile"
"auxprogs/filterBam/src/Makefile")
(("/usr/include/bamtools")
(string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
(substitute* "auxprogs/bam2wig/Makefile"
(("/usr/include/htslib")
(string-append (assoc-ref inputs "htslib") "/include/htslib")))))
(add-after 'unpack 'remove-googletest
(lambda* (#:key inputs #:allow-other-keys)
(let ((gtest (assoc-ref inputs "googletest")))
(delete-file-recursively "src/googletest")
(substitute* "src/Makefile"
(("unittest: googletest") "unittest:"))
(substitute* "src/unittests/Makefile"
(("\\.\\./googletest/include") (string-append gtest "/include"))
(("-L\\.\\./googletest") (string-append "-L" gtest "/lib"))))))
;; This mimics 'make install'.
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(scripts (string-append out "/share/augustus")))
(mkdir-p scripts)
(mkdir-p bin)
(copy-recursively "config" scripts)
(copy-recursively "bin" scripts)
(copy-recursively "scripts" scripts)
(for-each
(lambda (binary)
(symlink (string-append "../share/augustus/" binary)
(string-append bin "/" binary)))
'("augustus" "etraining" "prepareAlign" "fastBlockSearch"
"load2db" "getSeq")))))
(add-after 'install 'install-manpages
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(man1 (string-append out "/share/man/man1")))
(for-each
(lambda (adoc)
(invoke "asciidoctor"
"-a" "docdate=''"
"-b" "manpage"
(string-append "--destination-dir=" man1)
adoc))
(find-files "mansrc" "\\.adoc$"))))))))
(inputs
`(("bamtools" ,bamtools)
("boost" ,boost)
("gsl" ,gsl)
("htslib" ,htslib)
("lpsolve" ,lpsolve)
("mariadb:lib" ,mariadb "lib")
("mysql++" ,mysql++)
("perl" ,perl)
("python" ,python)
("sqlite" ,sqlite)
("suitesparse" ,suitesparse)
("zlib" ,zlib)))
(native-inputs
`(("asciidoctor" ,ruby-asciidoctor)
("googletest" ,googletest)
("mariadb:dev" ,mariadb "dev")))
(home-page "http://bioinf.uni-greifswald.de/webaugustus/")
(synopsis "Genome annotation with AUGUSTUS")
(description "AUGUSTUS is a gene prediction program. It can be used as an
ab initio program, which means it bases its prediction purely on the sequence.
AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic
sources such as EST, MS/MS, protein alignments and syntenic genomic alignments.")
(license license:artistic2.0)))
;; TODO: Replace GoMoMa-1.6.2.jar with https://github.com/Jstacs/Jstacs
(define-public gushr
(let ((commit "ee26d5c7eee97170c6183089d57477b338a7bc4b")
(revision "1"))
(package
(name "gushr")
(version (git-version "0.0.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Gaius-Augustus/GUSHR")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"00alkahjzc6zgzfm7f6zcayjvgcs3kb90fb9v855gpqcxv3y1s40"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'configure) ; No configure script.
(delete 'build)
;; Override the test.sh file.
(replace 'check
(lambda* (#:key tests? parallel-tests? inputs #:allow-other-keys)
(when tests?
(with-directory-excursion "example"
(invoke "../gushr.py"
"--AUGUSTUS_SCRIPTS_PATH"
(string-append (assoc-ref inputs "augustus")
"/share/augustus")
"--bam" (assoc-ref inputs "RNAseq.bam")
"--gtf" "augustus.gtf"
"--genome" "genome.fa"
"--outfile_name_stem" "gushr"
"--cores" (if parallel-tests?
(number->string (parallel-job-count))
"1"))))))
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(install-file "gushr.py" bin)
(install-file "GeMoMa-1.6.2.jar" bin)
(wrap-script (string-append bin "/gushr.py")
`("PATH" ":" prefix (,(string-append (assoc-ref inputs "java")
"/bin")
,(string-append (assoc-ref inputs "samtools")
"/bin"))))))))))
(inputs
`(("guile" ,guile-3.0) ; for wrap-script
("augustus" ,augustus-bio)
("java" ,icedtea-8 "jdk")
("python" ,python)
("samtools" ,samtools)))
(native-inputs
`(("RNAseq.bam"
,(origin
(method url-fetch)
(uri "http://bioinf.uni-greifswald.de/bioinf/braker/RNAseq.bam")
(sha256
(base32
"1apmgh9irwhfnbpqwvcjasfs524g03i284bxbb8czdkqfsa74w47"))))))
(home-page "https://github.com/Gaius-Augustus/GUSHR")
(synopsis "Generating UTRs from SHort Reads")
(description "Assembly-free construction of UTRs from short read RNA-Seq
data on the basis of coding sequence annotation. This tool has been adapted to
the format needs of AUGUSTUS/BRAKER and employs GeMoMa for generating UTRs from
RNA-Seq coverage data.")
(license license:gpl3+))))
