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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016, 2020 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018, 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
;;; Copyright © 2020 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu 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 gnu)
#:use-module (guix build-system cmake)
#:use-module (guix build-system go)
#:use-module (guix build-system haskell)
#:use-module (guix build-system meson)
#:use-module (guix build-system ocaml)
#:use-module (guix build-system perl)
#:use-module (guix build-system python)
#:use-module (guix build-system r)
#:use-module (guix build-system ruby)
#:use-module (guix build-system scons)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
#:use-module (gnu packages autotools)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages bash)
#:use-module (gnu packages bison)
#:use-module (gnu packages bioconductor)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages code)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
#:use-module (gnu packages cran)
#:use-module (gnu packages curl)
#:use-module (gnu packages documentation)
#:use-module (gnu packages databases)
#:use-module (gnu packages datastructures)
#:use-module (gnu packages dlang)
#:use-module (gnu packages file)
#:use-module (gnu packages flex)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gd)
#:use-module (gnu packages golang)
#:use-module (gnu packages glib)
#:use-module (gnu packages graph)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages groff)
#:use-module (gnu packages gtk)
#:use-module (gnu packages guile)
#:use-module (gnu packages guile-xyz)
#:use-module (gnu packages haskell-check)
#:use-module (gnu packages haskell-web)
#:use-module (gnu packages haskell-xyz)
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages java)
#:use-module (gnu packages java-compression)
#:use-module (gnu packages jemalloc)
#:use-module (gnu packages linux)
#:use-module (gnu packages lisp-xyz)
#:use-module (gnu packages logging)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages man)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages ocaml)
#:use-module (gnu packages pcre)
#:use-module (gnu packages parallel)
#:use-module (gnu packages pdf)
#:use-module (gnu packages perl)
#:use-module (gnu packages perl-check)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages python-compression)
#:use-module (gnu packages python-science)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
#:use-module (gnu packages shells)
#:use-module (gnu packages sphinx)
#:use-module (gnu packages statistics)
#:use-module (gnu packages swig)
#:use-module (gnu packages tbb)
#:use-module (gnu packages tex)
#:use-module (gnu packages texinfo)
#:use-module (gnu packages textutils)
#:use-module (gnu packages time)
#:use-module (gnu packages tls)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
#:use-module (gnu packages xorg)
#:use-module (srfi srfi-1)
#:use-module (ice-9 match))
(define-public aragorn
(package
(name "aragorn")
(version "1.2.38")
(source (origin
(method url-fetch)
(uri (string-append
"http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn"
version ".tgz"))
(sha256
(base32
"09i1rg716smlbnixfm7q1ml2mfpaa2fpn3hwjg625ysmfwwy712b"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are no tests
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'build
(lambda _
(invoke "gcc"
"-O3"
"-ffast-math"
"-finline-functions"
"-o"
"aragorn"
(string-append "aragorn" ,version ".c"))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(man (string-append out "/share/man/man1")))
(install-file "aragorn" bin)
(install-file "aragorn.1" man))
#t)))))
(home-page "http://mbio-serv2.mbioekol.lu.se/ARAGORN")
(synopsis "Detect tRNA, mtRNA and tmRNA genes in nucleotide sequences")
(description
"Aragorn identifies transfer RNA, mitochondrial RNA and
transfer-messenger RNA from nucleotide sequences, based on homology to known
tRNA consensus sequences and RNA structure. It also outputs the secondary
structure of the predicted RNA.")
(license license:gpl2)))
(define-public bamm
(package
(name "bamm")
(version "1.7.3")
(source (origin
(method git-fetch)
;; BamM is not available on pypi.
(uri (git-reference
(url "https://github.com/Ecogenomics/BamM.git")
(commit version)
(recursive? #t)))
(file-name (git-file-name name version))
(sha256
(base32
"1p83ahi984ipslxlg4yqy1gdnya9rkn1v71z8djgxkm9d2chw4c5"))
(modules '((guix build utils)))
(snippet
`(begin
;; Delete bundled htslib.
(delete-file-recursively "c/htslib-1.3.1")
#t))))
(build-system python-build-system)
(arguments
`(#:python ,python-2 ; BamM is Python 2 only.
;; Do not use bundled libhts. Do use the bundled libcfu because it has
;; been modified from its original form.
#:configure-flags
(let ((htslib (assoc-ref %build-inputs "htslib")))
(list "--with-libhts-lib" (string-append htslib "/lib")
"--with-libhts-inc" (string-append htslib "/include/htslib")))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'autogen
(lambda _
(with-directory-excursion "c"
(let ((sh (which "sh")))
(for-each make-file-writable (find-files "." ".*"))
;; Use autogen so that 'configure' works.
(substitute* "autogen.sh" (("/bin/sh") sh))
(setenv "CONFIG_SHELL" sh)
(invoke "./autogen.sh")))
#t))
(delete 'build)
;; Run tests after installation so compilation only happens once.
(delete 'check)
(add-after 'install 'wrap-executable
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(path (getenv "PATH")))
(wrap-program (string-append out "/bin/bamm")
`("PATH" ":" prefix (,path))))
#t))
(add-after 'wrap-executable 'post-install-check
(lambda* (#:key inputs outputs #:allow-other-keys)
(setenv "PATH"
(string-append (assoc-ref outputs "out")
"/bin:"
(getenv "PATH")))
(setenv "PYTHONPATH"
(string-append
(assoc-ref outputs "out")
"/lib/python"
(string-take (string-take-right
(assoc-ref inputs "python") 5) 3)
"/site-packages:"
(getenv "PYTHONPATH")))
;; There are 2 errors printed, but they are safe to ignore:
;; 1) [E::hts_open_format] fail to open file ...
;; 2) samtools view: failed to open ...
(invoke "nosetests")
#t)))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("libtool" ,libtool)
("zlib" ,zlib)
("python-nose" ,python2-nose)
("python-pysam" ,python2-pysam)))
(inputs
`(("htslib" ,htslib-1.3) ; At least one test fails on htslib-1.4+.
("samtools" ,samtools)
("bwa" ,bwa)
("grep" ,grep)
("sed" ,sed)
("coreutils" ,coreutils)))
(propagated-inputs
`(("python-numpy" ,python2-numpy)))
(home-page "https://ecogenomics.github.io/BamM/")
(synopsis "Metagenomics-focused BAM file manipulator")
(description
"BamM is a C library, wrapped in python, to efficiently generate and
parse BAM files, specifically for the analysis of metagenomic data. For
instance, it implements several methods to assess contig-wise read coverage.")
(license license:lgpl3+)))
(define-public bamtools
(package
(name "bamtools")
(version "2.5.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pezmaster31/bamtools.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0nfb2ypcx9959xnbz6wxh6py3xfizgmg8nrknxl95c507m9hmq8b"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ;no "check" target
#:phases
(modify-phases %standard-phases
(add-before
'configure 'set-ldflags
(lambda* (#:key outputs #:allow-other-keys)
(setenv "LDFLAGS"
(string-append
"-Wl,-rpath="
(assoc-ref outputs "out") "/lib/bamtools"))
#t)))))
(inputs `(("zlib" ,zlib)))
(home-page "https://github.com/pezmaster31/bamtools")
(synopsis "C++ API and command-line toolkit for working with BAM data")
(description
"BamTools provides both a C++ API and a command-line toolkit for handling
BAM files.")
(license license:expat)))
(define-public bcftools
(package
(name "bcftools")
(version "1.9")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/samtools/bcftools/"
"releases/download/"
version "/bcftools-" version ".tar.bz2"))
(sha256
(base32
"1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg"))
(modules '((guix build utils)))
(snippet '(begin
;; Delete bundled htslib.
(delete-file-recursively "htslib-1.9")
#t))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
(list "--enable-libgsl")
#:test-target "test"
#:phases
(modify-phases %standard-phases
(add-before 'check 'patch-tests
(lambda _
(substitute* "test/test.pl"
(("/bin/bash") (which "bash")))
#t)))))
(native-inputs
`(("htslib" ,htslib)
("perl" ,perl)))
(inputs
`(("gsl" ,gsl)
("zlib" ,zlib)))
(home-page "https://samtools.github.io/bcftools/")
(synopsis "Utilities for variant calling and manipulating VCFs and BCFs")
(description
"BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All commands work
transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
;; The sources are dual MIT/GPL, but becomes GPL-only when USE_GPL=1.
(license (list license:gpl3+ license:expat))))
(define-public bedops
(package
(name "bedops")
(version "2.4.35")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/bedops/bedops.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0mmgsgwz5r9w76hzgxkxc9s9lkdhhaf7vr6i02b09vbswvs1fyqx"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f
#:make-flags (list (string-append "BINDIR=" %output "/bin"))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'unpack-tarballs
(lambda _
;; FIXME: Bedops includes tarballs of minimally patched upstream
;; libraries jansson, zlib, and bzip2. We cannot just use stock
;; libraries because at least one of the libraries (zlib) is
;; patched to add a C++ function definition (deflateInit2cpp).
;; Until the Bedops developers offer a way to link against system
;; libraries we have to build the in-tree copies of these three
;; libraries.
;; See upstream discussion:
;; https://github.com/bedops/bedops/issues/124
;; Unpack the tarballs to benefit from shebang patching.
(with-directory-excursion "third-party"
(invoke "tar" "xvf" "jansson-2.6.tar.bz2")
(invoke "tar" "xvf" "zlib-1.2.7.tar.bz2")
(invoke "tar" "xvf" "bzip2-1.0.6.tar.bz2"))
;; Disable unpacking of tarballs in Makefile.
(substitute* "system.mk/Makefile.linux"
(("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
(("\\./configure") "CONFIG_SHELL=bash ./configure"))
(substitute* "third-party/zlib-1.2.7/Makefile.in"
(("^SHELL=.*$") "SHELL=bash\n"))
#t))
(delete 'configure))))
(home-page "https://github.com/bedops/bedops")
(synopsis "Tools for high-performance genomic feature operations")
(description
"BEDOPS is a suite of tools to address common questions raised in genomic
studies---mostly with regard to overlap and proximity relationships between
data sets. It aims to be scalable and flexible, facilitating the efficient
and accurate analysis and management of large-scale genomic data.
BEDOPS provides tools that perform highly efficient and scalable Boolean and
other set operations, statistical calculations, archiving, conversion and
other management of genomic data of arbitrary scale. Tasks can be easily
split by chromosome for distributing whole-genome analyses across a
computational cluster.")
(license license:gpl2+)))
(define-public bedtools
(package
(name "bedtools")
(version "2.29.2")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/arq5x/bedtools2/releases/"
"download/v" version "/"
"bedtools-" version ".tar.gz"))
(sha256
(base32
"0m3hk6548846w83a9s5drsczvy67n2azx41kj71n03klb2gbzwg3"))))
(build-system gnu-build-system)
(arguments
'(#:test-target "test"
#:make-flags
(list (string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
(delete 'configure))))
(native-inputs
`(("python" ,python-wrapper)))
(inputs
`(("samtools" ,samtools)
("zlib" ,zlib)))
(home-page "https://github.com/arq5x/bedtools2")
(synopsis "Tools for genome analysis and arithmetic")
(description
"Collectively, the bedtools utilities are a swiss-army knife of tools for
a wide-range of genomics analysis tasks. The most widely-used tools enable
genome arithmetic: that is, set theory on the genome. For example, bedtools
allows one to intersect, merge, count, complement, and shuffle genomic
intervals from multiple files in widely-used genomic file formats such as BAM,
BED, GFF/GTF, VCF.")
(license license:expat)))
;; Later releases of bedtools produce files with more columns than
;; what Ribotaper expects.
(define-public bedtools-2.18
(package (inherit bedtools)
(name "bedtools")
(version "2.18.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/arq5x/bedtools2/"
"releases/download/v" version
"/bedtools-" version ".tar.gz"))
(sha256
(base32
"11rvca19ncg03kxd0wzlfx5ws7r3nisd0z8s9j9n182d8ksp2pxz"))))
(arguments
'(#:test-target "test"
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(for-each (lambda (file)
(install-file file bin))
(find-files "bin" ".*")))
#t)))))))
(define-public pbbam
(package
(name "pbbam")
(version "0.23.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/PacificBiosciences/pbbam.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0h9gkrpf2lrxklxp72xfl5bi3h5zcm5hprrya9gf0hr3xwlbpp0x"))))
(build-system meson-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'find-googletest
(lambda* (#:key inputs #:allow-other-keys)
;; It doesn't find gtest_main because there's no pkg-config file
;; for it. Find it another way.
(substitute* "tests/meson.build"
(("pbbam_gtest_dep = dependency\\('gtest_main'.*")
(format #f "cpp = meson.get_compiler('cpp')
pbbam_gtest_dep = cpp.find_library('gtest_main', dirs : '~a')\n"
(assoc-ref inputs "googletest"))))
#t)))
;; TODO: tests/pbbam_test cannot be linked
;; ld: tests/59830eb@@pbbam_test@exe/src_test_Accuracy.cpp.o:
;; undefined reference to symbol '_ZTIN7testing4TestE'
;; ld: /gnu/store/...-googletest-1.8.0/lib/libgtest.so:
;; error adding symbols: DSO missing from command line
#:tests? #f
#:configure-flags '("-Dtests=false")))
;; These libraries are listed as "Required" in the pkg-config file.
(propagated-inputs
`(("htslib" ,htslib)
("zlib" ,zlib)))
(inputs
`(("boost" ,boost)
("samtools" ,samtools)))
(native-inputs
`(("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 blasr-libcpp
(package
(name "blasr-libcpp")
(version "5.3.3")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/PacificBiosciences/blasr_libcpp.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0cn5l42zyq67sj0g2imqkhayz2iqvv0a1pgpbmlq0qynjmsrbfd2"))))
(build-system meson-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'link-with-hdf5
(lambda* (#:key inputs #:allow-other-keys)
(let ((hdf5 (assoc-ref inputs "hdf5")))
(substitute* "meson.build"
(("libblasr_deps = \\[" m)
(string-append
m
(format #f "cpp.find_library('hdf5', dirs : '~a'), \
cpp.find_library('hdf5_cpp', dirs : '~a'), "
hdf5 hdf5)))))
#t))
(add-after 'unpack 'find-googletest
(lambda* (#:key inputs #:allow-other-keys)
;; It doesn't find gtest_main because there's no pkg-config file
;; for it. Find it another way.
(substitute* "unittest/meson.build"
(("libblasr_gtest_dep = dependency\\('gtest_main'.*")
(format #f "cpp = meson.get_compiler('cpp')
libblasr_gtest_dep = cpp.find_library('gtest_main', dirs : '~a')\n"
(assoc-ref inputs "googletest"))))
#t)))
;; TODO: unittest/libblasr_unittest cannot be linked
;; ld: ;; unittest/df08227@@libblasr_unittest@exe/alignment_utils_FileUtils_gtest.cpp.o:
;; undefined reference to symbol
;; '_ZN7testing8internal9DeathTest6CreateEPKcPKNS0_2REES3_iPPS1_'
;; ld: /gnu/store/...-googletest-1.8.0/lib/libgtest.so:
;; error adding symbols: DSO missing from command line
#:tests? #f
#:configure-flags '("-Dtests=false")))
(inputs
`(("boost" ,boost)
("hdf5" ,hdf5)
("pbbam" ,pbbam)
("zlib" ,zlib)))
(native-inputs
`(("googletest" ,googletest)
("pkg-config" ,pkg-config)))
(home-page "https://github.com/PacificBiosciences/blasr_libcpp")
(synopsis "Library for analyzing PacBio genomic sequences")
(description
"This package provides three libraries used by applications for analyzing
PacBio genomic sequences. This library contains three sub-libraries: pbdata,
hdf and alignment.")
(license license:bsd-3)))
(define-public blasr
(package
(name "blasr")
(version "5.3.3")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/PacificBiosciences/blasr.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1skgy2mvz8gsgfh1gc2nfgwvpyzb1hpmp2cf2773h5wsj8nw22kl"))))
(build-system meson-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'link-with-hdf5
(lambda* (#:key inputs #:allow-other-keys)
(let ((hdf5 (assoc-ref inputs "hdf5")))
(substitute* "meson.build"
(("blasr_deps = \\[" m)
(string-append
m
(format #f "cpp.find_library('hdf5', dirs : '~a'), \
cpp.find_library('hdf5_cpp', dirs : '~a'), "
hdf5 hdf5)))))
#t)))
;; Tests require "cram" executable, which is not packaged.
#:tests? #f
#:configure-flags '("-Dtests=false")))
(inputs
`(("boost" ,boost)
("blasr-libcpp" ,blasr-libcpp)
("hdf5" ,hdf5)
("pbbam" ,pbbam)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "https://github.com/PacificBiosciences/blasr")
(synopsis "PacBio long read aligner")
(description
"Blasr is a genomic sequence aligner for processing PacBio long reads.")
(license license:bsd-3)))
(define-public ribotaper
(package
(name "ribotaper")
(version "1.3.1")
(source (origin
(method url-fetch)
(uri (string-append "https://ohlerlab.mdc-berlin.de/"
"files/RiboTaper/RiboTaper_Version_"
version ".tar.gz"))
(sha256
(base32
"0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'install 'wrap-executables
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")))
(for-each
(lambda (script)
(wrap-program (string-append out "/bin/" script)
`("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
'("create_annotations_files.bash"
"create_metaplots.bash"
"Ribotaper_ORF_find.sh"
"Ribotaper.sh")))
#t)))))
(inputs
`(("bedtools" ,bedtools-2.18)
("samtools" ,samtools-0.1)
("r-minimal" ,r-minimal)
("r-foreach" ,r-foreach)
("r-xnomial" ,r-xnomial)
("r-domc" ,r-domc)
("r-multitaper" ,r-multitaper)
("r-seqinr" ,r-seqinr)))
(home-page "https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/")
(synopsis "Define translated ORFs using ribosome profiling data")
(description
"Ribotaper is a method for defining translated @dfn{open reading
frames} (ORFs) using ribosome profiling (ribo-seq) data. This package
provides the Ribotaper pipeline.")
(license license:gpl3+)))
(define-public ribodiff
(package
(name "ribodiff")
(version "0.2.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ratschlab/RiboDiff.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0x75nlp7qnmm64jasbi6l21f2cy99r2cjyl6b4hr8zf2bq22drnz"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:phases
(modify-phases %standard-phases
;; Generate an installable executable script wrapper.
(add-after 'unpack 'patch-setup.py
(lambda _
(substitute* "setup.py"
(("^(.*)packages=.*" line prefix)
(string-append line "\n"
prefix "scripts=['scripts/TE.py'],\n")))
#t)))))
(inputs
`(("python-numpy" ,python2-numpy)
("python-matplotlib" ,python2-matplotlib)
("python-scipy" ,python2-scipy)
("python-statsmodels" ,python2-statsmodels)))
(native-inputs
`(("python-mock" ,python2-mock)
("python-nose" ,python2-nose)))
(home-page "https://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/")
(synopsis "Detect translation efficiency changes from ribosome footprints")
(description "RiboDiff is a statistical tool that detects the protein
translational efficiency change from Ribo-Seq (ribosome footprinting) and
RNA-Seq data. It uses a generalized linear model to detect genes showing
difference in translational profile taking mRNA abundance into account. It
facilitates us to decipher the translational regulation that behave
independently with transcriptional regulation.")
(license license:gpl3+)))
(define-public bioawk
(package
(name "bioawk")
(version "1.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/lh3/bioawk.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1pxc3zdnirxbf9a0az698hd8xdik7qkhypm7v6hn922x8y9qmspm"))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)))
(native-inputs
`(("bison" ,bison)))
(arguments
`(#:tests? #f ; There are no tests to run.
;; Bison must generate files, before other targets can build.
#:parallel-build? #f
#:phases
(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase.
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(man (string-append out "/share/man/man1")))
(mkdir-p man)
(copy-file "awk.1" (string-append man "/bioawk.1"))
(install-file "bioawk" bin))
#t)))))
(home-page "https://github.com/lh3/bioawk")
(synopsis "AWK with bioinformatics extensions")
(description "Bioawk is an extension to Brian Kernighan's awk, adding the
support of several common biological data formats, including optionally gzip'ed
BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It
also adds a few built-in functions and a command line option to use TAB as the
input/output delimiter. When the new functionality is not used, bioawk is
intended to behave exactly the same as the original BWK awk.")
(license license:x11)))
(define-public python-pybedtools
(package
(name "python-pybedtools")
(version "0.8.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "pybedtools" version))
(sha256
(base32
"14w5i40gi25clrr7h4wa2pcpnyipya8hrqi7nq77553zc5wf0df0"))))
(build-system python-build-system)
(arguments
`(#:modules ((ice-9 ftw)
(srfi srfi-1)
(srfi srfi-26)
(guix build utils)
(guix build python-build-system))
;; See https://github.com/daler/pybedtools/issues/192
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'disable-broken-tests
(lambda _
(substitute* "pybedtools/test/test_scripts.py"
;; This test freezes.
(("def test_intron_exon_reads")
"def _do_not_test_intron_exon_reads")
;; This test fails in the Python 2 build.
(("def test_venn_mpl")
"def _do_not_test_venn_mpl"))
(substitute* "pybedtools/test/test_helpers.py"
;; Requires internet access.
(("def test_chromsizes")
"def _do_not_test_chromsizes")
;; Broken as a result of the workaround used in the check phase
;; (see: https://github.com/daler/pybedtools/issues/192).
(("def test_getting_example_beds")
"def _do_not_test_getting_example_beds"))
;; This issue still occurs on python2
(substitute* "pybedtools/test/test_issues.py"
(("def test_issue_303")
"def _test_issue_303"))
#t))
;; TODO: Remove phase after it's part of PYTHON-BUILD-SYSTEM.
;; build system.
;; Force the Cythonization of C++ files to guard against compilation
;; problems.
(add-after 'unpack 'remove-cython-generated-files
(lambda _
(let ((cython-sources (map (cut string-drop-right <> 4)
(find-files "." "\\.pyx$")))
(c/c++-files (find-files "." "\\.(c|cpp|cxx)$")))
(define (strip-extension filename)
(string-take filename (string-index-right filename #\.)))
(define (cythonized? c/c++-file)
(member (strip-extension c/c++-file) cython-sources))
(for-each delete-file (filter cythonized? c/c++-files))
#t)))
(add-after 'remove-cython-generated-files 'generate-cython-extensions
(lambda _
(invoke "python" "setup.py" "cythonize")))
(replace 'check
(lambda _
(let* ((cwd (getcwd))
(build-root-directory (string-append cwd "/build/"))
(build (string-append
build-root-directory
(find (cut string-prefix? "lib" <>)
(scandir (string-append
build-root-directory)))))
(scripts (string-append
build-root-directory
(find (cut string-prefix? "scripts" <>)
(scandir build-root-directory)))))
(setenv "PYTHONPATH"
(string-append build ":" (getenv "PYTHONPATH")))
;; Executable scripts such as 'intron_exon_reads.py' must be
;; available in the PATH.
(setenv "PATH"
(string-append scripts ":" (getenv "PATH"))))
;; The tests need to be run from elsewhere...
(mkdir-p "/tmp/test")
(copy-recursively "pybedtools/test" "/tmp/test")
(with-directory-excursion "/tmp/test"
(invoke "pytest" "-v" "--doctest-modules")))))))
(propagated-inputs
`(("bedtools" ,bedtools)
("samtools" ,samtools)
("python-matplotlib" ,python-matplotlib)
("python-pysam" ,python-pysam)
("python-pyyaml" ,python-pyyaml)))
(native-inputs
`(("python-numpy" ,python-numpy)
("python-pandas" ,python-pandas)
("python-cython" ,python-cython)
("kentutils" ,kentutils) ; for bedGraphToBigWig
("python-six" ,python-six)
;; For the test suite.
("python-pytest" ,python-pytest)
("python-psutil" ,python-psutil)))
(home-page "https://pythonhosted.org/pybedtools/")
(synopsis "Python wrapper for BEDtools programs")
(description
"pybedtools is a Python wrapper for Aaron Quinlan's BEDtools programs,
which are widely used for genomic interval manipulation or \"genome algebra\".
pybedtools extends BEDTools by offering feature-level manipulations from with
Python.")
(license license:gpl2+)))
(define-public python2-pybedtools
(let ((pybedtools (package-with-python2 python-pybedtools)))
(package
(inherit pybedtools)
(native-inputs
`(("python2-pathlib" ,python2-pathlib)
,@(package-native-inputs pybedtools))))))
(define-public python-biom-format
(package
(name "python-biom-format")
(version "2.1.7")
(source
(origin
(method git-fetch)
;; Use GitHub as source because PyPI distribution does not contain
;; test data: https://github.com/biocore/biom-format/issues/693
(uri (git-reference
(url "https://github.com/biocore/biom-format.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1rna16lyk5aqhnv0dp77wwaplias93f1vw28ad3jmyw6hwkai05v"))
(modules '((guix build utils)))
(snippet '(begin
;; Delete generated C files.
(for-each delete-file (find-files "." "\\.c"))
#t))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'use-cython
(lambda _ (setenv "USE_CYTHON" "1") #t))
(add-after 'unpack 'disable-broken-tests
(lambda _
(substitute* "biom/tests/test_cli/test_validate_table.py"
(("^(.+)def test_invalid_hdf5" m indent)
(string-append indent
"@npt.dec.skipif(True, msg='Guix')\n"
m)))
(substitute* "biom/tests/test_table.py"
(("^(.+)def test_from_hdf5_issue_731" m indent)
(string-append indent
"@npt.dec.skipif(True, msg='Guix')\n"
m)))
#t))
(add-before 'reset-gzip-timestamps 'make-files-writable
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(for-each (lambda (file) (chmod file #o644))
(find-files out "\\.gz"))
#t))))))
(propagated-inputs
`(("python-numpy" ,python-numpy)
("python-scipy" ,python-scipy)
("python-flake8" ,python-flake8)
("python-future" ,python-future)
("python-click" ,python-click)
("python-h5py" ,python-h5py)
("python-pandas" ,python-pandas)))
(native-inputs
`(("python-cython" ,python-cython)
("python-pytest" ,python-pytest)
("python-pytest-cov" ,python-pytest-cov)
("python-nose" ,python-nose)))
(home-page "http://www.biom-format.org")
(synopsis "Biological Observation Matrix (BIOM) format utilities")
(description
"The BIOM file format is designed to be a general-use format for
representing counts of observations e.g. operational taxonomic units, KEGG
orthology groups or lipid types, in one or more biological samples
e.g. microbiome samples, genomes, metagenomes.")
(license license:bsd-3)
(properties `((python2-variant . ,(delay python2-biom-format))))))
(define-public python2-biom-format
(let ((base (package-with-python2 (strip-python2-variant python-biom-format))))
(package
(inherit base)
(arguments
(substitute-keyword-arguments (package-arguments base)
((#:phases phases)
`(modify-phases ,phases
;; Do not require the unmaintained pyqi library.
(add-after 'unpack 'remove-pyqi
(lambda _
(substitute* "setup.py"
(("install_requires.append\\(\"pyqi\"\\)") "pass"))
#t)))))))))
(define-public python-pairtools
(package
(name "python-pairtools")
(version "0.3.0")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mirnylab/pairtools")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0gr8y13q7sd6yai6df4aavl2470n1f9s3cib6r473z4hr8hcbwmc"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-references
(lambda _
(substitute* '("pairtools/pairtools_merge.py"
"pairtools/pairtools_sort.py")
(("/bin/bash") (which "bash")))
#t))
(replace 'check
(lambda* (#:key inputs outputs #:allow-other-keys)
(add-installed-pythonpath inputs outputs)
(with-directory-excursion "/tmp"
(invoke "pytest" "-v")))))))
(native-inputs
`(("python-cython" ,python-cython)
("python-nose" ,python-nose)
("python-pytest" ,python-pytest)))
(inputs
`(("python" ,python-wrapper)))
(propagated-inputs
`(("htslib" ,htslib) ; for bgzip, looked up in PATH
("samtools" ,samtools) ; looked up in PATH
("lz4" ,lz4) ; for lz4c
("python-click" ,python-click)
("python-numpy" ,python-numpy)))
(home-page "https://github.com/mirnylab/pairtools")
(synopsis "Process mapped Hi-C data")
(description "Pairtools is a simple and fast command-line framework to
process sequencing data from a Hi-C experiment. Process pair-end sequence
alignments and perform the following operations:
@itemize
@item detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end
sequences of Hi-C DNA molecules
@item sort @code{.pairs} files for downstream analyses
@item detect, tag and remove PCR/optical duplicates
@item generate extensive statistics of Hi-C datasets
@item select Hi-C pairs given flexibly defined criteria
@item restore @code{.sam} alignments from Hi-C pairs.
@end itemize
")
(license license:expat)))
(define-public bioperl-minimal
(let* ((inputs `(("perl-module-build" ,perl-module-build)
("perl-data-stag" ,perl-data-stag)
("perl-libwww" ,perl-libwww)
("perl-uri" ,perl-uri)))
(transitive-inputs
(map (compose package-name cadr)
(delete-duplicates
(concatenate
(map (compose package-transitive-target-inputs cadr) inputs))))))
(package
(name "bioperl-minimal")
(version "1.7.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/bioperl/bioperl-live")
(commit (string-append "release-"
(string-map (lambda (c)
(if (char=? c #\.)
#\- c)) version)))))
(file-name (git-file-name name version))
(sha256
(base32
"0wl8yvzcls59pwwk6m8ahy87pwg6nnibzy5cldbvmcwg2x2w7783"))))
(build-system perl-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after
'install 'wrap-programs
(lambda* (#:key outputs #:allow-other-keys)
;; Make sure all executables in "bin" find the required Perl
;; modules at runtime. As the PERL5LIB variable contains also
;; the paths of native inputs, we pick the transitive target
;; inputs from %build-inputs.
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin/"))
(path (string-join
(cons (string-append out "/lib/perl5/site_perl")
(map (lambda (name)
(assoc-ref %build-inputs name))
',transitive-inputs))
":")))
(for-each (lambda (file)
(wrap-program file
`("PERL5LIB" ":" prefix (,path))))
(find-files bin "\\.pl$"))
#t))))))
(inputs inputs)
(native-inputs
`(("perl-test-most" ,perl-test-most)))
(home-page "https://metacpan.org/release/BioPerl")
(synopsis "Bioinformatics toolkit")
(description
"BioPerl is the product of a community effort to produce Perl code which
is useful in biology. Examples include Sequence objects, Alignment objects
and database searching objects. These objects not only do what they are
advertised to do in the documentation, but they also interact - Alignment
objects are made from the Sequence objects, Sequence objects have access to
Annotation and SeqFeature objects and databases, Blast objects can be
converted to Alignment objects, and so on. This means that the objects
provide a coordinated and extensible framework to do computational biology.")
(license license:perl-license))))
(define-public python-biopython
(package
(name "python-biopython")
(version "1.70")
(source (origin
(method url-fetch)
;; use PyPi rather than biopython.org to ease updating
(uri (pypi-uri "biopython" version))
(sha256
(base32
"0nz4n9d2y2dg849gn1z0vjlkwcpzzkzy3fij7x94a6ixy2c54z2a"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-before 'check 'set-home
;; Some tests require a home directory to be set.
(lambda _ (setenv "HOME" "/tmp") #t)))))
(propagated-inputs
`(("python-numpy" ,python-numpy)))
(home-page "https://biopython.org/")
(synopsis "Tools for biological computation in Python")
(description
"Biopython is a set of tools for biological computation including parsers
for bioinformatics files into Python data structures; interfaces to common
bioinformatics programs; a standard sequence class and tools for performing
common operations on them; code to perform data classification; code for
dealing with alignments; code making it easy to split up parallelizable tasks
into separate processes; and more.")
(license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))
(define-public python2-biopython
(package-with-python2 python-biopython))
(define-public python-fastalite
(package
(name "python-fastalite")
(version "0.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "fastalite" version))
(sha256
(base32
"1qli6pxp77i9xn2wfciq2zaxhl82bdxb33cpzqzj1z25yd036wqj"))))
(build-system python-build-system)
(arguments
`(#:tests? #f)) ; Test data is not distributed.
(home-page "https://github.com/nhoffman/fastalite")
(synopsis "Simplest possible FASTA parser")
(description "This library implements a FASTA and a FASTQ parser without
relying on a complex dependency tree.")
(license license:expat)))
(define-public python2-fastalite
(package-with-python2 python-fastalite))
(define-public bpp-core
;; The last release was in 2014 and the recommended way to install from source
;; is to clone the git repository, so we do this.
;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
(let ((commit "7d8bced0d1a87291ea8dd7046b7fb5ff9c35c582"))
(package
(name "bpp-core")
(version (string-append "2.2.0-1." (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
(url "http://biopp.univ-montp2.fr/git/bpp-core")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"10djsq5vlnkilv436gnmh4irpk49v29pa69r6xiryg32xmvn909j"))))
(build-system cmake-build-system)
(arguments
`(#:parallel-build? #f))
(home-page "http://biopp.univ-montp2.fr")
(synopsis "C++ libraries for Bioinformatics")
(description
"Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. It is
Object Oriented and is designed to be both easy to use and computer efficient.
Bio++ intends to help programmers to write computer expensive programs, by
providing them a set of re-usable tools.")
(license license:cecill-c))))
(define-public bpp-phyl
;; The last release was in 2014 and the recommended way to install from source
;; is to clone the git repository, so we do this.
;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
(let ((commit "0c07167b629f68b569bf274d1ad0c4af83276ae2"))
(package
(name "bpp-phyl")
(version (string-append "2.2.0-1." (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
(url "http://biopp.univ-montp2.fr/git/bpp-phyl")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"1ssjgchzwj3iai26kyly7gwkdv8sk59nqhkb1wpap3sf5m6kyllh"))))
(build-system cmake-build-system)
(arguments
`(#:parallel-build? #f
;; If out-of-source, test data is not copied into the build directory
;; so the tests fail.
#:out-of-source? #f))
(inputs
`(("bpp-core" ,bpp-core)
("bpp-seq" ,bpp-seq)))
(home-page "http://biopp.univ-montp2.fr")
(synopsis "Bio++ phylogenetic Library")
(description
"Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
library provides phylogenetics-related modules.")
(license license:cecill-c))))
(define-public bpp-popgen
;; The last release was in 2014 and the recommended way to install from source
;; is to clone the git repository, so we do this.
;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
(let ((commit "e472bac9b1a148803895d747cd6d0c5904f85d9f"))
(package
(name "bpp-popgen")
(version (string-append "2.2.0-1." (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
(url "http://biopp.univ-montp2.fr/git/bpp-popgen")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"0yn82dzn1n5629nzja68xfrhi655709rjanyryb36vzkmymy6dw5"))))
(build-system cmake-build-system)
(arguments
`(#:parallel-build? #f
#:tests? #f)) ; There are no tests.
(inputs
`(("bpp-core" ,bpp-core)
("bpp-seq" ,bpp-seq)))
(home-page "http://biopp.univ-montp2.fr")
(synopsis "Bio++ population genetics library")
(description
"Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
library provides population genetics-related modules.")
(license license:cecill-c))))
(define-public bpp-seq
;; The last release was in 2014 and the recommended way to install from source
;; is to clone the git repository, so we do this.
;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
(let ((commit "6cfa07965ce152e5598a89df2fa80a75973bfa33"))
(package
(name "bpp-seq")
(version (string-append "2.2.0-1." (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
(url "http://biopp.univ-montp2.fr/git/bpp-seq")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"1nys5jq7jqvdg40d91wsmj3q2yzy4276cp7sp44n67p468f27zf2"))))
(build-system cmake-build-system)
(arguments
`(#:parallel-build? #f
;; If out-of-source, test data is not copied into the build directory
;; so the tests fail.
#:out-of-source? #f))
(inputs
`(("bpp-core" ,bpp-core)))
(home-page "http://biopp.univ-montp2.fr")
(synopsis "Bio++ sequence library")
(description
"Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
library provides sequence-related modules.")
(license license:cecill-c))))
(define-public bppsuite
;; The last release was in 2014 and the recommended way to install from source
;; is to clone the git repository, so we do this.
;; http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
(let ((commit "c516147f57aa50961121cd505bed52cd7603698b"))
(package
(name "bppsuite")
(version (string-append "2.2.0-1." (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
(url "http://biopp.univ-montp2.fr/git/bppsuite")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"1y87pxvw0jxjizhq2dr9g2r91md45k1p9ih2sl1yy1y3p934l2kb"))))
(build-system cmake-build-system)
(arguments
`(#:parallel-build? #f
#:tests? #f)) ; There are no tests.
(native-inputs
`(("groff" ,groff)
("man-db" ,man-db)
("texinfo" ,texinfo)))
(inputs
`(("bpp-core" ,bpp-core)
("bpp-seq" ,bpp-seq)
("bpp-phyl" ,bpp-phyl)
("bpp-phyl" ,bpp-popgen)))
(home-page "http://biopp.univ-montp2.fr")
(synopsis "Bioinformatics tools written with the Bio++ libraries")
(description
"Bio++ is a set of C++ libraries for Bioinformatics, including sequence
analysis, phylogenetics, molecular evolution and population genetics. This
package provides command line tools using the Bio++ library.")
(license license:cecill-c))))
(define-public blast+
(package
(name "blast+")
(version "2.7.1")
(source (origin
(method url-fetch)
(uri (string-append
"ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/"
version "/ncbi-blast-" version "+-src.tar.gz"))
(sha256
(base32
"1jlq0afxxgczpp35k6mxh8mn4jzq7vqcnaixk166sfj10wq8v9qh"))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove bundled bzip2, zlib and pcre.
(delete-file-recursively "c++/src/util/compress/bzip2")
(delete-file-recursively "c++/src/util/compress/zlib")
(delete-file-recursively "c++/src/util/regexp")
(substitute* "c++/src/util/compress/Makefile.in"
(("bzip2 zlib api") "api"))
;; Remove useless msbuild directory
(delete-file-recursively
"c++/src/build-system/project_tree_builder/msbuild")
#t))))
(build-system gnu-build-system)
(arguments
`(;; There are two(!) tests for this massive library, and both fail with
;; "unparsable timing stats".
;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats)
;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats)
#:tests? #f
#:out-of-source? #t
#:parallel-build? #f ; not supported
#:phases
(modify-phases %standard-phases
(add-before 'configure 'set-HOME
;; $HOME needs to be set at some point during the configure phase
(lambda _ (setenv "HOME" "/tmp") #t))
(add-after 'unpack 'enter-dir
(lambda _ (chdir "c++") #t))
(add-after 'enter-dir 'fix-build-system
(lambda _
(define (which* cmd)
(cond ((string=? cmd "date")
;; make call to "date" deterministic
"date -d @0")
((which cmd)
=> identity)
(else
(format (current-error-port)
"WARNING: Unable to find absolute path for ~s~%"
cmd)
#f)))
;; Rewrite hardcoded paths to various tools
(substitute* (append '("src/build-system/configure.ac"
"src/build-system/configure"
"src/build-system/helpers/run_with_lock.c"
"scripts/common/impl/if_diff.sh"
"scripts/common/impl/run_with_lock.sh"
"src/build-system/Makefile.configurables.real"
"src/build-system/Makefile.in.top"
"src/build-system/Makefile.meta.gmake=no"
"src/build-system/Makefile.meta.in"
"src/build-system/Makefile.meta_l"
"src/build-system/Makefile.meta_p"
"src/build-system/Makefile.meta_r"
"src/build-system/Makefile.mk.in"
"src/build-system/Makefile.requirements"
"src/build-system/Makefile.rules_with_autodep.in")
(find-files "scripts/common/check" "\\.sh$"))
(("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
(or (which* cmd) all)))
(substitute* (find-files "src/build-system" "^config.*")
(("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
(("^PATH=.*") ""))
;; rewrite "/var/tmp" in check script
(substitute* "scripts/common/check/check_make_unix.sh"
(("/var/tmp") "/tmp"))
;; do not reset PATH
(substitute* (find-files "scripts/common/impl/" "\\.sh$")
(("^ *PATH=.*") "")
(("action=/bin/") "action=")
(("export PATH") ":"))
#t))
(replace 'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out"))
(lib (string-append (assoc-ref outputs "lib") "/lib"))
(include (string-append (assoc-ref outputs "include")
"/include/ncbi-tools++")))
;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'.
(invoke "./configure.orig"
(string-append "--with-build-root=" (getcwd) "/build")
(string-append "--prefix=" out)
(string-append "--libdir=" lib)
(string-append "--includedir=" include)
(string-append "--with-bz2="
(assoc-ref inputs "bzip2"))
(string-append "--with-z="
(assoc-ref inputs "zlib"))
(string-append "--with-pcre="
(assoc-ref inputs "pcre"))
;; Each library is built twice by default, once
;; with "-static" in its name, and again
;; without.
"--without-static"
"--with-dll")
#t))))))
(outputs '("out" ; 21 MB
"lib" ; 226 MB
"include")) ; 33 MB
(inputs
`(("bzip2" ,bzip2)
("lmdb" ,lmdb)
("zlib" ,zlib)
("pcre" ,pcre)
("perl" ,perl)
("python" ,python-wrapper)))
(native-inputs
`(("cpio" ,cpio)))
(home-page "https://blast.ncbi.nlm.nih.gov")
(synopsis "Basic local alignment search tool")
(description
"BLAST is a popular method of performing a DNA or protein sequence
similarity search, using heuristics to produce results quickly. It also
calculates an “expect value” that estimates how many matches would have
occurred at a given score by chance, which can aid a user in judging how much
confidence to have in an alignment.")
;; Most of the sources are in the public domain, with the following
;; exceptions:
;; * Expat:
;; * ./c++/include/util/bitset/
;; * ./c++/src/html/ncbi_menu*.js
;; * Boost license:
;; * ./c++/include/util/impl/floating_point_comparison.hpp
;; * LGPL 2+:
;; * ./c++/include/dbapi/driver/odbc/unix_odbc/
;; * ASL 2.0:
;; * ./c++/src/corelib/teamcity_*
(license (list license:public-domain
license:expat
license:boost1.0
license:lgpl2.0+
license:asl2.0))))
(define-public bless
(package
(name "bless")
(version "1p02")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/bless-ec/bless.v"
version ".tgz"))
(sha256
(base32
"0rm0gw2s18dqwzzpl3c2x1z05ni2v0xz5dmfk3d33j6g4cgrlrdd"))
(modules '((guix build utils)))
(snippet
`(begin
;; Remove bundled boost, pigz, zlib, and .git directory
;; FIXME: also remove bundled sources for murmurhash3 and
;; kmc once packaged.
(delete-file-recursively "boost")
(delete-file-recursively "pigz")
(delete-file-recursively "google-sparsehash")
(delete-file-recursively "zlib")
(delete-file-recursively ".git")
#t))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target
#:make-flags
(list (string-append "ZLIB="
(assoc-ref %build-inputs "zlib:static")
"/lib/libz.a")
(string-append "LDFLAGS="
(string-join '("-lboost_filesystem"
"-lboost_system"
"-lboost_iostreams"
"-lz"
"-fopenmp"))))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'do-not-build-bundled-pigz
(lambda* (#:key inputs outputs #:allow-other-keys)
(substitute* "Makefile"
(("cd pigz/pigz-2.3.3; make") ""))
#t))
(add-after 'unpack 'patch-paths-to-executables
(lambda* (#:key inputs outputs #:allow-other-keys)
(substitute* "parse_args.cpp"
(("kmc_binary = .*")
(string-append "kmc_binary = \""
(assoc-ref outputs "out")
"/bin/kmc\";"))
(("pigz_binary = .*")
(string-append "pigz_binary = \""
(assoc-ref inputs "pigz")
"/bin/pigz\";")))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
(for-each (lambda (file)
(install-file file bin))
'("bless" "kmc/bin/kmc"))
#t)))
(delete 'configure))))
(native-inputs
`(("perl" ,perl)))
(inputs
`(("openmpi" ,openmpi)
("boost" ,boost)
("sparsehash" ,sparsehash)
("pigz" ,pigz)
("zlib:static" ,zlib "static")
("zlib" ,zlib)))
(supported-systems '("x86_64-linux"))
(home-page "https://sourceforge.net/p/bless-ec/wiki/Home/")
(synopsis "Bloom-filter-based error correction tool for NGS reads")
(description
"@dfn{Bloom-filter-based error correction solution for high-throughput
sequencing reads} (BLESS) uses a single minimum-sized bloom filter is a
correction tool for genomic reads produced by @dfn{Next-generation
sequencing} (NGS). BLESS produces accurate correction results with much less
memory compared with previous solutions and is also able to tolerate a higher
false-positive rate. BLESS can extend reads like DNA assemblers to correct
errors at the end of reads.")
(license license:gpl3+)))
(define-public bowtie
(package
(name "bowtie")
(version "2.3.4.3")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/BenLangmead/bowtie2.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1zl3cf327y2p7p03cavymbh7b00djc7lncfaqih33n96iy9q8ibp"))
(modules '((guix build utils)))
(snippet
'(begin
(substitute* "Makefile"
;; replace BUILD_HOST and BUILD_TIME for deterministic build
(("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
(("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
#t))))
(build-system gnu-build-system)
(arguments
'(#:make-flags
(list "allall"
"WITH_TBB=1"
(string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'check
(lambda _
(invoke "perl"
"scripts/test/simple_tests.pl"
"--bowtie2=./bowtie2"
"--bowtie2-build=./bowtie2-build")
#t)))))
(inputs
`(("tbb" ,tbb)
("zlib" ,zlib)
("python" ,python-wrapper)))
(native-inputs
`(("perl" ,perl)
("perl-clone" ,perl-clone)
("perl-test-deep" ,perl-test-deep)
("perl-test-simple" ,perl-test-simple)))
(home-page "http://bowtie-bio.sourceforge.net/bowtie2/index.shtml")
(synopsis "Fast and sensitive nucleotide sequence read aligner")
(description
"Bowtie 2 is a fast and memory-efficient tool for aligning sequencing
reads to long reference sequences. It is particularly good at aligning reads
of about 50 up to 100s or 1,000s of characters, and particularly good at
aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the
genome with an FM Index to keep its memory footprint small: for the human
genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports
gapped, local, and paired-end alignment modes.")
(supported-systems '("x86_64-linux"))
(license license:gpl3+)))
(define-public bowtie1
(package
(name "bowtie1")
(version "1.2.3")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/bowtie-bio/bowtie/"
version "/bowtie-src-x86_64.zip"))
(sha256
(base32
"0vmiqdhc9dzyfy9sh6vgi7k9xy2hiw8g87vbamnc6cgpm179zsa4"))
(modules '((guix build utils)))
(snippet
'(substitute* "Makefile"
;; replace BUILD_HOST and BUILD_TIME for deterministic build
(("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
(("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ; no "check" target
#:make-flags
(list "all"
(string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
(delete 'configure))))
(inputs
`(("tbb" ,tbb)
("zlib" ,zlib)))
(supported-systems '("x86_64-linux"))
(home-page "http://bowtie-bio.sourceforge.net/index.shtml")
(synopsis "Fast aligner for short nucleotide sequence reads")
(description
"Bowtie is a fast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to
keep its memory footprint small: typically about 2.2 GB for the human
genome (2.9 GB for paired-end).")
(license license:artistic2.0)))
(define-public tophat
(package
(name "tophat")
(version "2.1.1")
(source (origin
(method url-fetch)
(uri (string-append
"http://ccb.jhu.edu/software/tophat/downloads/tophat-"
version ".tar.gz"))
(sha256
(base32
"19add02kv2xhd6ihd779dr7x35ggym3jqr0m5c4315i1yfb0p11p"))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove bundled SeqAn and samtools
(delete-file-recursively "src/SeqAn-1.4.2")
(delete-file-recursively "src/samtools-0.1.18")
#t))))
(build-system gnu-build-system)
(arguments
'(#:parallel-build? #f ; not supported
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'use-system-samtools
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "src/Makefile.in"
(("(noinst_LIBRARIES = )\\$\\(SAMLIB\\)" _ prefix) prefix)
(("\\$\\(SAMPROG\\): \\$\\(SAMLIB\\)") "")
(("SAMPROG = samtools_0\\.1\\.18") "")
(("\\$\\(samtools_0_1_18_SOURCES\\)") "")
(("am__EXEEXT_1 = samtools_0\\.1\\.18\\$\\(EXEEXT\\)") ""))
(substitute* '("src/common.cpp"
"src/tophat.py")
(("samtools_0.1.18") (which "samtools")))
(substitute* '("src/common.h"
"src/bam2fastx.cpp")
(("#include \"bam.h\"") "#include <samtools/bam.h>")
(("#include \"sam.h\"") "#include <samtools/sam.h>"))
(substitute* '("src/bwt_map.h"
"src/map2gtf.h"
"src/align_status.h")
(("#include <bam.h>") "#include <samtools/bam.h>")
(("#include <sam.h>") "#include <samtools/sam.h>"))
#t)))))
(native-inputs
`(("gcc" ,gcc-5))) ;; doesn't build with later versions
(inputs
`(("boost" ,boost)
("bowtie" ,bowtie)
("ncurses" ,ncurses)
("perl" ,perl)
("python" ,python-2)
("samtools" ,samtools-0.1)
("seqan" ,seqan-1)
("zlib" ,zlib)))
(home-page "https://ccb.jhu.edu/software/tophat/index.shtml")
(synopsis "Spliced read mapper for RNA-Seq data")
(description
"TopHat is a fast splice junction mapper for nucleotide sequence
reads produced by the RNA-Seq method. It aligns RNA-Seq reads to
mammalian-sized genomes using the ultra high-throughput short read
aligner Bowtie, and then analyzes the mapping results to identify
splice junctions between exons.")
;; TopHat is released under the Boost Software License, Version 1.0
;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121589893
(license license:boost1.0)))
(define-public bwa
(package
(name "bwa")
(version "0.7.17")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/lh3/bwa/releases/download/v"
version "/bwa-" version ".tar.bz2"))
(sha256
(base32
"1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target
#:phases
(modify-phases %standard-phases
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(lib (string-append out "/lib"))
(doc (string-append out "/share/doc/bwa"))
(man (string-append out "/share/man/man1")))
(install-file "bwa" bin)
(install-file "libbwa.a" lib)
(install-file "README.md" doc)
(install-file "bwa.1" man))
#t))
;; no "configure" script
(delete 'configure))))
(inputs `(("zlib" ,zlib)))
;; Non-portable SSE instructions are used so building fails on platforms
;; other than x86_64.
(supported-systems '("x86_64-linux"))
(home-page "http://bio-bwa.sourceforge.net/")
(synopsis "Burrows-Wheeler sequence aligner")
(description
"BWA is a software package for mapping low-divergent sequences against a
large reference genome, such as the human genome. It consists of three
algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is
designed for Illumina sequence reads up to 100bp, while the rest two for
longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar
features such as long-read support and split alignment, but BWA-MEM, which is
the latest, is generally recommended for high-quality queries as it is faster
and more accurate. BWA-MEM also has better performance than BWA-backtrack for
70-100bp Illumina reads.")
(license license:gpl3+)))
(define-public bwa-pssm
(package (inherit bwa)
(name "bwa-pssm")
(version "0.5.11")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/pkerpedjiev/bwa-pssm.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"076c4q0cdqz8jgylb067y9zmvxglppnzi3qiscn0xiypgc6lgb5r"))))
(build-system gnu-build-system)
(inputs
`(("gdsl" ,gdsl)
("zlib" ,zlib)
("perl" ,perl)))
(home-page "http://bwa-pssm.binf.ku.dk/")
(synopsis "Burrows-Wheeler transform-based probabilistic short read mapper")
(description
"BWA-PSSM is a probabilistic short genomic sequence read aligner based on
the use of @dfn{position specific scoring matrices} (PSSM). Like many of the
existing aligners it is fast and sensitive. Unlike most other aligners,
however, it is also adaptible in the sense that one can direct the alignment
based on known biases within the data set. It is coded as a modification of
the original BWA alignment program and shares the genome index structure as
well as many of the command line options.")
(license license:gpl3+)))
(define-public bwa-meth
(package
(name "bwa-meth")
(version "0.2.2")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/brentp/bwa-meth.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"17j31i7zws5j7mhsq9x3qgkxly6mlmrgwhfq0qbflgxrmx04yaiz"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'keep-references-to-bwa
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "bwameth.py"
(("bwa (mem|index)" _ command)
(string-append (which "bwa") " " command))
;; There's an ill-advised check for "samtools" on PATH.
(("^checkX.*") ""))
#t)))))
(inputs
`(("bwa" ,bwa)))
(native-inputs
`(("python-toolshed" ,python-toolshed)))
(home-page "https://github.com/brentp/bwa-meth")
(synopsis "Fast and accurante alignment of BS-Seq reads")
(description
"BWA-Meth works for single-end reads and for paired-end reads from the
directional protocol (most common). It uses the method employed by
methylcoder and Bismark of in silico conversion of all C's to T's in both
reference and reads. It recovers the original read (needed to tabulate
methylation) by attaching it as a comment which BWA appends as a tag to the
read. It performs favorably to existing aligners gauged by number of on and
off-target reads for a capture method that targets CpG-rich region.")
(license license:expat)))
(define-public python-bx-python
(package
(name "python-bx-python")
(version "0.8.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "bx-python" version))
(sha256
(base32
"11kksg2rbzihpmcid823xvg42xi88m7sz58rzk29abybkxy0rszs"))))
(build-system python-build-system)
;; Tests fail because test data are not included
(arguments '(#:tests? #f))
(propagated-inputs
`(("python-numpy" ,python-numpy)
("python-six" ,python-six)))
(inputs
`(("zlib" ,zlib)))
(native-inputs
`(("python-lzo" ,python-lzo)
("python-nose" ,python-nose)
("python-cython" ,python-cython)))
(home-page "https://github.com/bxlab/bx-python")
(synopsis "Tools for manipulating biological data")
(description
"bx-python provides tools for manipulating biological data, particularly
multiple sequence alignments.")
(license license:expat)))
(define-public python2-bx-python
(package-with-python2 python-bx-python))
(define-public python-pysam
(package
(name "python-pysam")
(version "0.15.1")
(source (origin
(method git-fetch)
;; Test data is missing on PyPi.
(uri (git-reference
(url "https://github.com/pysam-developers/pysam.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1vj367w6xbn9bpmksm162l1aipf7cj97h1q83y7jcpm33ihwpf7x"))
(modules '((guix build utils)))
(snippet '(begin
;; Drop bundled htslib. TODO: Also remove samtools
;; and bcftools.
(delete-file-recursively "htslib")
#t))))
(build-system python-build-system)
(arguments
`(#:modules ((ice-9 ftw)
(srfi srfi-26)
(guix build python-build-system)
(guix build utils))
#:phases
(modify-phases %standard-phases
(add-before 'build 'set-flags
(lambda* (#:key inputs #:allow-other-keys)
(setenv "HTSLIB_MODE" "external")
(setenv "HTSLIB_LIBRARY_DIR"
(string-append (assoc-ref inputs "htslib") "/lib"))
(setenv "HTSLIB_INCLUDE_DIR"
(string-append (assoc-ref inputs "htslib") "/include"))
(setenv "LDFLAGS" "-lncurses")
(setenv "CFLAGS" "-D_CURSES_LIB=1")
#t))
(replace 'check
(lambda* (#:key inputs outputs #:allow-other-keys)
;; This file contains tests that require a connection to the
;; internet.
(delete-file "tests/tabix_test.py")
;; FIXME: This test fails
(delete-file "tests/AlignmentFile_test.py")
;; Add first subdirectory of "build" directory to PYTHONPATH.
(setenv "PYTHONPATH"
(string-append
(getenv "PYTHONPATH")
":" (getcwd) "/build/"
(car (scandir "build"
(negate (cut string-prefix? "." <>))))))
;; Step out of source dir so python does not import from CWD.
(with-directory-excursion "tests"
(setenv "HOME" "/tmp")
(invoke "make" "-C" "pysam_data")
(invoke "make" "-C" "cbcf_data")
;; Running nosetests without explicitly asking for a single
;; process leads to a crash. Running with multiple processes
;; fails because the tests are not designed to run in parallel.
;; FIXME: tests keep timing out on some systems.
(invoke "nosetests" "-v" "--processes" "1")))))))
(propagated-inputs
`(("htslib" ,htslib))) ; Included from installed header files.
(inputs
`(("ncurses" ,ncurses)
("curl" ,curl)
("zlib" ,zlib)))
(native-inputs
`(("python-cython" ,python-cython)
;; Dependencies below are are for tests only.
("samtools" ,samtools)
("bcftools" ,bcftools)
("python-nose" ,python-nose)))
(home-page "https://github.com/pysam-developers/pysam")
(synopsis "Python bindings to the SAMtools C API")
(description
"Pysam is a Python module for reading and manipulating files in the
SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It
also includes an interface for tabix.")
(license license:expat)))
(define-public python2-pysam
(package-with-python2 python-pysam))
(define-public python-twobitreader
(package
(name "python-twobitreader")
(version "3.1.6")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/benjschiller/twobitreader")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1qbxvv1h58cismbk1anpjrkpghsaiy64a11ir3lhy6qch6xf8n62"))))
(build-system python-build-system)
;; Tests are not included
(arguments '(#:tests? #f))
(native-inputs
`(("python-sphinx" ,python-sphinx)))
(home-page "https://github.com/benjschiller/twobitreader")
(synopsis "Python library for reading .2bit files")
(description
"twobitreader is a Python library for reading .2bit files as used by the
UCSC genome browser.")
(license license:artistic2.0)))
(define-public python2-twobitreader
(package-with-python2 python-twobitreader))
(define-public python-plastid
(package
(name "python-plastid")
(version "0.4.8")
(source (origin
(method url-fetch)
(uri (pypi-uri "plastid" version))
(sha256
(base32
"0l24dd3q66if8yj042m4s0g95n6acn7im1imqd3p6h8ns43kxhj8"))))
(build-system python-build-system)
(arguments
;; Some test files are not included.
`(#:tests? #f))
(propagated-inputs
`(("python-numpy" ,python-numpy)
("python-scipy" ,python-scipy)
("python-pandas" ,python-pandas)
("python-pysam" ,python-pysam)
("python-matplotlib" ,python-matplotlib)
("python-biopython" ,python-biopython)
("python-twobitreader" ,python-twobitreader)
("python-termcolor" ,python-termcolor)))
(native-inputs
`(("python-cython" ,python-cython)
("python-nose" ,python-nose)))
(home-page "https://github.com/joshuagryphon/plastid")
(synopsis "Python library for genomic analysis")
(description
"plastid is a Python library for genomic analysis – in particular,
high-throughput sequencing data – with an emphasis on simplicity.")
(license license:bsd-3)))
(define-public python2-plastid
(package-with-python2 python-plastid))
(define-public tetoolkit
(package
(name "tetoolkit")
(version "2.0.3")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mhammell-laboratory/tetoolkit.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1yzi0kfpzip8zpjb82x1ik6h22yzfyjiz2dv85v6as2awwqvk807"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2 ; not guaranteed to work with Python 3
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'make-writable
(lambda _
(for-each make-file-writable (find-files "."))
#t))
(add-after 'unpack 'patch-invocations
(lambda* (#:key inputs #:allow-other-keys)
(substitute* '("bin/TEtranscripts"
"bin/TEcount")
(("'sort ")
(string-append "'" (which "sort") " "))
(("'rm -f ")
(string-append "'" (which "rm") " -f "))
(("'Rscript'") (string-append "'" (which "Rscript") "'")))
(substitute* "TEToolkit/IO/ReadInputs.py"
(("BamToBED") (which "bamToBed")))
(substitute* "TEToolkit/Normalization.py"
(("\"Rscript\"")
(string-append "\"" (which "Rscript") "\"")))
#t))
(add-after 'install 'wrap-program
(lambda* (#:key outputs #:allow-other-keys)
;; Make sure the executables find R packages.
(let ((out (assoc-ref outputs "out")))
(for-each
(lambda (script)
(wrap-program (string-append out "/bin/" script)
`("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
'("TEtranscripts"
"TEcount")))
#t)))))
(inputs
`(("coreutils" ,coreutils)
("bedtools" ,bedtools)
("python-argparse" ,python2-argparse)
("python-pysam" ,python2-pysam)
("r-minimal" ,r-minimal)
("r-deseq2" ,r-deseq2)))
(home-page "https://github.com/mhammell-laboratory/tetoolkit")
(synopsis "Transposable elements in differential enrichment analysis")
(description
"This is package for including transposable elements in differential
enrichment analysis of sequencing datasets. TEtranscripts and TEcount take
RNA-seq (and similar data) and annotates reads to both genes and transposable
elements. TEtranscripts then performs differential analysis using DESeq2.
Note that TEtranscripts and TEcount rely on specially curated GTF files, which
are not included due to their size.")
(license license:gpl3+)))
(define-public cd-hit
(package
(name "cd-hit")
(version "4.6.8")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/weizhongli/cdhit"
"/releases/download/V" version
"/cd-hit-v" version
"-2017-0621-source.tar.gz"))
(sha256
(base32
"1b4mwm2520ixjbw57sil20f9iixzw4bkdqqwgg1fc3pzm6rz4zmn"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are no tests
#:make-flags
;; Executables are copied directly to the PREFIX.
(list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin")
;; Support longer sequences (e.g. Pacbio sequences)
"MAX_SEQ=60000000")
#:phases
(modify-phases %standard-phases
;; No "configure" script
(delete 'configure)
;; Remove sources of non-determinism
(add-after 'unpack 'be-timeless
(lambda _
(substitute* "cdhit-utility.c++"
((" \\(built on \" __DATE__ \"\\)") ""))
(substitute* "cdhit-common.c++"
(("__DATE__") "\"0\"")
(("\", %s, \" __TIME__ \"\\\\n\", date") ""))
#t))
;; The "install" target does not create the target directory.
(add-before 'install 'create-target-dir
(lambda* (#:key outputs #:allow-other-keys)
(mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
#t)))))
(inputs
`(("perl" ,perl)))
(home-page "http://weizhongli-lab.org/cd-hit/")
(synopsis "Cluster and compare protein or nucleotide sequences")
(description
"CD-HIT is a program for clustering and comparing protein or nucleotide
sequences. CD-HIT is designed to be fast and handle extremely large
databases.")
;; The manual says: "It can be copied under the GNU General Public License
;; version 2 (GPLv2)."
(license license:gpl2)))
(define-public clipper
(package
(name "clipper")
(version "1.2.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/YeoLab/clipper.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0fja1rj84wp9vpj8rxpj3n8zqzcqq454m904yp9as1w4phccirjb"))
(modules '((guix build utils)))
(snippet
'(begin
;; remove unnecessary setup dependency
(substitute* "setup.py"
(("setup_requires = .*") ""))
#t))))
(build-system python-build-system)
(arguments
`(#:python ,python-2 ; only Python 2 is supported
#:phases
(modify-phases %standard-phases
;; This is fixed in upstream commit
;; f6c2990198f906bf97730d95695b4bd5a6d01ddb.
(add-after 'unpack 'fix-typo
(lambda _
(substitute* "clipper/src/readsToWiggle.pyx"
(("^sc.*") ""))
#t)))))
(inputs
`(("htseq" ,python2-htseq)
("python-pybedtools" ,python2-pybedtools)
("python-cython" ,python2-cython)
("python-scikit-learn" ,python2-scikit-learn)
("python-matplotlib" ,python2-matplotlib)
("python-pandas" ,python2-pandas)
("python-pysam" ,python2-pysam)
("python-numpy" ,python2-numpy)
("python-scipy" ,python2-scipy)))
(native-inputs
`(("python-mock" ,python2-mock) ; for tests
("python-nose" ,python2-nose) ; for tests
("python-pytz" ,python2-pytz))) ; for tests
(home-page "https://github.com/YeoLab/clipper")
(synopsis "CLIP peak enrichment recognition")
(description
"CLIPper is a tool to define peaks in CLIP-seq datasets.")
(license license:gpl2)))
(define-public codingquarry
(package
(name "codingquarry")
(version "2.0")
(source (origin
(method url-fetch)
(uri (string-append
"mirror://sourceforge/codingquarry/CodingQuarry_v"
version ".tar.gz"))
(sha256
(base32
"0115hkjflsnfzn36xppwf9h9avfxlavr43djqmshkkzbgjzsz60i"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ; no "check" target
#:phases
(modify-phases %standard-phases
(delete 'configure)
(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/codingquarry")))
(install-file "INSTRUCTIONS.pdf" doc)
(copy-recursively "QuarryFiles"
(string-append out "/QuarryFiles"))
(install-file "CodingQuarry" bin)
(install-file "CufflinksGTF_to_CodingQuarryGFF3.py" bin))
#t)))))
(inputs `(("openmpi" ,openmpi)))
(native-search-paths
(list (search-path-specification
(variable "QUARRY_PATH")
(files '("QuarryFiles")))))
(native-inputs `(("python" ,python-2))) ; Only Python 2 is supported
(synopsis "Fungal gene predictor")
(description "CodingQuarry is a highly accurate, self-training GHMM fungal
gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
(home-page "https://sourceforge.net/projects/codingquarry/")
(license license:gpl3+)))
(define-public couger
(package
(name "couger")
(version "1.8.2")
(source (origin
(method url-fetch)
(uri (string-append
"http://couger.oit.duke.edu/static/assets/COUGER"
version ".zip"))
(sha256
(base32
"04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(replace
'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(copy-recursively "src" (string-append out "/src"))
(mkdir bin)
;; Add "src" directory to module lookup path.
(substitute* "couger"
(("from argparse")
(string-append "import sys\nsys.path.append(\""
out "\")\nfrom argparse")))
(install-file "couger" bin))
#t))
(add-after
'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Make sure 'couger' runs with the correct PYTHONPATH.
(let* ((out (assoc-ref outputs "out"))
(path (getenv "PYTHONPATH")))
(wrap-program (string-append out "/bin/couger")
`("PYTHONPATH" ":" prefix (,path))))
#t)))))
(inputs
`(("python" ,python-2)
("python2-pillow" ,python2-pillow)
("python2-numpy" ,python2-numpy)
("python2-scipy" ,python2-scipy)
("python2-matplotlib" ,python2-matplotlib)))
(propagated-inputs
`(("r-minimal" ,r-minimal)
("libsvm" ,libsvm)
("randomjungle" ,randomjungle)))
(native-inputs
`(("unzip" ,unzip)))
(home-page "http://couger.oit.duke.edu")
(synopsis "Identify co-factors in sets of genomic regions")
(description
"COUGER can be applied to any two sets of genomic regions bound by
paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify
putative co-factors that provide specificity to each TF. The framework
determines the genomic targets uniquely-bound by each TF, and identifies a
small set of co-factors that best explain the in vivo binding differences
between the two TFs.
COUGER uses classification algorithms (support vector machines and random
forests) with features that reflect the DNA binding specificities of putative
co-factors. The features are generated either from high-throughput TF-DNA
binding data (from protein binding microarray experiments), or from large
collections of DNA motifs.")
(license license:gpl3+)))
(define-public clustal-omega
(package
(name "clustal-omega")
(version "1.2.4")
(source (origin
(method url-fetch)
(uri (string-append "http://www.clustal.org/omega/clustal-omega-"
version ".tar.gz"))
(sha256
(base32
"1vm30mzncwdv881vrcwg11vzvrsmwy4wg80j5i0lcfk6dlld50w6"))))
(build-system gnu-build-system)
(inputs
`(("argtable" ,argtable)))
(home-page "http://www.clustal.org/omega/")
(synopsis "Multiple sequence aligner for protein and DNA/RNA")
(description
"Clustal-Omega is a general purpose multiple sequence alignment (MSA)
program for protein and DNA/RNA. It produces high quality MSAs and is capable
of handling data-sets of hundreds of thousands of sequences in reasonable
time.")
(license license:gpl2+)))
(define-public crossmap
(package
(name "crossmap")
(version "0.3.8")
(source (origin
(method url-fetch)
(uri (pypi-uri "CrossMap" version))
(sha256
(base32
"1sb2f2qbxya4fzw3yjl09vbrs8vfmw22zrygrvz004sf9gb1vkan"))))
(build-system python-build-system)
(inputs
`(("python-bx-python" ,python-bx-python)
("python-numpy" ,python-numpy)
("python-pybigwig" ,python-pybigwig)
("python-pysam" ,python-pysam)
("zlib" ,zlib)))
(native-inputs
`(("python-cython" ,python-cython)
("python-nose" ,python-nose)))
(home-page "http://crossmap.sourceforge.net/")
(synopsis "Convert genome coordinates between assemblies")
(description
"CrossMap is a program for conversion of genome coordinates or annotation
files between different genome assemblies. It supports most commonly used
file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
(license license:gpl2+)))
(define-public python-dnaio
(package
(name "python-dnaio")
(version "0.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "dnaio" version))
(sha256
(base32
"0f16m7hdlm0fz1n7y5asy0v9ghyrq17ni1p9iybq22ddzyd49r27"))))
(build-system python-build-system)
(native-inputs
`(("python-cython" ,python-cython)
("python-pytest" ,python-pytest)
("python-xopen" ,python-xopen)))
(home-page "https://github.com/marcelm/dnaio/")
(synopsis "Read FASTA and FASTQ files efficiently")
(description
"dnaio is a Python library for fast parsing of FASTQ and also FASTA
files. The code was previously part of the cutadapt tool.")
(license license:expat)))
(define-public python-deeptoolsintervals
(package
(name "python-deeptoolsintervals")
(version "0.1.9")
(source (origin
(method url-fetch)
(uri (pypi-uri "deeptoolsintervals" version))
(sha256
(base32
"1xnl80nblysj6dylj4683wgrfa425rkx4dp5k65hvwdns9pw753x"))))
(build-system python-build-system)
(inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/deeptools/deeptools_intervals")
(synopsis "Create GTF-based interval trees with associated meta-data")
(description
"This package provides a Python module creating/accessing GTF-based
interval trees with associated meta-data. It is primarily used by the
@code{deeptools} package.")
(license license:expat)))
(define-public python-deeptools
(package
(name "python-deeptools")
(version "3.4.3")
(source (origin
(method url-fetch)
(uri (pypi-uri "deepTools" version))
(sha256
(base32
"1azgjniss5ff6a90nicdjkxyjwqmi3gzfn09gra42hwlz19hipxb"))))
(build-system python-build-system)
(propagated-inputs
`(("python-matplotlib" ,python-matplotlib)
("python-numpy" ,python-numpy)
("python-numpydoc" ,python-numpydoc)
("python-py2bit" ,python-py2bit)
("python-pybigwig" ,python-pybigwig)
("python-pysam" ,python-pysam)
("python-scipy" ,python-scipy)
("python-deeptoolsintervals" ,python-deeptoolsintervals)
("python-plotly" ,python-plotly)))
(home-page "https://pypi.org/project/deepTools/")
(synopsis "Useful tools for exploring deep sequencing data")
(description "This package addresses the challenge of handling large amounts
of data that are now routinely generated from DNA sequencing centers.
@code{deepTools} contains useful modules to process the mapped reads data for
multiple quality checks, creating normalized coverage files in standard bedGraph
and bigWig file formats, that allow comparison between different files. Finally,
using such normalized and standardized files, deepTools can create many
publication-ready visualizations to identify enrichments and for functional
annotations of the genome.")
;; The file deeptools/cm.py is licensed under the BSD license. The
;; remainder of the code is licensed under the MIT license.
(license (list license:bsd-3 license:expat))))
(define-public cutadapt
(package
(name "cutadapt")
(version "2.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "cutadapt" version))
(sha256
(base32
"1vqmsfkm6llxzmsz9wcfcvzx9a9f8iabvwik2rbyn7nc4wm25z89"))))
(build-system python-build-system)
(inputs
`(("python-dnaio" ,python-dnaio)
("python-xopen" ,python-xopen)))
(native-inputs
`(("python-cython" ,python-cython)
("python-pytest" ,python-pytest)
("python-setuptools-scm" ,python-setuptools-scm)))
(home-page "https://cutadapt.readthedocs.io/en/stable/")
(synopsis "Remove adapter sequences from nucleotide sequencing reads")
(description
"Cutadapt finds and removes adapter sequences, primers, poly-A tails and
other types of unwanted sequence from high-throughput sequencing reads.")
(license license:expat)))
(define-public libbigwig
(package
(name "libbigwig")
(version "0.4.4")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/dpryan79/libBigWig.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"09693dmf1scdac5pyq6qyn8b4mcipvnmc370k9a5z41z81m3dcsj"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
#:tests? #f ; tests require access to the web
#:make-flags
(list "CC=gcc"
(string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
(delete 'configure))))
(inputs
`(("zlib" ,zlib)
("curl" ,curl)))
(native-inputs
`(("doxygen" ,doxygen)
;; Need for tests
("python" ,python-2)))
(home-page "https://github.com/dpryan79/libBigWig")
(synopsis "C library for handling bigWig files")
(description
"This package provides a C library for parsing local and remote BigWig
files.")
(license license:expat)))
(define-public python-pybigwig
(package
(name "python-pybigwig")
(version "0.3.17")
(source (origin
(method url-fetch)
(uri (pypi-uri "pyBigWig" version))
(sha256
(base32
"157x6v48y299zm382krf1dw08fdxg95im8lnabhp5vc94s04zxj1"))
(modules '((guix build utils)))
(snippet
'(begin
;; Delete bundled libBigWig sources
(delete-file-recursively "libBigWig")
#t))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'link-with-libBigWig
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "setup.py"
(("libs=\\[") "libs=[\"BigWig\", "))
#t)))))
(propagated-inputs
`(("python-numpy" ,python-numpy)))
(inputs
`(("libbigwig" ,libbigwig)
("zlib" ,zlib)
("curl" ,curl)))
(home-page "https://github.com/dpryan79/pyBigWig")
(synopsis "Access bigWig files in Python using libBigWig")
(description
"This package provides Python bindings to the libBigWig library for
accessing bigWig files.")
(license license:expat)))
(define-public python2-pybigwig
(package-with-python2 python-pybigwig))
(define-public python-dendropy
(package
(name "python-dendropy")
(version "4.4.0")
(source
(origin
(method git-fetch)
;; Source from GitHub so that tests are included.
(uri (git-reference
(url "https://github.com/jeetsukumaran/DendroPy.git")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"097hfyv2kaf4x92i4rjx0paw2cncxap48qivv8zxng4z7nhid0x9"))))
(build-system python-build-system)
(home-page "https://dendropy.org/")
(synopsis "Library for phylogenetics and phylogenetic computing")
(description
"DendroPy is a library for phylogenetics and phylogenetic computing: reading,
writing, simulation, processing and manipulation of phylogenetic
trees (phylogenies) and characters.")
(license license:bsd-3)))
(define-public python2-dendropy
(let ((base (package-with-python2 python-dendropy)))
(package
(inherit base)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'remove-failing-test
(lambda _
;; This test fails when the full test suite is run, as documented
;; at https://github.com/jeetsukumaran/DendroPy/issues/74
(substitute* "tests/test_dataio_nexml_reader_tree_list.py"
(("test_collection_comments_and_annotations")
"do_not_test_collection_comments_and_annotations"))
#t)))
,@(package-arguments base))))))
(define-public python-py2bit
(package
(name "python-py2bit")
(version "0.3.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "py2bit" version))
(sha256
(base32
"1vw2nvw1yrl7ikkqsqs1pg239yr5nspvd969r1x9arms1k25a1a5"))))
(build-system python-build-system)
(home-page "https://github.com/dpryan79/py2bit")
(synopsis "Access 2bit files using lib2bit")
(description
"This package provides Python bindings for lib2bit to access 2bit files
with Python.")
(license license:expat)))
(define-public deeptools
(package
(name "deeptools")
(version "3.1.3")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/deeptools/deepTools.git")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
;; This phase fails, but it's not needed.
(delete 'reset-gzip-timestamps))))
(inputs
`(("python-plotly" ,python-plotly)
("python-scipy" ,python-scipy)
("python-numpy" ,python-numpy)
("python-numpydoc" ,python-numpydoc)
("python-matplotlib" ,python-matplotlib)
("python-pysam" ,python-pysam)
("python-py2bit" ,python-py2bit)
("python-pybigwig" ,python-pybigwig)))
(native-inputs
`(("python-mock" ,python-mock) ;for tests
("python-nose" ,python-nose) ;for tests
("python-pytz" ,python-pytz))) ;for tests
(home-page "https://github.com/deeptools/deepTools")
(synopsis "Tools for normalizing and visualizing deep-sequencing data")
(description
"DeepTools addresses the challenge of handling the large amounts of data
that are now routinely generated from DNA sequencing centers. To do so,
deepTools contains useful modules to process the mapped reads data to create
coverage files in standard bedGraph and bigWig file formats. By doing so,
deepTools allows the creation of normalized coverage files or the comparison
between two files (for example, treatment and control). Finally, using such
normalized and standardized files, multiple visualizations can be created to
identify enrichments with functional annotations of the genome.")