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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;;
;;; 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 perl)
#:use-module (guix build-system python)
#:use-module (guix build-system r)
#:use-module (guix build-system ruby)
#: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 bison)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
#:use-module (gnu packages curl)
#:use-module (gnu packages documentation)
#:use-module (gnu packages datastructures)
#:use-module (gnu packages file)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gd)
#:use-module (gnu packages image)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
#:use-module (gnu packages logging)
#: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 pcre)
#:use-module (gnu packages pdf)
#:use-module (gnu packages perl)
#: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 readline)
#:use-module (gnu packages ruby)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
#: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 (gnu packages zip)
#:use-module (srfi srfi-1))
(define-public aragorn
(package
(name "aragorn")
(version "1.2.36")
(source (origin
(method url-fetch)
(uri (string-append
"http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn"
version ".tgz"))
(sha256
(base32
"1dg7jlz1qpqy88igjxd6ncs11ccsirb36qv1z01a0np4i4jh61mb"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are no tests
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'build
(lambda _
(zero? (system* "gcc"
"-O3"
"-ffast-math"
"-finline-functions"
"-o"
"aragorn"
(string-append "aragorn" ,version ".c")))))
(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 bin)
(copy-file "aragorn"
(string-append bin "/aragorn"))
(mkdir-p man)
(copy-file "aragorn.1"
(string-append man "/aragorn.1")))
#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 bamtools
(package
(name "bamtools")
(version "2.3.0")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/pezmaster31/bamtools/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1brry29bw2xr2l9pqn240rkqwayg85b8qq78zk2zs6nlspk4d018"))))
(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")))))))
(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 bedops
(package
(name "bedops")
(version "2.4.14")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/bedops/bedops/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f
#:make-flags (list (string-append "BINDIR=" %output "/bin"))
#:phases
(alist-cons-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"
(and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
(zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
(zero? (system* "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")))
(alist-delete 'configure %standard-phases))))
(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 "2.25.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1ywcy3yfwzhl905b51l0ffjia55h75vv3mw5xkvib04pp6pj548m"))))
(build-system gnu-build-system)
(native-inputs `(("python" ,python-2)))
(inputs `(("samtools" ,samtools)
("zlib" ,zlib)))
(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)))))
(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:gpl2)))
(define-public bioawk
(package
(name "bioawk")
(version "1.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/lh3/bioawk/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw"))))
(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)))))))
(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 python2-pybedtools
(package
(name "python2-pybedtools")
(version "0.6.9")
(source (origin
(method url-fetch)
(uri (string-append
"https://pypi.python.org/packages/source/p/pybedtools/pybedtools-"
version ".tar.gz"))
(sha256
(base32
"1ldzdxw1p4y3g2ignmggsdypvqkcwqwzhdha4rbgpih048z5p4an"))))
(build-system python-build-system)
(arguments `(#:python ,python-2)) ; no Python 3 support
(inputs
`(("python-cython" ,python2-cython)
("python-matplotlib" ,python2-matplotlib)))
(propagated-inputs
`(("bedtools" ,bedtools)
("samtools" ,samtools)))
(native-inputs
`(("python-pyyaml" ,python2-pyyaml)
("python-nose" ,python2-nose)
("python-setuptools" ,python2-setuptools)))
(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 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 "1.6.924")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-"
version ".tar.gz"))
(sha256
(base32
"1l3npcvvvwjlhkna9dndpfv1hklhrgva013kw96m0n1wpd37ask1"))))
(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 "http://search.cpan.org/dist/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 (package-license perl)))))
(define-public python-biopython
(package
(name "python-biopython")
(version "1.66")
(source (origin
(method url-fetch)
;; use PyPi rather than biopython.org to ease updating
(uri (pypi-uri "biopython" version))
(sha256
(base32
"1gdv92593klimg22icf5j9by7xiq86jnwzkpz4abaa05ylkdf6hp"))))
(build-system python-build-system)
(inputs
`(("python-numpy" ,python-numpy)))
(native-inputs
`(("python-setuptools" ,python2-setuptools)))
(home-page "http://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 (inherit (package-with-python2 python-biopython))
(inputs
`(("python2-numpy" ,python2-numpy)))))
(define-public blast+
(package
(name "blast+")
(version "2.4.0")
(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
"14n9jik6vhiwjd3m7bach4xj1pzfn0szbsbyfxybd9l9cc43b6mb"))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove bundled bzip2 and zlib
(delete-file-recursively "c++/src/util/compress/bzip2")
(delete-file-recursively "c++/src/util/compress/zlib")
(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 three(!) tests for this massive library, and all fail with
;; "unparsable timing stats".
;; ERR [127] -- [util/regexp] test_pcre.sh (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
;; $HOME needs to be set at some point during the configure phase
(lambda _ (setenv "HOME" "/tmp") #t))
(add-after
'unpack 'enter-dir
(lambda _ (chdir "c++") #t))
(add-after
'enter-dir 'fix-build-system
(lambda _
(define (which* cmd)
(cond ((string=? cmd "date")
;; make call to "date" deterministic
"date -d @0")
((which cmd)
=> identity)
(else
(format (current-error-port)
"WARNING: Unable to find absolute path for ~s~%"
cmd)
#f)))
;; Rewrite hardcoded paths to various tools
(substitute* (append '("src/build-system/configure.ac"
"src/build-system/configure"
"scripts/common/impl/if_diff.sh"
"scripts/common/impl/run_with_lock.sh"
"src/build-system/Makefile.configurables.real"
"src/build-system/Makefile.in.top"
"src/build-system/Makefile.meta.gmake=no"
"src/build-system/Makefile.meta.in"
"src/build-system/Makefile.meta_l"
"src/build-system/Makefile.meta_p"
"src/build-system/Makefile.meta_r"
"src/build-system/Makefile.mk.in"
"src/build-system/Makefile.requirements"
"src/build-system/Makefile.rules_with_autodep.in")
(find-files "scripts/common/check" "\\.sh$"))
(("(/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'.
(zero? (system* "./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"))
;; Each library is built twice by default, once
;; with "-static" in its name, and again
;; without.
"--without-static"
"--with-dll"))))))))
(outputs '("out" ; 19 MB
"lib" ; 203 MB
"include")) ; 32 MB
(inputs
`(("bzip2" ,bzip2)
("zlib" ,zlib)))
(native-inputs
`(("cpio" ,cpio)))
(home-page "http://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")
"/lib/libz.a")
(string-append "LDFLAGS="
(string-join '("-lboost_filesystem"
"-lboost_system"
"-lboost_iostreams"
"-lz"
"-fopenmp"
"-std=c++11"))))
#: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" ,zlib)))
(supported-systems '("x86_64-linux"))
(home-page "http://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 "2.2.6")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BenLangmead/bowtie2/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1ssfvymxfrap6f9pf86s9bvsbqdgka4abr2r7j3mgr4w1l289m86"))
(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)
(inputs `(("perl" ,perl)
("perl-clone" ,perl-clone)
("perl-test-deep" ,perl-test-deep)
("perl-test-simple" ,perl-test-simple)
("python" ,python-2)
("tbb" ,tbb)))
(arguments
'(#:make-flags
(list "allall"
"WITH_TBB=1"
(string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
(alist-delete
'configure
(alist-replace
'check
(lambda* (#:key outputs #:allow-other-keys)
(system* "perl"
"scripts/test/simple_tests.pl"
"--bowtie2=./bowtie2"
"--bowtie2-build=./bowtie2-build"))
%standard-phases))))
(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 tophat
(package
(name "tophat")
(version "2.1.0")
(source (origin
(method url-fetch)
(uri (string-append
"http://ccb.jhu.edu/software/tophat/downloads/tophat-"
version ".tar.gz"))
(sha256
(base32
"168zlzykq622zbgkh90a90f1bdgsxkscq2zxzbj8brq80hbjpyp7"))
(patches (search-patches "tophat-build-with-later-seqan.patch"))
(modules '((guix build utils)))
(snippet
'(begin
;; Remove bundled SeqAn and samtools
(delete-file-recursively "src/SeqAn-1.3")
(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)))))
(inputs
`(("boost" ,boost)
("bowtie" ,bowtie)
("samtools" ,samtools-0.1)
("ncurses" ,ncurses)
("python" ,python-2)
("perl" ,perl)
("zlib" ,zlib)
("seqan" ,seqan)))
(home-page "http://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 "0.7.12")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/bio-bwa/bwa-"
version ".tar.bz2"))
(sha256
(base32
"1330dpqncv0px3pbhjzz1gwgg39kkcv2r9qp2xs0sixf8z8wl7bh"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target
#:phases
(alist-replace
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append
(assoc-ref outputs "out") "/bin"))
(doc (string-append
(assoc-ref outputs "out") "/share/doc/bwa"))
(man (string-append
(assoc-ref outputs "out") "/share/man/man1")))
(mkdir-p bin)
(mkdir-p doc)
(mkdir-p man)
(install-file "bwa" bin)
(install-file "README.md" doc)
(install-file "bwa.1" man)))
;; no "configure" script
(alist-delete 'configure %standard-phases))))
(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 url-fetch)
(uri (string-append "https://github.com/pkerpedjiev/bwa-pssm/"
"archive/" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"02p7mpbs4mlxmn84g2x4ghak638vbj4lqix2ipx5g84pz9bhdavg"))))
(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 python2-bx-python
(package
(name "python2-bx-python")
(version "0.7.2")
(source (origin
(method url-fetch)
(uri (string-append
"https://pypi.python.org/packages/source/b/bx-python/bx-python-"
version ".tar.gz"))
(sha256
(base32
"0ld49idhc5zjdvbhvjq1a2qmpjj7h5v58rqr25dzmfq7g34b50xh"))
(modules '((guix build utils)))
(snippet
'(substitute* "setup.py"
;; remove dependency on outdated "distribute" module
(("^from distribute_setup import use_setuptools") "")
(("^use_setuptools\\(\\)") "")))))
(build-system python-build-system)
(arguments
`(#:tests? #f ;tests fail because test data are not included
#:python ,python-2))
(inputs
`(("python-numpy" ,python2-numpy)
("zlib" ,zlib)))
(native-inputs
`(("python-nose" ,python2-nose)
("python-setuptools" ,python2-setuptools)))
(home-page "http://bitbucket.org/james_taylor/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 python-pysam
(package
(name "python-pysam")
(version "0.8.4")
(source (origin
(method url-fetch)
(uri (pypi-uri "pysam" version))
(sha256
(base32
"1slx5mb94mzm5qzk52q270sab0sar95j67w1g1k452nz3s9j7krh"))))
(build-system python-build-system)
(arguments
`(#:tests? #f ; tests are excluded in the manifest
#:phases
(alist-cons-before
'build 'set-flags
(lambda _
(setenv "LDFLAGS" "-lncurses")
(setenv "CFLAGS" "-D_CURSES_LIB=1"))
%standard-phases)))
(inputs
`(("ncurses" ,ncurses)
("zlib" ,zlib)))
(native-inputs
`(("python-cython" ,python-cython)
("python-setuptools" ,python-setuptools)))
(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 "3.1.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "twobitreader" version))
(sha256
(base32
"0y408fp6psqzwxpcpqn0wp7fr41dwz8d54wpj6j261fj5q8vs169"))))
(properties `((python2-variant . ,(delay python2-twobitreader))))
(build-system python-build-system)
(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
(let ((base (package-with-python2 (strip-python2-variant python-twobitreader))))
(package
(inherit base)
(native-inputs `(("python2-setuptools" ,python2-setuptools)
,@(package-native-inputs base))))))
(define-public python-plastid
(package
(name "python-plastid")
(version "0.4.5")
(source (origin
(method url-fetch)
(uri (pypi-uri "plastid" version))
(sha256
(base32
"1nhxw8a5gn9as58i2ih52c5cjwj48ik418pzsjwph3s66mmy9yvq"))))
(properties `((python2-variant . ,(delay python2-plastid))))
(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)))
(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
(let ((base (package-with-python2 (strip-python2-variant python-plastid))))
(package
(inherit base)
;; setuptools is required at runtime
(propagated-inputs `(("python2-setuptools" ,python2-setuptools)
,@(package-propagated-inputs base))))))
(define-public cd-hit
(package
(name "cd-hit")
(version "4.6.5")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/weizhongli/cdhit"
"/releases/download/V" version
"/cd-hit-v" version "-2016-0304.tar.gz"))
(sha256
(base32
"15db0hq38yyifwqx9b6l34z14jcq576dmjavhj8a426c18lvnhp3"))))
(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"))
#: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 "0.3.0")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/YeoLab/clipper/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1q7jpimsqln7ic44i8v2rx2haj5wvik8hc1s2syd31zcn0xk1iyq"))
(modules '((guix build utils)))
(snippet
;; remove unnecessary setup dependency
'(substitute* "setup.py"
(("setup_requires = .*") "")))))
(build-system python-build-system)
(arguments `(#:python ,python-2)) ; only Python 2 is supported
(inputs
`(("htseq" ,htseq)
("python-pybedtools" ,python2-pybedtools)
("python-cython" ,python2-cython)
("python-scikit-learn" ,python2-scikit-learn)
("python-matplotlib" ,python2-matplotlib)
("python-pysam" ,python2-pysam)
("python-numpy" ,python2-numpy)
("python-scipy" ,python2-scipy)))
(native-inputs
`(("python-mock" ,python2-mock) ; for tests
("python-pytz" ,python2-pytz) ; for tests
("python-setuptools" ,python2-setuptools)))
(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)))))))
(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")))
(copy-recursively "src" (string-append out "/src"))
(mkdir (string-append out "/bin"))
;; Add "src" directory to module lookup path.
(substitute* "couger"
(("from argparse")
(string-append "import sys\nsys.path.append(\""
out "\")\nfrom argparse")))
(copy-file "couger" (string-append out "/bin/couger")))
#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" ,r)
("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 "1.2.1")
(source (origin
(method url-fetch)
(uri (string-append
"http://www.clustal.org/omega/clustal-omega-"
version ".tar.gz"))
(sha256
(base32
"02ibkx0m0iwz8nscg998bh41gg251y56cgh86bvyrii5m8kjgwqf"))))
(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 "0.2.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
version ".tar.gz"))
(sha256
(base32
"07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f"))
;; This patch has been sent upstream already and is available
;; for download from Sourceforge, but it has not been merged.
(patches (search-patches "crossmap-allow-system-pysam.patch"))
(modules '((guix build utils)))
;; remove bundled copy of pysam
(snippet
'(delete-file-recursively "lib/pysam"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:phases
(alist-cons-after
'unpack 'set-env
(lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1"))
%standard-phases)))
(inputs
`(("python-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam)
("zlib" ,zlib)))
(native-inputs
`(("python-cython" ,python2-cython)
("python-nose" ,python2-nose)
("python-setuptools" ,python2-setuptools)))
(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 cufflinks
(package
(name "cufflinks")
(version "2.2.1")
(source (origin
(method url-fetch)
(uri (string-append "http://cole-trapnell-lab.github.io/"
"cufflinks/assets/downloads/cufflinks-"
version ".tar.gz"))
(sha256
(base32
"1bnm10p8m7zq4qiipjhjqb24csiqdm1pwc8c795z253r2xk6ncg8"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
(list
;; The includes for "eigen" are located in a subdirectory.
(string-append "EIGEN_CPPFLAGS="
"-I" (assoc-ref %build-inputs "eigen")
"/include/eigen3/")
;; Cufflinks must be linked with various boost libraries.
(string-append "LDFLAGS="
(string-join '("-lboost_system"
"-lboost_serialization"
"-lboost_thread"))))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-search-for-bam
(lambda _
(substitute* '("ax_bam.m4"
"configure"
"src/hits.h")
(("<bam/sam\\.h>") "<samtools/sam.h>")
(("<bam/bam\\.h>") "<samtools/bam.h>")
(("<bam/version\\.hpp>") "<samtools/version.h>"))
#t)))
#:configure-flags
(list (string-append "--with-bam="
(assoc-ref %build-inputs "samtools")))))
(inputs
`(("eigen" ,eigen)
("samtools" ,samtools-0.1)
("htslib" ,htslib)
("boost" ,boost)
("python" ,python-2)
("zlib" ,zlib)))
(home-page "http://cole-trapnell-lab.github.io/cufflinks/")
(synopsis "Transcriptome assembly and RNA-Seq expression analysis")
(description
"Cufflinks assembles RNA transcripts, estimates their abundances,
and tests for differential expression and regulation in RNA-Seq
samples. It accepts aligned RNA-Seq reads and assembles the
alignments into a parsimonious set of transcripts. Cufflinks then
estimates the relative abundances of these transcripts based on how
many reads support each one, taking into account biases in library
preparation protocols.")
(license license:boost1.0)))
(define-public cutadapt
(package
(name "cutadapt")
(version "1.8")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/marcelm/cutadapt/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"161bp87y6gd6r5bmvjpn2b1k942i3fizfpa139f0jn6jv1wcp5h5"))))
(build-system python-build-system)
(arguments
;; tests must be run after install
`(#:phases (alist-cons-after
'install 'check
(lambda* (#:key inputs outputs #:allow-other-keys)
(setenv "PYTHONPATH"
(string-append
(getenv "PYTHONPATH")
":" (assoc-ref outputs "out")
"/lib/python"
(string-take (string-take-right
(assoc-ref inputs "python") 5) 3)
"/site-packages"))
(zero? (system* "nosetests" "-P" "tests")))
(alist-delete 'check %standard-phases))))
(native-inputs
`(("python-cython" ,python-cython)
("python-nose" ,python-nose)
("python-setuptools" ,python-setuptools)))
(home-page "https://code.google.com/p/cutadapt/")
(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 "0.1.4")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/dpryan79/libBigWig/"
"archive/" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
#:make-flags
(list "CC=gcc"
(string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-before 'check 'disable-curl-test
(lambda _
(substitute* "Makefile"
(("./test/testRemote.*") ""))
#t))
;; This has been fixed with the upstream commit 4ff6959cd8a0, but
;; there has not yet been a release containing this change.
(add-before 'install 'create-target-dirs
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(mkdir-p (string-append out "/lib"))
(mkdir-p (string-append out "/include"))
#t))))))
(inputs
`(("zlib" ,zlib)
("curl" ,curl)))
(native-inputs
`(("doxygen" ,doxygen)))
(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 "0.2.5")
(source (origin
(method url-fetch)
(uri (pypi-uri "pyBigWig" version))
(sha256
(base32
"0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d"))
(modules '((guix build utils)))
(snippet
'(begin
;; Delete bundled libBigWig sources
(delete-file-recursively "libBigWig")))))
(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)))))
(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
(let ((pybigwig (package-with-python2 python-pybigwig)))
(package (inherit pybigwig)
(native-inputs
`(("python-setuptools" ,python2-setuptools))))))
(define-public deeptools
(package
(name "deeptools")
(version "2.1.1")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/fidelram/deepTools/"
"archive/" version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1nmfin0zjdby3vay3r4flvz94dr6qjhj41ax4yz3vx13j6wz8izd"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2))
(inputs
`(("python-scipy" ,python2-scipy)
("python-numpy" ,python2-numpy)
("python-numpydoc" ,python2-numpydoc)
("python-matplotlib" ,python2-matplotlib)
("python-bx-python" ,python2-bx-python)
("python-pysam" ,python2-pysam)
("python-pybigwig" ,python2-pybigwig)))
(native-inputs
`(("python-mock" ,python2-mock) ;for tests
("python-pytz" ,python2-pytz) ;for tests
("python-setuptools" ,python2-setuptools)))
(home-page "https://github.com/fidelram/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.")
(license license:gpl3+)))
(define-public diamond
(package
(name "diamond")
(version "0.8.9")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/bbuchfink/diamond/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1g0j24qcx48mp04hbk0hpbvh0gbw5wmifpliyaq95zp4qwwcs5x4"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'remove-native-compilation
(lambda _
(substitute* "CMakeLists.txt" (("-march=native") ""))
#t)))))
(inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/bbuchfink/diamond")
(synopsis "Accelerated BLAST compatible local sequence aligner")
(description
"DIAMOND is a BLAST-compatible local aligner for mapping protein and
translated DNA query sequences against a protein reference database (BLASTP
and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short
reads at a typical sensitivity of 90-99% relative to BLAST depending on the
data and settings.")
;; diamond fails to build on other platforms
;; https://github.com/bbuchfink/diamond/issues/18
(supported-systems '("x86_64-linux"))
(license (license:non-copyleft "file://src/COPYING"
"See src/COPYING in the distribution."))))
(define-public edirect
(package
(name "edirect")
(version "4.10")
(source (origin
(method url-fetch)
(uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
"versions/2016-05-03/edirect.tar.gz"))
(sha256
(base32
"15zsprak5yh8c1yrz4r1knmb5s8qcmdid4xdhkh3lqcv64l60hli"))))
(build-system perl-build-system)
(arguments
`(#:tests? #f ;no "check" target
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build)
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((target (string-append (assoc-ref outputs "out")
"/bin")))
(mkdir-p target)
(copy-file "edirect.pl"
(string-append target "/edirect.pl"))
#t)))
(add-after
'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Make sure 'edirect.pl' finds all perl inputs at runtime.
(let* ((out (assoc-ref outputs "out"))
(path (getenv "PERL5LIB")))
(wrap-program (string-append out "/bin/edirect.pl")
`("PERL5LIB" ":" prefix (,path)))))))))
(inputs
`(("perl-html-parser" ,perl-html-parser)
("perl-encode-locale" ,perl-encode-locale)
("perl-file-listing" ,perl-file-listing)
("perl-html-tagset" ,perl-html-tagset)
("perl-html-tree" ,perl-html-tree)
("perl-http-cookies" ,perl-http-cookies)
("perl-http-date" ,perl-http-date)
("perl-http-message" ,perl-http-message)
("perl-http-negotiate" ,perl-http-negotiate)
("perl-lwp-mediatypes" ,perl-lwp-mediatypes)
("perl-lwp-protocol-https" ,perl-lwp-protocol-https)
("perl-net-http" ,perl-net-http)
("perl-uri" ,perl-uri)
("perl-www-robotrules" ,perl-www-robotrules)
("perl" ,perl)))
(home-page "http://www.ncbi.nlm.nih.gov/books/NBK179288/")
(synopsis "Tools for accessing the NCBI's set of databases")
(description
"Entrez Direct (EDirect) is a method for accessing the National Center
for Biotechnology Information's (NCBI) set of interconnected
databases (publication, sequence, structure, gene, variation, expression,
etc.) from a terminal. Functions take search terms from command-line
arguments. Individual operations are combined to build multi-step queries.
Record retrieval and formatting normally complete the process.
EDirect also provides an argument-driven function that simplifies the
extraction of data from document summaries or other results that are returned
in structured XML format. This can eliminate the need for writing custom
software to answer ad hoc questions.")
(license license:public-domain)))
(define-public express
(package
(name "express")
(version "1.5.1")
(source (origin
(method url-fetch)
(uri
(string-append
"http://bio.math.berkeley.edu/eXpress/downloads/express-"
version "/express-" version "-src.tgz"))
(sha256
(base32
"03rczxd0gjp2l1jxcmjfmf5j94j77zqyxa6x063zsc585nj40n0c"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #f ;no "check" target
#:phases
(alist-cons-after
'unpack 'use-shared-boost-libs-and-set-bamtools-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "CMakeLists.txt"
(("set\\(Boost_USE_STATIC_LIBS ON\\)")
"set(Boost_USE_STATIC_LIBS OFF)")
(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
(string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
(substitute* "src/CMakeLists.txt"
(("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
(string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
#t)
%standard-phases)))
(inputs
`(("boost" ,boost)
("bamtools" ,bamtools)
("protobuf" ,protobuf)
("zlib" ,zlib)))
(home-page "http://bio.math.berkeley.edu/eXpress")
(synopsis "Streaming quantification for high-throughput genomic sequencing")
(description
"eXpress is a streaming tool for quantifying the abundances of a set of
target sequences from sampled subsequences. Example applications include
transcript-level RNA-Seq quantification, allele-specific/haplotype expression
analysis (from RNA-Seq), transcription factor binding quantification in
ChIP-Seq, and analysis of metagenomic data.")
(license license:artistic2.0)))
(define-public express-beta-diversity
(package
(name "express-beta-diversity")
(version "1.0.7")
(source (origin
(method url-fetch)
(uri
(string-append
"https://github.com/dparks1134/ExpressBetaDiversity/archive/v"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1djvdlmqvjf6h0zq7w36y8cl5cli6rgj86x65znl48agnwmzxfxr"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-before 'build 'enter-source (lambda _ (chdir "source") #t))
(replace 'check
(lambda _ (zero? (system* "../bin/ExpressBetaDiversity"
"-u"))))
(add-after 'check 'exit-source (lambda _ (chdir "..") #t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out")
"/bin")))
(mkdir-p bin)
(copy-file "scripts/convertToEBD.py"
(string-append bin "/convertToEBD.py"))
(copy-file "bin/ExpressBetaDiversity"
(string-append bin "/ExpressBetaDiversity"))
#t))))))
(inputs
`(("python" ,python-2)))
(home-page "http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity")
(synopsis "Taxon- and phylogenetic-based beta diversity measures")
(description
"Express Beta Diversity (EBD) calculates ecological beta diversity
(dissimilarity) measures between biological communities. EBD implements a
variety of diversity measures including those that make use of phylogenetic
similarity of community members.")
(license license:gpl3+)))
(define-public fasttree
(package
(name "fasttree")
(version "2.1.8")
(source (origin
(method url-fetch)
(uri (string-append
"http://www.microbesonline.org/fasttree/FastTree-"
version ".c"))
(sha256
(base32
"0dzqc9vr9iiiw21y159xfjl2z90vw0y7r4x6456pcaxiy5hd2wmi"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no "check" target
#:phases
(modify-phases %standard-phases
(delete 'unpack)
(delete 'configure)
(replace 'build
(lambda* (#:key source #:allow-other-keys)
(and (zero? (system* "gcc"
"-O3"
"-finline-functions"
"-funroll-loops"
"-Wall"
"-o"
"FastTree"
source
"-lm"))
(zero? (system* "gcc"
"-DOPENMP"
"-fopenmp"
"-O3"
"-finline-functions"
"-funroll-loops"
"-Wall"
"-o"
"FastTreeMP"
source
"-lm")))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out")
"/bin")))
(mkdir-p bin)
(copy-file "FastTree"
(string-append bin "/FastTree"))
(copy-file "FastTreeMP"
(string-append bin "/FastTreeMP"))
#t))))))
(home-page "http://www.microbesonline.org/fasttree")
(synopsis "Infers approximately-maximum-likelihood phylogenetic trees")
(description
"FastTree can handle alignments with up to a million of sequences in a
reasonable amount of time and memory. For large alignments, FastTree is
100-1,000 times faster than PhyML 3.0 or RAxML 7.")
(license license:gpl2+)))
(define-public fastx-toolkit
(package
(name "fastx-toolkit")
(version "0.0.14")
(source (origin
(method url-fetch)
(uri
(string-append
"https://github.com/agordon/fastx_toolkit/releases/download/"
version "/fastx_toolkit-" version ".tar.bz2"))
(sha256
(base32
"01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy"))))
(build-system gnu-build-system)
(inputs
`(("libgtextutils" ,libgtextutils)))
(native-inputs
`(("pkg-config" ,pkg-config)))
(home-page "http://hannonlab.cshl.edu/fastx_toolkit/")
(synopsis "Tools for FASTA/FASTQ file preprocessing")
(description
"The FASTX-Toolkit is a collection of command line tools for Short-Reads
FASTA/FASTQ files preprocessing.
Next-Generation sequencing machines usually produce FASTA or FASTQ files,
containing multiple short-reads sequences. The main processing of such
FASTA/FASTQ files is mapping the sequences to reference genomes. However, it
is sometimes more productive to preprocess the files before mapping the
sequences to the genome---manipulating the sequences to produce better mapping
results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
(license license:agpl3+)))
(define-public flexbar
(package
(name "flexbar")
(version "2.5")
(source (origin
(method url-fetch)
(uri
(string-append "mirror://sourceforge/flexbar/"
version "/flexbar_v" version "_src.tgz"))
(sha256
(base32
"13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags (list
(string-append "-DFLEXBAR_BINARY_DIR="
(assoc-ref %outputs "out")
"/bin/"))
#:phases
(alist-replace
'check
(lambda* (#:key outputs #:allow-other-keys)
(setenv "PATH" (string-append
(assoc-ref outputs "out") "/bin:"
(getenv "PATH")))
(chdir "../flexbar_v2.5_src/test")
(zero? (system* "bash" "flexbar_validate.sh")))
(alist-delete 'install %standard-phases))))
(inputs
`(("tbb" ,tbb)
("zlib" ,zlib)))
(native-inputs
`(("pkg-config" ,pkg-config)
("seqan" ,seqan)))
(home-page "http://flexbar.sourceforge.net")
(synopsis "Barcode and adapter removal tool for sequencing platforms")
(description
"Flexbar preprocesses high-throughput nucleotide sequencing data
efficiently. It demultiplexes barcoded runs and removes adapter sequences.
Moreover, trimming and filtering features are provided. Flexbar increases
read mapping rates and improves genome and transcriptome assemblies. It
supports next-generation sequencing data in fasta/q and csfasta/q format from
Illumina, Roche 454, and the SOLiD platform.")
(license license:gpl3)))
(define-public fraggenescan
(package
(name "fraggenescan")
(version "1.20")
(source
(origin
(method url-fetch)
(uri
(string-append "mirror://sourceforge/fraggenescan/"
"FragGeneScan" version ".tar.gz"))
(sha256
(base32 "1zzigqmvqvjyqv4945kv6nc5ah2xxm1nxgrlsnbzav3f5c0n0pyj"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-before 'build 'patch-paths
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append (assoc-ref outputs "out")))
(share (string-append out "/share/fraggenescan/")))
(substitute* "run_FragGeneScan.pl"
(("system\\(\"rm")
(string-append "system(\"" (which "rm")))
(("system\\(\"mv")
(string-append "system(\"" (which "mv")))
;; This script and other programs expect the training files
;; to be in the non-standard location bin/train/XXX. Change
;; this to be share/fraggenescan/train/XXX instead.
(("^\\$train.file = \\$dir.*")
(string-append "$train_file = \""
share
"train/\".$FGS_train_file;")))
(substitute* "run_hmm.c"
(("^ strcat\\(train_dir, \\\"train/\\\"\\);")
(string-append " strcpy(train_dir, \"" share "/train/\");")))
(substitute* "post_process.pl"
(("^my \\$dir = substr.*")
(string-append "my $dir = \"" share "\";"))))
#t))
(replace 'build
(lambda _ (and (zero? (system* "make" "clean"))
(zero? (system* "make" "fgs")))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append (assoc-ref outputs "out")))
(bin (string-append out "/bin/"))
(share (string-append out "/share/fraggenescan/train")))
(install-file "run_FragGeneScan.pl" bin)
(install-file "FragGeneScan" bin)
(install-file "FGS_gff.py" bin)
(install-file "post_process.pl" bin)
(copy-recursively "train" share))))
(delete 'check)
(add-after 'install 'post-install-check
;; In lieu of 'make check', run one of the examples and check the
;; output files gets created.
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (string-append (assoc-ref outputs "out")))
(bin (string-append out "/bin/")))
(and (zero? (system* (string-append bin "run_FragGeneScan.pl")
"-genome=./example/NC_000913.fna"
"-out=./test2"
"-complete=1"
"-train=complete"))
(file-exists? "test2.faa")
(file-exists? "test2.ffn")
(file-exists? "test2.gff")
(file-exists? "test2.out"))))))))
(inputs
`(("perl" ,perl)
("python" ,python-2))) ;not compatible with python 3.
(home-page "https://sourceforge.net/projects/fraggenescan/")
(synopsis "Finds potentially fragmented genes in short reads")
(description
"FragGeneScan is a program for predicting bacterial and archaeal genes in
short and error-prone DNA sequencing reads. It can also be applied to predict
genes in incomplete assemblies or complete genomes.")
;; GPL3+ according to private correspondense with the authors.
(license license:gpl3+)))
(define-public fxtract
(let ((util-commit "776ca85a18a47492af3794745efcb4a905113115"))
(package
(name "fxtract")
(version "2.3")
(source
(origin
(method url-fetch)
(uri (string-append
"https://github.com/ctSkennerton/fxtract/archive/"
version ".tar.gz"))
(file-name (string-append "ctstennerton-util-"
(string-take util-commit 7)
"-checkout"))
(sha256
(base32
"0275cfdhis8517hm01is62062swmi06fxzifq7mr3knbbxjlaiwj"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags (list
(string-append "PREFIX=" (assoc-ref %outputs "out"))
"CC=gcc")
#:test-target "fxtract_test"
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-before 'build 'copy-util
(lambda* (#:key inputs #:allow-other-keys)
(rmdir "util")
(copy-recursively (assoc-ref inputs "ctskennerton-util") "util")
#t))
;; Do not use make install as this requires additional dependencies.
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out"/bin")))
(install-file "fxtract" bin)
#t))))))
(inputs
`(("pcre" ,pcre)
("zlib" ,zlib)))
(native-inputs
;; ctskennerton-util is licensed under GPL2.
`(("ctskennerton-util"
,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ctSkennerton/util.git")
(commit util-commit)))
(file-name (string-append
"ctstennerton-util-" util-commit "-checkout"))
(sha256
(base32
"0cls1hd4vgj3f36fpzzg4xc77d6f3hpc60cbpfmn2gdr7ykzzad7"))))))
(home-page "https://github.com/ctSkennerton/fxtract")
(synopsis "Extract sequences from FASTA and FASTQ files")
(description
"Fxtract extracts sequences from a protein or nucleotide fastx (FASTA
or FASTQ) file given a subsequence. It uses a simple substring search for
basic tasks but can change to using POSIX regular expressions, PCRE, hash
lookups or multi-pattern searching as required. By default fxtract looks in
the sequence of each record but can also be told to look in the header,
comment or quality sections.")
(license license:expat))))
(define-public grit
(package
(name "grit")
(version "2.0.2")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/nboley/grit/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:phases
(alist-cons-after
'unpack 'generate-from-cython-sources
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Delete these C files to force fresh generation from pyx sources.
(delete-file "grit/sparsify_support_fns.c")
(delete-file "grit/call_peaks_support_fns.c")
(substitute* "setup.py"
(("Cython.Setup") "Cython.Build")
;; Add numpy include path to fix compilation
(("pyx\", \\]")
(string-append "pyx\", ], include_dirs = ['"
(assoc-ref inputs "python-numpy")
"/lib/python2.7/site-packages/numpy/core/include/"
"']"))) #t)
%standard-phases)))
(inputs
`(("python-scipy" ,python2-scipy)
("python-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam)
("python-networkx" ,python2-networkx)))
(native-inputs
`(("python-cython" ,python2-cython)
("python-setuptools" ,python2-setuptools)))
(home-page "http://grit-bio.org")
(synopsis "Tool for integrative analysis of RNA-seq type assays")
(description
"GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
full length transcript models. When none of these data sources are available,
GRIT can be run by providing a candidate set of TES or TSS sites. In
addition, GRIT can merge in reference junctions and gene boundaries. GRIT can
also be run in quantification mode, where it uses a provided GTF file and just
estimates transcript expression.")
(license license:gpl3+)))
(define-public hisat
(package
(name "hisat")
(version "0.1.4")
(source (origin
(method url-fetch)
(uri (string-append
"http://ccb.jhu.edu/software/hisat/downloads/hisat-"
version "-beta-source.zip"))
(sha256
(base32
"1k381ydranqxp09yf2y7w1d0chz5d59vb6jchi89hbb0prq19lk5"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ;no check target
#:make-flags '("allall"
;; Disable unsupported `popcnt' instructions on
;; architectures other than x86_64
,@(if (string-prefix? "x86_64"
(or (%current-target-system)
(%current-system)))
'()
'("POPCNT_CAPABILITY=0")))
#:phases
(alist-cons-after
'unpack 'patch-sources
(lambda _
;; XXX Cannot use snippet because zip files are not supported
(substitute* "Makefile"
(("^CC = .*$") "CC = gcc")
(("^CPP = .*$") "CPP = g++")
;; replace BUILD_HOST and BUILD_TIME for deterministic build
(("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
(("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
(substitute* '("hisat-build" "hisat-inspect")
(("/usr/bin/env") (which "env"))))
(alist-replace
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bi/")))
(for-each (lambda (file)
(install-file file bin))
(find-files
"."
"hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))
(alist-delete 'configure %standard-phases)))))
(native-inputs
`(("unzip" ,unzip)))
(inputs
`(("perl" ,perl)
("python" ,python)
("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://ccb.jhu.edu/software/hisat/index.shtml")
(synopsis "Hierarchical indexing for spliced alignment of transcripts")
(description
"HISAT is a fast and sensitive spliced alignment program for mapping
RNA-seq reads. In addition to one global FM index that represents a whole
genome, HISAT uses a large set of small FM indexes that collectively cover the
whole genome. These small indexes (called local indexes) combined with
several alignment strategies enable effective alignment of RNA-seq reads, in
particular, reads spanning multiple exons.")
(license license:gpl3+)))
(define-public hmmer
(package
(name "hmmer")
(version "3.1b2")
(source (origin
(method url-fetch)
(uri (string-append
"http://eddylab.org/software/hmmer"
(version-prefix version 1) "/"
version "/hmmer-" version ".tar.gz"))
(sha256
(base32
"0djmgc0pfli0jilfx8hql1axhwhqxqb8rxg2r5rg07aw73sfs5nx"))))
(build-system gnu-build-system)
(native-inputs `(("perl" ,perl)))
(home-page "http://hmmer.org/")
(synopsis "Biosequence analysis using profile hidden Markov models")
(description
"HMMER is used for searching sequence databases for homologs of protein
sequences, and for making protein sequence alignments. It implements methods
using probabilistic models called profile hidden Markov models (profile
HMMs).")
(license (list license:gpl3+
;; The bundled library 'easel' is distributed
;; under The Janelia Farm Software License.
(license:non-copyleft
"file://easel/LICENSE"
"See easel/LICENSE in the distribution.")))))
(define-public htseq
(package
(name "htseq")
(version "0.6.1")
(source (origin
(method url-fetch)
(uri (string-append
"https://pypi.python.org/packages/source/H/HTSeq/HTSeq-"
version ".tar.gz"))
(sha256
(base32
"1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv"))))
(build-system python-build-system)
(arguments `(#:python ,python-2)) ; only Python 2 is supported
;; Numpy needs to be propagated when htseq is used as a Python library.
(propagated-inputs
`(("python-numpy" ,python2-numpy)))
(inputs
`(("python-pysam" ,python2-pysam)))
(native-inputs
`(("python-setuptools" ,python2-setuptools)))
(home-page "http://www-huber.embl.de/users/anders/HTSeq/")
(synopsis "Analysing high-throughput sequencing data with Python")
(description
"HTSeq is a Python package that provides infrastructure to process data
from high-throughput sequencing assays.")
(license license:gpl3+)))
(define-public java-htsjdk
(package
(name "java-htsjdk")
(version "1.129")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/samtools/htsjdk/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"0asdk9b8jx2ij7yd6apg9qx03li8q7z3ml0qy2r2qczkra79y6fw"))
(modules '((guix build utils)))
;; remove build dependency on git
(snippet '(substitute* "build.xml"
(("failifexecutionfails=\"true\"")
"failifexecutionfails=\"false\"")))))
(build-system ant-build-system)
(arguments
`(#:tests? #f ; test require Internet access
#:make-flags
(list (string-append "-Ddist=" (assoc-ref %outputs "out")
"/share/java/htsjdk/"))
#:build-target "all"
#:phases
(modify-phases %standard-phases
;; The build phase also installs the jars
(delete 'install))))
(home-page "http://samtools.github.io/htsjdk/")
(synopsis "Java API for high-throughput sequencing data (HTS) formats")
(description
"HTSJDK is an implementation of a unified Java library for accessing
common file formats, such as SAM and VCF, used for high-throughput
sequencing (HTS) data. There are also an number of useful utilities for
manipulating HTS data.")
(license license:expat)))
(define-public htslib
(package
(name "htslib")
(version "1.3.1")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/samtools/htslib/releases/download/"
version "/htslib-" version ".tar.bz2"))
(sha256
(base32
"1rja282fwdc25ql6izkhdyh8ppw8x2fs0w0js78zgkmqjlikmma9"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after
'unpack 'patch-tests
(lambda _
(substitute* "test/test.pl"
(("/bin/bash") (which "bash")))
#t)))))
(inputs
`(("zlib" ,zlib)))
(native-inputs
`(("perl" ,perl)))
(home-page "http://www.htslib.org")
(synopsis "C library for reading/writing high-throughput sequencing data")
(description
"HTSlib is a C library for reading/writing high-throughput sequencing
data. It also provides the bgzip, htsfile, and tabix utilities.")
;; Files under cram/ are released under the modified BSD license;
;; the rest is released under the Expat license
(license (list license:expat license:bsd-3))))
(define-public idr
(package
(name "idr")
(version "2.0.0")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/nboley/idr/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1k3x44biak00aiv3hpm1yd6nn4hhp7n0qnbs3zh2q9sw7qr1qj5r"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after
'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(python-version (string-take (string-take-right
(assoc-ref inputs "python") 5) 3))
(path (string-join
(map (lambda (name)
(string-append (assoc-ref inputs name)
"/lib/python" python-version
"/site-packages"))
'("python-scipy"
"python-numpy"
"python-matplotlib"))
":")))
(wrap-program (string-append out "/bin/idr")
`("PYTHONPATH" ":" prefix (,path))))
#t)))))
(inputs
`(("python-scipy" ,python-scipy)
("python-numpy" ,python-numpy)
("python-matplotlib" ,python-matplotlib)))
(native-inputs
`(("python-cython" ,python-cython)
("python-setuptools" ,python-setuptools)))
(home-page "https://github.com/nboley/idr")
(synopsis "Tool to measure the irreproducible discovery rate (IDR)")
(description
"The IDR (Irreproducible Discovery Rate) framework is a unified approach
to measure the reproducibility of findings identified from replicate
experiments and provide highly stable thresholds based on reproducibility.")
(license license:gpl3+)))
(define-public jellyfish
(package
(name "jellyfish")
(version "2.2.4")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/gmarcais/Jellyfish/"
"releases/download/v" version
"/jellyfish-" version ".tar.gz"))
(sha256
(base32
"0a6xnynqy2ibfbfz86b9g2m2dgm7f1469pmymkpam333gi3p26nk"))))
(build-system gnu-build-system)
(outputs '("out" ;for library
"ruby" ;for Ruby bindings
"python")) ;for Python bindings
(arguments
`(#:configure-flags
(list (string-append "--enable-ruby-binding="
(assoc-ref %outputs "ruby"))
(string-append "--enable-python-binding="
(assoc-ref %outputs "python")))
#:phases
(modify-phases %standard-phases
(add-before 'check 'set-SHELL-variable
(lambda _
;; generator_manager.hpp either uses /bin/sh or $SHELL
;; to run tests.
(setenv "SHELL" (which "bash"))
#t)))))
(native-inputs
`(("bc" ,bc)
("time" ,time)
("ruby" ,ruby)
("python" ,python-2)))
(synopsis "Tool for fast counting of k-mers in DNA")
(description
"Jellyfish is a tool for fast, memory-efficient counting of k-mers in
DNA. A k-mer is a substring of length k, and counting the occurrences of all
such substrings is a central step in many analyses of DNA sequence. Jellyfish
is a command-line program that reads FASTA and multi-FASTA files containing
DNA sequences. It outputs its k-mer counts in a binary format, which can be
translated into a human-readable text format using the @code{jellyfish dump}
command, or queried for specific k-mers with @code{jellyfish query}.")
(home-page "http://www.genome.umd.edu/jellyfish.html")
;; The combined work is published under the GPLv3 or later. Individual
;; files such as lib/jsoncpp.cpp are released under the Expat license.
(license (list license:gpl3+ license:expat))))
(define-public khmer
(package
(name "khmer")
(version "2.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "khmer" version))
(sha256
(base32
"0wb05shqh77v00256qlm68vbbx3kl76fyzihszbz5nhanl4ni33a"))
(patches (search-patches "khmer-use-libraries.patch"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'set-paths
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Delete bundled libraries.
(delete-file-recursively "third-party/zlib")
(delete-file-recursively "third-party/bzip2")
;; Replace bundled seqan.
(let* ((seqan-all "third-party/seqan")
(seqan-include (string-append
seqan-all "/core/include")))
(delete-file-recursively seqan-all)
(copy-recursively (string-append (assoc-ref inputs "seqan")
"/include/seqan")
(string-append seqan-include "/seqan")))
;; We do not replace the bundled MurmurHash as the canonical
;; repository for this code 'SMHasher' is unsuitable for
;; providing a library. See
;; https://lists.gnu.org/archive/html/guix-devel/2016-06/msg00977.html
#t))
(add-after 'unpack 'set-cc
(lambda _
(setenv "CC" "gcc")
#t))
;; It is simpler to test after installation.
(delete 'check)
(add-after 'install 'post-install-check
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(setenv "PATH"
(string-append
(getenv "PATH")
":"
(assoc-ref outputs "out")
"/bin"))
(setenv "PYTHONPATH"
(string-append
(getenv "PYTHONPATH")
":"
out
"/lib/python"
(string-take (string-take-right
(assoc-ref inputs "python") 5) 3)
"/site-packages"))
(with-directory-excursion "build"
(zero? (system* "nosetests" "khmer" "--attr"
"!known_failing")))))))))
(native-inputs
`(("seqan" ,seqan)
("python-nose" ,python-nose)))
(inputs
`(("zlib" ,zlib)
("bzip2" ,bzip2)
("python-screed" ,python-screed)
("python-bz2file" ,python-bz2file)))
(home-page "https://khmer.readthedocs.org/")
(synopsis "K-mer counting, filtering and graph traversal library")
(description "The khmer software is a set of command-line tools for
working with DNA shotgun sequencing data from genomes, transcriptomes,
metagenomes and single cells. Khmer can make de novo assemblies faster, and
sometimes better. Khmer can also identify and fix problems with shotgun
data.")
(license license:bsd-3)))
(define-public macs
(package
(name "macs")
(version "2.1.0.20151222")
(source (origin
(method url-fetch)
(uri (pypi-uri "MACS2" version))
(sha256
(base32
"1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2 ; only compatible with Python 2.7
#:tests? #f)) ; no test target
(inputs
`(("python-numpy" ,python2-numpy)))
(native-inputs
`(("python-setuptools" ,python2-setuptools)))
(home-page "http://github.com/taoliu/MACS/")
(synopsis "Model based analysis for ChIP-Seq data")
(description
"MACS is an implementation of a ChIP-Seq analysis algorithm for
identifying transcript factor binding sites named Model-based Analysis of
ChIP-Seq (MACS). MACS captures the influence of genome complexity to evaluate
the significance of enriched ChIP regions and it improves the spatial
resolution of binding sites through combining the information of both
sequencing tag position and orientation.")
(license license:bsd-3)))
(define-public mafft
(package
(name "mafft")
(version "7.299")
(source (origin
(method url-fetch)
(uri (string-append
"http://mafft.cbrc.jp/alignment/software/mafft-" version
"-without-extensions-src.tgz"))
(file-name (string-append name "-" version ".tgz"))
(sha256
(base32
"1pwwdy5a17ggx8h9v9y712ilswj27dc3d23r65l56jgjz67y5zc0"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no automated tests, though there are tests in the read me
#:make-flags (let ((out (assoc-ref %outputs "out")))
(list (string-append "PREFIX=" out)
(string-append "BINDIR="
(string-append out "/bin"))))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'enter-dir
(lambda _ (chdir "core") #t))
(add-after 'enter-dir 'patch-makefile
(lambda _
;; on advice from the MAFFT authors, there is no need to
;; distribute mafft-profile, mafft-distance, or
;; mafft-homologs.rb as they are too "specialised".
(substitute* "Makefile"
;; remove mafft-homologs.rb from SCRIPTS
(("^SCRIPTS = mafft mafft-homologs.rb")
"SCRIPTS = mafft")
;; remove mafft-homologs from MANPAGES
(("^MANPAGES = mafft.1 mafft-homologs.1")
"MANPAGES = mafft.1")
;; remove mafft-distance from PROGS
(("^PROGS = dvtditr dndfast7 dndblast sextet5 mafft-distance")
"PROGS = dvtditr dndfast7 dndblast sextet5")
;; remove mafft-profile from PROGS
(("splittbfast disttbfast tbfast mafft-profile 2cl mccaskillwrap")
"splittbfast disttbfast tbfast f2cl mccaskillwrap")
(("^rm -f mafft-profile mafft-profile.exe") "#")
(("^rm -f mafft-distance mafft-distance.exe") ")#")
;; do not install MAN pages in libexec folder
(("^\t\\$\\(INSTALL\\) -m 644 \\$\\(MANPAGES\\) \
\\$\\(DESTDIR\\)\\$\\(LIBDIR\\)") "#"))
#t))
(add-after 'enter-dir 'patch-paths
(lambda* (#:key inputs #:allow-other-keys)
(substitute* '("pairash.c"
"mafft.tmpl")
(("perl") (which "perl"))
(("([\"`| ])awk" _ prefix)
(string-append prefix (which "awk")))
(("grep") (which "grep")))
#t))
(delete 'configure))))
(inputs
`(("perl" ,perl)
("gawk" ,gawk)
("grep" ,grep)))
(propagated-inputs
`(("coreutils" ,coreutils)))
(home-page "http://mafft.cbrc.jp/alignment/software/")
(synopsis "Multiple sequence alignment program")
(description
"MAFFT offers a range of multiple alignment methods for nucleotide and
protein sequences. For instance, it offers L-INS-i (accurate; for alignment
of <~200 sequences) and FFT-NS-2 (fast; for alignment of <~30,000
sequences).")
(license (license:non-copyleft
"http://mafft.cbrc.jp/alignment/software/license.txt"
"BSD-3 with different formatting"))))
(define-public metabat
(package
(name "metabat")
(version "0.26.3")
(source (origin
(method url-fetch)
(uri (string-append
"https://bitbucket.org/berkeleylab/metabat/get/"
version ".tar.bz2"))
(file-name (string-append name "-" version ".tar.bz2"))
(sha256
(base32
"1vpfvgsn8wdsv1g7z73zxcncskx7dy7bw5msg1hhibk25ay11pyg"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-includes
(lambda _
(substitute* "src/BamUtils.h"
(("^#include \"bam/bam\\.h\"")
"#include \"samtools/bam.h\"")
(("^#include \"bam/sam\\.h\"")
"#include \"samtools/sam.h\""))
(substitute* "src/KseqReader.h"
(("^#include \"bam/kseq\\.h\"")
"#include \"htslib/kseq.h\""))
#t))
(add-after 'unpack 'fix-scons
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "SConstruct"
(("^htslib_dir = 'samtools'")
(string-append "hitslib_dir = '"
(assoc-ref inputs "htslib")
"'"))
(("^samtools_dir = 'samtools'")
(string-append "samtools_dir = '"
(assoc-ref inputs "htslib")
"'"))
(("^findStaticOrShared\\('bam', hts_lib")
(string-append "findStaticOrShared('bam', '"
(assoc-ref inputs "samtools")
"/lib'"))
;; Do not distribute README.
(("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") ""))
#t))
(delete 'configure)
(replace 'build
(lambda* (#:key inputs outputs #:allow-other-keys)
(mkdir (assoc-ref outputs "out"))
(zero? (system* "scons"
(string-append
"PREFIX="
(assoc-ref outputs "out"))
(string-append
"BOOST_ROOT="
(assoc-ref inputs "boost"))
"install"))))
;; Check and install are carried out during build phase.
(delete 'check)
(delete 'install))))
(inputs
`(("zlib" ,zlib)
("perl" ,perl)
("samtools" ,samtools)
("htslib" ,htslib)
("boost" ,boost)))
(native-inputs
`(("scons" ,scons)))
(home-page "https://bitbucket.org/berkeleylab/metabat")
(synopsis
"Reconstruction of single genomes from complex microbial communities")
(description
"Grouping large genomic fragments assembled from shotgun metagenomic
sequences to deconvolute complex microbial communities, or metagenome binning,
enables the study of individual organisms and their interactions. MetaBAT is
an automated metagenome binning software, which integrates empirical
probabilistic distances of genome abundance and tetranucleotide frequency.")
(license (license:non-copyleft "file://license.txt"
"See license.txt in the distribution."))))
(define-public miso
(package
(name "miso")
(version "0.5.3")
(source (origin
(method url-fetch)
(uri (string-append
"https://pypi.python.org/packages/source/m/misopy/misopy-"
version ".tar.gz"))
(sha256
(base32
"0x446867az8ir0z8c1vjqffkp0ma37wm4sylixnkhgawllzx8v5w"))
(modules '((guix build utils)))
(snippet
'(substitute* "setup.py"
;; Use setuptools, or else the executables are not
;; installed.
(("distutils.core") "setuptools")
;; use "gcc" instead of "cc" for compilation
(("^defines")
"cc.set_executables(
compiler='gcc',
compiler_so='gcc',
linker_exe='gcc',
linker_so='gcc -shared'); defines")))))
(build-system python-build-system)
(arguments
`(#:python ,python-2 ; only Python 2 is supported
#:tests? #f)) ; no "test" target
(inputs
`(("samtools" ,samtools)
("python-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam)
("python-scipy" ,python2-scipy)
("python-matplotlib" ,python2-matplotlib)))
(native-inputs
`(("python-mock" ,python2-mock) ;for tests
("python-pytz" ,python2-pytz) ;for tests
("python-setuptools" ,python2-setuptools)))
(home-page "http://genes.mit.edu/burgelab/miso/index.html")
(synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
(description
"MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates
the expression level of alternatively spliced genes from RNA-Seq data, and
identifies differentially regulated isoforms or exons across samples. By
modeling the generative process by which reads are produced from isoforms in
RNA-Seq, the MISO model uses Bayesian inference to compute the probability
that a read originated from a particular isoform.")
(license license:gpl2)))
(define-public muscle
(package
(name "muscle")
(version "3.8.1551")
(source (origin
(method url-fetch/tarbomb)
(file-name (string-append name "-" version))
(uri (string-append
"http://www.drive5.com/muscle/muscle_src_"
version ".tar.gz"))
(sha256
(base32
"0bj8kj7sdizy3987zx6w7axihk40fk8rn76mpbqqjcnd64i5a367"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags (list "LDLIBS = -lm")
#:phases
(modify-phases %standard-phases
(delete 'configure)
(replace 'check
;; There are no tests, so just test if it runs.
(lambda _ (zero? (system* "./muscle" "-version"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin")))
(install-file "muscle" bin)))))))