;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2014, 2015 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2015 Pjotr Prins <pjotr.guix@thebird.nl>
+;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (guix git-download)
#: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 boost)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages cpio)
+ #:use-module (gnu packages file)
#:use-module (gnu packages java)
+ #:use-module (gnu packages linux)
+ #:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
+ #:use-module (gnu packages mpi)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
+ #:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
+ #:use-module (gnu packages ruby)
#:use-module (gnu packages statistics)
- #:use-module (gnu packages swig)
#:use-module (gnu packages tbb)
#:use-module (gnu packages textutils)
+ #:use-module (gnu packages tls)
#:use-module (gnu packages vim)
+ #:use-module (gnu packages web)
#:use-module (gnu packages xml)
- #:use-module (gnu packages zip))
+ #: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 "2.4.5")
+ (version "2.4.14")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/bedops/bedops/archive/v"
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0wmg6j0icimlrnsidaxrzf3hfgjvlkkcwvpdg7n4gg7hdv2m9ni5"))))
+ "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f
(define-public bedtools
(package
(name "bedtools")
- (version "2.22.0")
+ (version "2.24.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/arq5x/bedtools2/archive/v"
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "16aq0w3dmbd0853j32xk9jin4vb6v6fgakfyvrsmsjizzbn3fpfl"))))
+ "0lnxrjvs3nnmb4bmskag1wg3h2hd80przz5q3xd0bvs7vyxrvpbl"))
+ (patches (list (search-patch "bedtools-32bit-compilation.patch")))))
(build-system gnu-build-system)
(native-inputs `(("python" ,python-2)))
(inputs `(("samtools" ,samtools)
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
- (mkdir-p bin)
(for-each (lambda (file)
- (copy-file file (string-append bin (basename file))))
+ (install-file file bin))
(find-files "bin" ".*"))))
%standard-phases)))))
(home-page "https://github.com/arq5x/bedtools2")
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")
(inputs
`(("python2-numpy" ,python2-numpy)))))
+(define-public blast+
+ (package
+ (name "blast+")
+ (version "2.2.31")
+ (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
+ "19gq6as4k1jrgsd26158ads6h7v4jca3h4r5dzg1y0m6ya50x5ph"))
+ (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 google-sparsehash,
+ ;; murmurhash3, kmc once packaged.
+ (delete-file-recursively "boost")
+ (delete-file-recursively "pigz")
+ (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)
+ ("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")
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
- (mkdir-p bin)
(for-each (lambda (file)
- (copy-file file (string-append bin file)))
+ (install-file file bin))
(find-files "." "bowtie2.*"))))
(alist-replace
'check
(mkdir-p bin)
(mkdir-p doc)
(mkdir-p man)
- (copy-file "bwa" (string-append bin "/bwa"))
- (copy-file "README.md" (string-append doc "/README.md"))
- (copy-file "bwa.1" (string-append man "/bwa.1"))))
+ (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
(uri (string-append
"https://github.com/YeoLab/clipper/archive/"
version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1q7jpimsqln7ic44i8v2rx2haj5wvik8hc1s2syd31zcn0xk1iyq"))
"CLIPper is a tool to define peaks in CLIP-seq datasets.")
(license license:gpl2)))
+(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")
(define-public crossmap
(package
(name "crossmap")
- (version "0.1.6")
+ (version "0.2.1")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/crossmap/CrossMap-"
version ".tar.gz"))
(sha256
(base32
- "163hi5gjgij6cndxlvbkp5jjwr0k4wbm9im6d2210278q7k9kpnp"))
- ;; patch has been sent upstream already
+ "07y179f63d7qnzdvkqcziwk9bs3k4zhp81q392fp1hwszjdvy22f"))
+ ;; This patch has been sent upstream already and is available
+ ;; for download from Sourceforge, but it has not been merged.
(patches (list
(search-patch "crossmap-allow-system-pysam.patch")))
(modules '((guix build utils)))
other types of unwanted sequence from high-throughput sequencing reads.")
(license license:expat)))
+(define-public deeptools
+ (package
+ (name "deeptools")
+ (version "1.5.11")
+ (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
+ "1kaagygcbvjs9sxd9cqmskd02wcfp9imvb735r087w7hwqpvz6fs"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2))
+ (propagated-inputs
+ `(("python-scipy" ,python2-scipy)
+ ("python-numpy" ,python2-numpy)
+ ("python-matplotlib" ,python2-matplotlib)
+ ("python-bx-python" ,python2-bx-python)
+ ("python-pysam" ,python2-pysam)))
+ (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 "0.7.9")
+ (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
+ "0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15"))
+ (snippet '(begin
+ (delete-file "bin/diamond")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:tests? #f ;no "check" target
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'enter-source-dir
+ (lambda _
+ (chdir "src")
+ #t))
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (mkdir-p bin)
+ (copy-file "../bin/diamond"
+ (string-append bin "/diamond"))
+ #t))))))
+ (native-inputs
+ `(("bc" ,bc)))
+ (inputs
+ `(("boost" ,boost)
+ ("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 "2.50")
+ (source (origin
+ (method url-fetch)
+ ;; Note: older versions are not retained.
+ (uri "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.zip")
+ (sha256
+ (base32
+ "08afhz2ph66h8h381hl1mqyxkdi5nbvzsyj9gfw3jfbdijnpi4qj"))))
+ (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)))
+ (native-inputs
+ `(("unzip" ,unzip)))
+ (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")
"13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
(build-system cmake-build-system)
(arguments
- `(;; There is no test target, although there is a directory containing
- ;; test data and scripts (launched by flexbar_validate.sh).
- #:tests? #f
- #:configure-flags (list
+ `(#:configure-flags (list
(string-append "-DFLEXBAR_BINARY_DIR="
(assoc-ref %outputs "out")
"/bin/"))
#:phases
- (alist-delete 'install %standard-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)))
(alist-replace
'install
(lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
- (mkdir-p bin)
- (for-each
- (lambda (file)
- (copy-file file (string-append bin file)))
- (find-files
- "."
- "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))
+ (let ((bin (string-append (assoc-ref outputs "out") "/bi/")))
+ (for-each (lambda (file)
+ (install-file file bin))
+ (find-files
+ "."
+ "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))
(alist-delete 'configure %standard-phases)))))
(native-inputs
`(("unzip" ,unzip)))
`(("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
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://selab.janelia.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.janelia.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")
"1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv"))))
(build-system python-build-system)
(arguments `(#:python ,python-2)) ; only Python 2 is supported
- (inputs
- `(("python-numpy" ,python2-numpy)
- ("python-setuptools" ,python2-setuptools)))
+ ;; Numpy needs to be propagated when htseq is used as a Python library.
+ (propagated-inputs
+ `(("python-numpy" ,python2-numpy)))
+ (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
manipulating HTS data.")
(license license:expat)))
+(define-public htslib
+ (package
+ (name "htslib")
+ (version "1.2.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/samtools/htslib/releases/download/"
+ version "/htslib-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "1c32ssscbnjwfw3dra140fq7riarp2x990qxybh34nr1p5r17nxx"))))
+ (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 macs
(package
(name "macs")
sequencing tag position and orientation.")
(license license:bsd-3)))
+(define-public mafft
+ (package
+ (name "mafft")
+ (version "7.221")
+ (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
+ "0xi7klbsgi049vsrk6jiwh9wfj3b770gz3c8c7zwij448v0dr73d"))))
+ (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-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))
+ (delete 'configure))))
+ (inputs
+ `(("perl" ,perl)))
+ (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 "0.26.1")
+ (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
+ "0vgrhbaxg4dkxyax2kbigak7w0arhqvw0szwp6gd9wmyilc44kfa"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'fix-includes
+ (lambda _
+ (substitute* "SConstruct"
+ (("/include/bam/bam.h")
+ "/include/samtools/bam.h"))
+ (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 \"samtools/kseq.h\""))
+ #t))
+ (add-after 'unpack 'fix-scons
+ (lambda _
+ (substitute* "SConstruct" ; 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
+ "HTSLIB_DIR="
+ (assoc-ref inputs "htslib"))
+ (string-append
+ "SAMTOOLS_DIR="
+ (assoc-ref inputs "samtools"))
+ (string-append
+ "BOOST_ROOT="
+ (assoc-ref inputs "boost"))
+ "install"))))
+ ;; check and install 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")
(source (origin
(method url-fetch)
(uri (string-append
- "http://pypi.python.org/packages/source/m/misopy/misopy-"
+ "https://pypi.python.org/packages/source/m/misopy/misopy-"
version ".tar.gz"))
(sha256
(base32
"0x446867az8ir0z8c1vjqffkp0ma37wm4sylixnkhgawllzx8v5w"))
(modules '((guix build utils)))
- ;; use "gcc" instead of "cc" for compilation
(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',
("python-scipy" ,python2-scipy)
("python-matplotlib" ,python2-matplotlib)))
(native-inputs
- `(("python-setuptools" ,python2-setuptools)))
+ `(("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
that a read originated from a particular isoform.")
(license license:gpl2)))
-(define-public python2-pbcore
+(define-public orfm
(package
- (name "python2-pbcore")
- (version "0.9.3")
+ (name "orfm")
+ (version "0.4.1")
(source (origin
(method url-fetch)
(uri (string-append
- "https://github.com/PacificBiosciences/pbcore/archive/"
+ "https://github.com/wwood/OrfM/releases/download/v"
+ version "/orfm-" version ".tar.gz"))
+ (sha256
+ (base32
+ "05fmw145snk646ly076zby0fjav0k7ysbclck5d4s9pmgcfpijc2"))))
+ (build-system gnu-build-system)
+ (inputs `(("zlib" ,zlib)))
+ (synopsis "Simple and not slow open reading frame (ORF) caller")
+ (description
+ "An ORF caller finds stretches of DNA that when translated are not
+interrupted by stop codons. OrfM finds and prints these ORFs.")
+ (home-page "https://github.com/wwood/OrfM")
+ (license license:lgpl3+)))
+
+(define-public python2-pbcore
+ (package
+ (name "python2-pbcore")
+ (version "0.9.3")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/PacificBiosciences/pbcore/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
files and writing bioinformatics applications.")
(license license:bsd-3)))
+(define-public python2-warpedlmm
+ (package
+ (name "python2-warpedlmm")
+ (version "0.21")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-"
+ version ".zip"))
+ (sha256
+ (base32
+ "1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2 ; requires Python 2.7
+ #:phases
+ (modify-phases %standard-phases
+ (add-after
+ 'install 'remove-bin-directory
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; The "bin" directory only contains wrappers for running
+ ;; the module tests. They are not needed after the
+ ;; "check" phase.
+ (delete-file-recursively
+ (string-append (assoc-ref outputs "out") "/bin"))
+ #t)))))
+ (propagated-inputs
+ `(("python-scipy" ,python2-scipy)
+ ("python-numpy" ,python2-numpy)
+ ("python-matplotlib" ,python2-matplotlib)
+ ("python-fastlmm" ,python2-fastlmm)
+ ("python-pandas" ,python2-pandas)
+ ("python-pysnptools" ,python2-pysnptools)))
+ (native-inputs
+ `(("python-setuptools" ,python2-setuptools)
+ ("python-mock" ,python2-mock)
+ ("python-nose" ,python2-nose)
+ ("unzip" ,unzip)))
+ (home-page "https://github.com/PMBio/warpedLMM")
+ (synopsis "Implementation of warped linear mixed models")
+ (description
+ "WarpedLMM is a Python implementation of the warped linear mixed model,
+which automatically learns an optimal warping function (or transformation) for
+the phenotype as it models the data.")
+ (license license:asl2.0)))
+
(define-public pbtranscript-tofu
- (let ((commit "c7bbd5472"))
+ (let ((commit "8f5467fe6"))
(package
(name "pbtranscript-tofu")
- (version (string-append "0.4.1." commit))
+ (version (string-append "2.2.3." commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/PacificBiosciences/cDNA_primer.git")
(commit commit)))
- (file-name (string-append name "-" version ".tar.gz"))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "148xkzi689c49g6fdhckp6mnmj2qhjdf1j4wifm6ja7ij95d7fxx"))))
+ "1lgnpi35ihay42qx0b6yl3kkgra723i413j33kvs0kvs61h82w0f"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; remove bundled Cython sources
+ (delete-file "pbtranscript-tofu/pbtranscript/Cython-0.20.1.tar.gz")
+ #t))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:configure-flags '("--single-version-externally-managed"
"--record=pbtranscript-tofu.txt")
#:phases
- (alist-cons-after
- 'unpack 'enter-directory-and-clean-up
- (lambda _
- (chdir "pbtranscript-tofu/pbtranscript/")
- ;; Delete clutter
- (delete-file-recursively "dist/")
- (delete-file-recursively "build/")
- (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/")
- (delete-file-recursively "pbtools.pbtranscript.egg-info")
- (delete-file "Cython-0.20.1.tar.gz")
- (delete-file "setuptools_cython-0.2.1-py2.7.egg")
- (delete-file "setuptools_cython-0.2.1.tar.gz")
- (delete-file "setup.cfg")
- (for-each delete-file
- (find-files "." "\\.so$"))
- ;; files should be writable for install phase
- (for-each (lambda (f) (chmod f #o755))
- (find-files "." "\\.py$")))
- %standard-phases)))
+ (modify-phases %standard-phases
+ (add-after 'unpack 'enter-directory
+ (lambda _
+ (chdir "pbtranscript-tofu/pbtranscript/")
+ #t))
+ ;; With setuptools version 18.0 and later this setup.py hack causes
+ ;; a build error, so we disable it.
+ (add-after 'enter-directory 'patch-setuppy
+ (lambda _
+ (substitute* "setup.py"
+ (("if 'setuptools.extension' in sys.modules:")
+ "if False:"))
+ #t)))))
(inputs
- `(("python-cython" ,python2-cython)
- ("python-numpy" ,python2-numpy)
+ `(("python-numpy" ,python2-numpy)
("python-bx-python" ,python2-bx-python)
("python-networkx" ,python2-networkx)
("python-scipy" ,python2-scipy)
- ("python-pbcore" ,python2-pbcore)))
+ ("python-pbcore" ,python2-pbcore)
+ ("python-h5py" ,python2-h5py)))
(native-inputs
- `(("python-nose" ,python2-nose)
+ `(("python-cython" ,python2-cython)
+ ("python-nose" ,python2-nose)
("python-setuptools" ,python2-setuptools)))
(home-page "https://github.com/PacificBiosciences/cDNA_primer")
(synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
generated using the PacBio Iso-Seq protocol.")
(license license:bsd-3))))
+(define-public prodigal
+ (package
+ (name "prodigal")
+ (version "2.6.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/hyattpd/Prodigal/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0m8sb0fg6lmxrlpzna0am6svbnlmd3dckrhgzxxgb3gxr5fyj284"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ;no check target
+ #:make-flags (list (string-append "INSTALLDIR="
+ (assoc-ref %outputs "out")
+ "/bin"))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure))))
+ (home-page "http://prodigal.ornl.gov")
+ (synopsis "Protein-coding gene prediction for Archaea and Bacteria")
+ (description
+ "Prodigal runs smoothly on finished genomes, draft genomes, and
+metagenomes, providing gene predictions in GFF3, Genbank, or Sequin table
+format. It runs quickly, in an unsupervised fashion, handles gaps, handles
+partial genes, and identifies translation initiation sites.")
+ (license license:gpl3+)))
+
+(define-public rsem
+ (package
+ (name "rsem")
+ (version "1.2.20")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append "http://deweylab.biostat.wisc.edu/rsem/src/rsem-"
+ version ".tar.gz"))
+ (sha256
+ (base32 "0nzdc0j0hjllhsd5f2xli95dafm3nawskigs140xzvjk67xh0r9q"))
+ (patches (list (search-patch "rsem-makefile.patch")))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; remove bundled copy of boost
+ (delete-file-recursively "boost")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ;no "check" target
+ #:phases
+ (modify-phases %standard-phases
+ ;; No "configure" script.
+ ;; Do not build bundled samtools library.
+ (replace 'configure
+ (lambda _
+ (substitute* "Makefile"
+ (("^all : sam/libbam.a") "all : "))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (string-append (assoc-ref outputs "out")))
+ (bin (string-append out "/bin/"))
+ (perl (string-append out "/lib/perl5/site_perl")))
+ (mkdir-p bin)
+ (mkdir-p perl)
+ (for-each (lambda (file)
+ (copy-file file
+ (string-append bin (basename file))))
+ (find-files "." "rsem-.*"))
+ (copy-file "rsem_perl_utils.pm"
+ (string-append perl "/rsem_perl_utils.pm")))
+ #t))
+ (add-after
+ 'install 'wrap-program
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (for-each (lambda (prog)
+ (wrap-program (string-append out "/bin/" prog)
+ `("PERL5LIB" ":" prefix
+ (,(string-append out "/lib/perl5/site_perl")))))
+ '("rsem-plot-transcript-wiggles"
+ "rsem-calculate-expression"
+ "rsem-generate-ngvector"
+ "rsem-run-ebseq"
+ "rsem-prepare-reference")))
+ #t)))))
+ (inputs
+ `(("boost" ,boost)
+ ("ncurses" ,ncurses)
+ ("r" ,r)
+ ("perl" ,perl)
+ ("samtools" ,samtools-0.1)
+ ("zlib" ,zlib)))
+ (home-page "http://deweylab.biostat.wisc.edu/rsem/")
+ (synopsis "Estimate gene expression levels from RNA-Seq data")
+ (description
+ "RSEM is a software package for estimating gene and isoform expression
+levels from RNA-Seq data. The RSEM package provides a user-friendly
+interface, supports threads for parallel computation of the EM algorithm,
+single-end and paired-end read data, quality scores, variable-length reads and
+RSPD estimation. In addition, it provides posterior mean and 95% credibility
+interval estimates for expression levels. For visualization, it can generate
+BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
+ (license license:gpl3+)))
+
(define-public rseqc
(package
(name "rseqc")
(define-public samtools
(package
(name "samtools")
- (version "1.1")
+ (version "1.2")
(source
(origin
(method url-fetch)
version "/samtools-" version ".tar.bz2"))
(sha256
(base32
- "1y5p2hs4gif891b4ik20275a8xf3qrr1zh9wpysp4g8m0g1jckf2"))))
+ "1akdqb685pk9xk1nb6sa9aq8xssjjhvvc06kp4cpdqvz2157l3j2"))))
(build-system gnu-build-system)
(arguments
`(;; There are 87 test failures when building on non-64-bit architectures
;; systems.
#:tests? ,(string=? (or (%current-system) (%current-target-system))
"x86_64-linux")
- #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
+ #:modules ((ice-9 ftw)
+ (ice-9 regex)
+ (guix build gnu-build-system)
+ (guix build utils))
+ #:make-flags (list "LIBCURSES=-lncurses"
+ (string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
(alist-cons-after
'unpack
- 'patch-makefile-curses
- (lambda _
- (substitute* "Makefile"
- (("-lcurses") "-lncurses")))
+ 'patch-tests
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((bash (assoc-ref inputs "bash")))
+ (substitute* "test/test.pl"
+ ;; The test script calls out to /bin/bash
+ (("/bin/bash")
+ (string-append bash "/bin/bash"))
+ ;; There are two failing tests upstream relating to the "stats"
+ ;; subcommand in test_usage_subcommand ("did not have Usage"
+ ;; and "usage did not mention samtools stats"), so we disable
+ ;; them.
+ (("(test_usage_subcommand\\(.*\\);)" cmd)
+ (string-append "unless ($subcommand eq 'stats') {" cmd "};")))))
(alist-cons-after
- 'unpack
- 'patch-tests
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((bash (assoc-ref inputs "bash")))
- (substitute* "test/test.pl"
- ;; The test script calls out to /bin/bash
- (("/bin/bash")
- (string-append bash "/bin/bash"))
- ;; There are two failing tests upstream relating to the "stats"
- ;; subcommand in test_usage_subcommand ("did not have Usage"
- ;; and "usage did not mention samtools stats"), so we disable
- ;; them.
- (("(test_usage_subcommand\\(.*\\);)" cmd)
- (string-append "unless ($subcommand eq 'stats') {" cmd "};")))))
- (alist-delete
- 'configure
- %standard-phases)))))
+ 'install 'install-library
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((lib (string-append (assoc-ref outputs "out") "/lib")))
+ (install-file "libbam.a" lib)))
+ (alist-cons-after
+ 'install 'install-headers
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((include (string-append (assoc-ref outputs "out")
+ "/include/samtools/")))
+ (for-each (lambda (file)
+ (install-file file include))
+ (scandir "." (lambda (name) (string-match "\\.h$" name))))
+ #t))
+ (alist-delete 'configure %standard-phases))))))
(native-inputs `(("pkg-config" ,pkg-config)))
(inputs `(("ncurses" ,ncurses)
("perl" ,perl)
viewer.")
(license license:expat)))
+(define-public samtools-0.1
+ ;; This is the most recent version of the 0.1 line of samtools. The input
+ ;; and output formats differ greatly from that used and produced by samtools
+ ;; 1.x and is still used in many bioinformatics pipelines.
+ (package (inherit samtools)
+ (version "0.1.19")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append "mirror://sourceforge/samtools/"
+ version "/samtools-" version ".tar.bz2"))
+ (sha256
+ (base32 "1m33xsfwz0s8qi45lylagfllqg7fphf4dr0780rsvw75av9wk06h"))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments samtools)
+ ((#:tests? tests) #f) ;no "check" target
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append
+ (assoc-ref outputs "out") "/bin")))
+ (mkdir-p bin)
+ (copy-file "samtools"
+ (string-append bin "/samtools")))))
+ (delete 'patch-tests)))))))
+
+(define-public mosaik
+ (let ((commit "5c25216d"))
+ (package
+ (name "mosaik")
+ (version "2.2.30")
+ (source (origin
+ ;; There are no release tarballs nor tags.
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/wanpinglee/MOSAIK.git")
+ (commit commit)))
+ (file-name (string-append name "-" version))
+ (sha256
+ (base32
+ "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no tests
+ #:make-flags (list "CC=gcc")
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda _ (chdir "src") #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (mkdir-p bin)
+ (copy-recursively "../bin" bin)
+ #t))))))
+ (inputs
+ `(("perl" ,perl)
+ ("zlib" ,zlib)))
+ (supported-systems '("x86_64-linux"))
+ (home-page "https://code.google.com/p/mosaik-aligner/")
+ (synopsis "Map nucleotide sequence reads to reference genomes")
+ (description
+ "MOSAIK is a program for mapping second and third-generation sequencing
+reads to a reference genome. MOSAIK can align reads generated by all the
+major sequencing technologies, including Illumina, Applied Biosystems SOLiD,
+Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
+ ;; MOSAIK is released under the GPLv2+ with the exception of third-party
+ ;; code released into the public domain:
+ ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/
+ ;; 2. MD5 implementation - RSA Data Security, RFC 1321
+ (license (list license:gpl2+ license:public-domain)))))
+
(define-public ngs-sdk
(package
(name "ngs-sdk")
- (version "1.1.0")
+ (version "1.2.2")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "09fakv9w87lfg9g70kwzmnryqdjj1sz2c7kw01i6drjf787gkjhw"))))
+ "0rvq61zfw2h9jcz6a33b9xrl20r7s5a9rldvv6rs2qy42khpmf5j"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-build? #f ; not supported
'configure
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
- ;; Only replace the version suffix, not the version number in the
- ;; directory name; fixed in commit 46d4509fa8 (no release yet).
- (substitute* "setup/konfigure.perl"
- (((string-append "\\$\\(subst "
- "(\\$\\(VERSION[^\\)]*\\)),"
- "(\\$\\([^\\)]+\\)),"
- "(\\$\\([^\\)]+\\)|\\$\\@)"
- "\\)")
- _ pattern replacement target)
- (string-append "$(patsubst "
- "%" pattern ","
- "%" replacement ","
- target ")")))
-
;; The 'configure' script doesn't recognize things like
;; '--enable-fast-install'.
(zero? (system* "./configure"
(lambda _ (chdir "ngs-sdk") #t)
%standard-phases))))
(native-inputs `(("perl" ,perl)))
+ ;; According to the test
+ ;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i)
+ ;; in ngs-sdk/setup/konfigure.perl
+ (supported-systems '("i686-linux" "x86_64-linux"))
(home-page "https://github.com/ncbi/ngs")
(synopsis "API for accessing Next Generation Sequencing data")
(description
(srfi srfi-26))
,@(package-arguments ngs-sdk))
((#:phases phases)
- `(alist-cons-after
- 'enter-dir 'fix-java-symlink-installation
- (lambda _
- ;; Only replace the version suffix, not the version number in
- ;; the directory name. Reported here:
- ;; https://github.com/ncbi/ngs/pull/4
- (substitute* "Makefile.java"
- (((string-append "\\$\\(subst "
- "(\\$\\(VERSION[^\\)]*\\)),"
- "(\\$\\([^\\)]+\\)),"
- "(\\$\\([^\\)]+\\)|\\$\\@)"
- "\\)")
- _ pattern replacement target)
- (string-append "$(patsubst "
- "%" pattern ","
- "%" replacement ","
- target ")"))))
- (alist-replace
- 'enter-dir (lambda _ (chdir "ngs-java") #t)
- ,phases))))))
+ `(modify-phases ,phases
+ (replace 'enter-dir (lambda _ (chdir "ngs-java") #t)))))))
(inputs
`(("jdk" ,icedtea6 "jdk")
("ngs-sdk" ,ngs-sdk)))
(synopsis "Java bindings for NGS SDK")))
+(define-public ncbi-vdb
+ (package
+ (name "ncbi-vdb")
+ (version "2.5.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append "https://github.com/ncbi/ncbi-vdb/archive/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1rcnyc4xkdfcjww2i0s0qrbapys0cxbjcx2sy3qkpslf9f400fgj"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:parallel-build? #f ; not supported
+ #:tests? #f ; no "check" target
+ #:phases
+ (alist-replace
+ 'configure
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ ;; Override include path for libmagic
+ (substitute* "setup/package.prl"
+ (("name => 'magic', Include => '/usr/include'")
+ (string-append "name=> 'magic', Include => '"
+ (assoc-ref inputs "libmagic")
+ "/include" "'")))
+
+ ;; Install kdf5 library (needed by sra-tools)
+ (substitute* "build/Makefile.install"
+ (("LIBRARIES_TO_INSTALL =")
+ "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
+
+ ;; The 'configure' script doesn't recognize things like
+ ;; '--enable-fast-install'.
+ (zero? (system*
+ "./configure"
+ (string-append "--build-prefix=" (getcwd) "/build")
+ (string-append "--prefix=" (assoc-ref outputs "out"))
+ (string-append "--debug")
+ (string-append "--with-xml2-prefix="
+ (assoc-ref inputs "libxml2"))
+ (string-append "--with-ngs-sdk-prefix="
+ (assoc-ref inputs "ngs-sdk"))
+ (string-append "--with-ngs-java-prefix="
+ (assoc-ref inputs "ngs-java"))
+ (string-append "--with-hdf5-prefix="
+ (assoc-ref inputs "hdf5"))))))
+ (alist-cons-after
+ 'install 'install-interfaces
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Install interface libraries. On i686 the interface libraries
+ ;; are installed to "linux/gcc/i386", so we need to use the Linux
+ ;; architecture name ("i386") instead of the target system prefix
+ ;; ("i686").
+ (mkdir (string-append (assoc-ref outputs "out") "/ilib"))
+ (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
+ ,(system->linux-architecture
+ (or (%current-target-system)
+ (%current-system)))
+ "/rel/ilib")
+ (string-append (assoc-ref outputs "out")
+ "/ilib"))
+ ;; Install interface headers
+ (copy-recursively "interfaces"
+ (string-append (assoc-ref outputs "out")
+ "/include")))
+ %standard-phases))))
+ (inputs
+ `(("libxml2" ,libxml2)
+ ("ngs-sdk" ,ngs-sdk)
+ ("ngs-java" ,ngs-java)
+ ("libmagic" ,file)
+ ("hdf5" ,hdf5)))
+ (native-inputs `(("perl" ,perl)))
+ (home-page "https://github.com/ncbi/ncbi-vdb")
+ (synopsis "Database engine for genetic information")
+ (description
+ "The NCBI-VDB library implements a highly compressed columnar data
+warehousing engine that is most often used to store genetic information.
+Databases are stored in a portable image within the file system, and can be
+accessed/downloaded on demand across HTTP.")
+ (license license:public-domain)))
+
+(define-public plink
+ (package
+ (name "plink")
+ (version "1.07")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-"
+ version "-src.zip"))
+ (sha256
+ (base32 "0as8gxm4pjyc8dxmm1sl873rrd7wn5qs0l29nqfnl31x8i467xaa"))
+ (patches (list (search-patch "plink-1.07-unclobber-i.patch")))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:tests? #f ;no "check" target
+ #:make-flags (list (string-append "LIB_LAPACK="
+ (assoc-ref %build-inputs "lapack")
+ "/lib/liblapack.so")
+ "WITH_LAPACK=1"
+ "FORCE_DYNAMIC=1"
+ ;; disable phoning home
+ "WITH_WEBCHECK=")
+ #:phases
+ (modify-phases %standard-phases
+ ;; no "configure" script
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin/")))
+ (install-file "plink" bin)
+ #t))))))
+ (inputs
+ `(("zlib" ,zlib)
+ ("lapack" ,lapack)))
+ (native-inputs
+ `(("unzip" ,unzip)))
+ (home-page "http://pngu.mgh.harvard.edu/~purcell/plink/")
+ (synopsis "Whole genome association analysis toolset")
+ (description
+ "PLINK is a whole genome association analysis toolset, designed to
+perform a range of basic, large-scale analyses in a computationally efficient
+manner. The focus of PLINK is purely on analysis of genotype/phenotype data,
+so there is no support for steps prior to this (e.g. study design and
+planning, generating genotype or CNV calls from raw data). Through
+integration with gPLINK and Haploview, there is some support for the
+subsequent visualization, annotation and storage of results.")
+ ;; Code is released under GPLv2, except for fisher.h, which is under
+ ;; LGPLv2.1+
+ (license (list license:gpl2 license:lgpl2.1+))))
+
+(define-public preseq
+ (package
+ (name "preseq")
+ (version "1.0.2")
+ (source (origin
+ (method url-fetch)
+ (uri
+ (string-append "http://smithlabresearch.org/downloads/preseq-"
+ version ".tar.bz2"))
+ (sha256
+ (base32 "0r7sw07p6nv8ygvc17gd78lisbw5336v3vhs86b5wv8mw3pwqksc"))
+ (patches (list (search-patch "preseq-1.0.2-install-to-PREFIX.patch")
+ (search-patch "preseq-1.0.2-link-with-libbam.patch")))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Remove bundled samtools.
+ '(delete-file-recursively "preseq-master/samtools"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ;no "check" target
+ #:phases
+ (modify-phases %standard-phases
+ (add-after
+ 'unpack 'enter-dir
+ (lambda _
+ (chdir "preseq-master")
+ #t))
+ (add-after
+ 'enter-dir 'use-samtools-headers
+ (lambda _
+ (substitute* '("smithlab_cpp/SAM.cpp"
+ "smithlab_cpp/SAM.hpp")
+ (("sam.h") "samtools/sam.h"))
+ #t))
+ (delete 'configure))
+ #:make-flags (list (string-append "PREFIX="
+ (assoc-ref %outputs "out"))
+ (string-append "LIBBAM="
+ (assoc-ref %build-inputs "samtools")
+ "/lib/libbam.a"))))
+ (inputs
+ `(("gsl" ,gsl)
+ ("samtools" ,samtools-0.1)
+ ("zlib" ,zlib)))
+ (home-page "http://smithlabresearch.org/software/preseq/")
+ (synopsis "Program for analyzing library complexity")
+ (description
+ "The preseq package is aimed at predicting and estimating the complexity
+of a genomic sequencing library, equivalent to predicting and estimating the
+number of redundant reads from a given sequencing depth and how many will be
+expected from additional sequencing using an initial sequencing experiment.
+The estimates can then be used to examine the utility of further sequencing,
+optimize the sequencing depth, or to screen multiple libraries to avoid low
+complexity samples.")
+ (license license:gpl3+)))
+
+(define-public sra-tools
+ (package
+ (name "sra-tools")
+ (version "2.4.5-5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append "https://github.com/ncbi/sra-tools/archive/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "11nrnvz7a012f4iryf0wiwrid0h111grsfxbxa9j51h3f2xbvgns"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:parallel-build? #f ; not supported
+ #:tests? #f ; no "check" target
+ #:phases
+ (alist-replace
+ 'configure
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; The build system expects a directory containing the sources and
+ ;; raw build output of ncbi-vdb, including files that are not
+ ;; installed. Since we are building against an installed version of
+ ;; ncbi-vdb, the following modifications are needed.
+ (substitute* "setup/konfigure.perl"
+ ;; Make the configure script look for the "ilib" directory of
+ ;; "ncbi-vdb" without first checking for the existence of a
+ ;; matching library in its "lib" directory.
+ (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);")
+ "my $f = File::Spec->catdir($ilibdir, $ilib);")
+ ;; Look for interface libraries in ncbi-vdb's "ilib" directory.
+ (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);")
+ "my $ilibdir = File::Spec->catdir($dir, 'ilib');"))
+
+ ;; The 'configure' script doesn't recognize things like
+ ;; '--enable-fast-install'.
+ (zero? (system*
+ "./configure"
+ (string-append "--build-prefix=" (getcwd) "/build")
+ (string-append "--prefix=" (assoc-ref outputs "out"))
+ (string-append "--debug")
+ (string-append "--with-fuse-prefix="
+ (assoc-ref inputs "fuse"))
+ (string-append "--with-magic-prefix="
+ (assoc-ref inputs "libmagic"))
+ ;; TODO: building with libxml2 fails with linker errors
+ ;; (string-append "--with-xml2-prefix="
+ ;; (assoc-ref inputs "libxml2"))
+ (string-append "--with-ncbi-vdb-sources="
+ (assoc-ref inputs "ncbi-vdb"))
+ (string-append "--with-ncbi-vdb-build="
+ (assoc-ref inputs "ncbi-vdb"))
+ (string-append "--with-ngs-sdk-prefix="
+ (assoc-ref inputs "ngs-sdk"))
+ (string-append "--with-hdf5-prefix="
+ (assoc-ref inputs "hdf5")))))
+ %standard-phases)))
+ (native-inputs `(("perl" ,perl)))
+ (inputs
+ `(("ngs-sdk" ,ngs-sdk)
+ ("ncbi-vdb" ,ncbi-vdb)
+ ("libmagic" ,file)
+ ("fuse" ,fuse)
+ ("hdf5" ,hdf5)
+ ("zlib" ,zlib)))
+ (home-page "http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software")
+ (synopsis "Tools and libraries for reading and writing sequencing data")
+ (description
+ "The SRA Toolkit from NCBI is a collection of tools and libraries for
+reading of sequencing files from the Sequence Read Archive (SRA) database and
+writing files into the .sra format.")
+ (license license:public-domain)))
+
(define-public seqan
(package
(name "seqan")
bioinformatics file formats, sequence alignment, and more.")
(license license:bsd-3)))
+(define-public seqmagick
+ (package
+ (name "seqmagick")
+ (version "0.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://pypi.python.org/packages/source/s/seqmagick/seqmagick-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0cgn477n74gsl4qdaakrrhi953kcsd4q3ivk2lr18x74s3g4ma1d"))))
+ (build-system python-build-system)
+ (arguments
+ ;; python2 only, see https://github.com/fhcrc/seqmagick/issues/56
+ `(#:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ ;; Current test in setup.py does not work as of 0.6.1,
+ ;; so use nose to run tests instead for now. See
+ ;; https://github.com/fhcrc/seqmagick/issues/55
+ (replace 'check (lambda _ (zero? (system* "nosetests")))))))
+ (inputs
+ `(("python-biopython" ,python2-biopython)))
+ (native-inputs
+ `(("python-setuptools" ,python2-setuptools)
+ ("python-nose" ,python2-nose)))
+ (home-page "http://github.com/fhcrc/seqmagick")
+ (synopsis "Tools for converting and modifying sequence files")
+ (description
+ "Bioinformaticians often have to convert sequence files between formats
+and do little manipulations on them, and it's not worth writing scripts for
+that. Seqmagick is a utility to expose the file format conversion in
+BioPython in a convenient way. Instead of having a big mess of scripts, there
+is one that takes arguments.")
+ (license license:gpl3)))
+
(define-public star
(package
(name "star")
- (version "2.4.0j")
+ (version "2.4.2a")
(source (origin
(method url-fetch)
(uri (string-append
version ".tar.gz"))
(sha256
(base32
- "1y3bciych1aw6s7k8sy1saj23dcan9wk4d4f96an499slkxwz712"))
+ "1c3rnm7r5l0kl3d04gl1g7938xqf1c2l0mla87rlplqg1hcns5mc"))
(modules '((guix build utils)))
(snippet
'(substitute* "source/Makefile"
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
- (mkdir-p bin)
- (copy-file "STAR" (string-append bin "STAR"))))
+ (install-file "STAR" bin)))
(alist-delete
'configure %standard-phases)))))
(native-inputs
;; STAR is licensed under GPLv3 or later; htslib is MIT-licensed.
(license license:gpl3+)))
-(define-public shogun
+(define-public subread
(package
- (name "shogun")
- (version "4.0.0")
- (source
- (origin
- (method url-fetch)
- (uri (string-append
- "ftp://shogun-toolbox.org/shogun/releases/"
- (version-major+minor version)
- "/sources/shogun-" version ".tar.bz2"))
- (sha256
- (base32
- "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb"))))
- (build-system cmake-build-system)
+ (name "subread")
+ (version "1.4.6-p2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "mirror://sourceforge/subread/subread-"
+ version "-source.tar.gz"))
+ (sha256
+ (base32
+ "06sv9mpcsdj6p68y15d6gi70lca3lxmzk0dn61hg0kfsa7rxmsr3"))))
+ (build-system gnu-build-system)
(arguments
- '(#:tests? #f ;no check target
+ `(#:tests? #f ;no "check" target
+ ;; The CC and CCFLAGS variables are set to contain a lot of x86_64
+ ;; optimizations by default, so we override these flags such that x86_64
+ ;; flags are only added when the build target is an x86_64 system.
+ #:make-flags
+ (list (let ((system ,(or (%current-target-system)
+ (%current-system)))
+ (flags '("-ggdb" "-fomit-frame-pointer"
+ "-ffast-math" "-funroll-loops"
+ "-fmessage-length=0"
+ "-O9" "-Wall" "-DMAKE_FOR_EXON"
+ "-DMAKE_STANDALONE"
+ "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\""))
+ (flags64 '("-mmmx" "-msse" "-msse2" "-msse3")))
+ (if (string-prefix? "x86_64" system)
+ (string-append "CCFLAGS=" (string-join (append flags flags64)))
+ (string-append "CCFLAGS=" (string-join flags))))
+ "-f" "Makefile.Linux"
+ "CC=gcc ${CCFLAGS}")
#:phases
(alist-cons-after
- 'unpack 'delete-broken-symlinks
- (lambda _
- (for-each delete-file '("applications/arts/data"
- "applications/asp/data"
- "applications/easysvm/data"
- "applications/msplicer/data"
- "applications/ocr/data"
- "examples/documented/data"
- "examples/documented/matlab_static"
- "examples/documented/octave_static"
- "examples/undocumented/data"
- "examples/undocumented/matlab_static"
- "examples/undocumented/octave_static"
- "tests/integration/data"
- "tests/integration/matlab_static"
- "tests/integration/octave_static"
- "tests/integration/python_modular/tests"))
- #t)
- (alist-cons-after
- 'unpack 'change-R-target-path
+ 'unpack 'enter-dir
+ (lambda _ (chdir "src") #t)
+ (alist-replace
+ 'install
(lambda* (#:key outputs #:allow-other-keys)
- (substitute* '("src/interfaces/r_modular/CMakeLists.txt"
- "src/interfaces/r_static/CMakeLists.txt"
- "examples/undocumented/r_modular/CMakeLists.txt")
- (("\\$\\{R_COMPONENT_LIB_PATH\\}")
- (string-append (assoc-ref outputs "out")
- "/lib/R/library/")))
- #t)
- (alist-cons-after
- 'unpack 'fix-octave-modules
- (lambda* (#:key outputs #:allow-other-keys)
- (substitute* '("src/interfaces/octave_modular/CMakeLists.txt"
- "src/interfaces/octave_static/CMakeLists.txt")
- (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
- "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave"))
-
- ;; change target directory
- (substitute* "src/interfaces/octave_modular/CMakeLists.txt"
- (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
- (string-append (assoc-ref outputs "out")
- "/share/octave/packages")))
- #t)
- (alist-cons-before
- 'build 'set-HOME
- ;; $HOME needs to be set at some point during the build phase
- (lambda _ (setenv "HOME" "/tmp") #t)
- %standard-phases))))
- #:configure-flags
- (list "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
- ;;"-DJavaModular=ON" ;requires unpackaged jblas
- ;;"-DRubyModular=ON" ;requires unpackaged ruby-narray
- ;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist
- ;;"-DLuaModular=ON" ;fails because lua doesn't build pkgconfig file
- "-DOctaveModular=ON"
- "-DOctaveStatic=ON"
- "-DPythonModular=ON"
- "-DPythonStatic=ON"
- "-DRModular=ON"
- "-DRStatic=ON"
- "-DCmdLineStatic=ON")))
- (inputs
- `(("python" ,python)
- ("numpy" ,python-numpy)
- ("r" ,r)
- ("octave" ,octave)
- ("swig" ,swig)
- ("hdf5" ,hdf5)
- ("atlas" ,atlas)
- ("arpack" ,arpack-ng)
- ("lapack" ,lapack)
- ("glpk" ,glpk)
- ("libxml2" ,libxml2)
- ("lzo" ,lzo)
- ("zlib" ,zlib)))
- (native-inputs
- `(("pkg-config" ,pkg-config)))
- (home-page "http://shogun-toolbox.org/")
- (synopsis "Machine learning toolbox")
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (mkdir-p bin)
+ (copy-recursively "../bin" bin)))
+ ;; no "configure" script
+ (alist-delete 'configure %standard-phases)))))
+ (inputs `(("zlib" ,zlib)))
+ (home-page "http://bioinf.wehi.edu.au/subread-package/")
+ (synopsis "Tool kit for processing next-gen sequencing data")
(description
- "The Shogun Machine learning toolbox provides a wide range of unified and
-efficient Machine Learning (ML) methods. The toolbox seamlessly allows to
-combine multiple data representations, algorithm classes, and general purpose
-tools. This enables both rapid prototyping of data pipelines and extensibility
-in terms of new algorithms.")
+ "The subread package contains the following tools: subread aligner, a
+general-purpose read aligner; subjunc aligner: detecting exon-exon junctions
+and mapping RNA-seq reads; featureCounts: counting mapped reads for genomic
+features; exactSNP: a SNP caller that discovers SNPs by testing signals
+against local background noises.")
(license license:gpl3+)))
(define-public vcftools
(arguments
`(#:tests? #f ; no "check" target
#:make-flags (list
+ "CFLAGS=-O2" ; override "-m64" flag
(string-append "PREFIX=" (assoc-ref %outputs "out"))
(string-append "MANDIR=" (assoc-ref %outputs "out")
"/share/man/man1"))
;; The license is declared as LGPLv3 in the README and
;; at http://vcftools.sourceforge.net/license.html
(license license:lgpl3)))
+
+(define-public vsearch
+ (package
+ (name "vsearch")
+ (version "1.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/torognes/vsearch/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0b1359wbzgb2cm04h7dq05v80vik88hnsv298xxd1q1f2q4ydni7"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Remove bundled cityhash and '-mtune=native'.
+ (substitute* "src/Makefile.am"
+ (("^AM_CXXFLAGS=-I\\$\\{srcdir\\}/cityhash \
+-O3 -mtune=native -Wall -Wsign-compare")
+ (string-append "AM_CXXFLAGS=-lcityhash"
+ " -O3 -Wall -Wsign-compare"))
+ (("^__top_builddir__bin_vsearch_SOURCES = cityhash/city.h \\\\")
+ "__top_builddir__bin_vsearch_SOURCES = \\")
+ (("^cityhash/config.h \\\\") "\\")
+ (("^cityhash/city.cc \\\\") "\\"))
+ (substitute* "src/vsearch.h"
+ (("^\\#include \"cityhash/city.h\"")
+ "#include <city.h>"))
+ (delete-file-recursively "src/cityhash")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'configure 'autogen
+ (lambda _ (zero? (system* "autoreconf" "-vif")))))))
+ (inputs
+ `(("zlib" ,zlib)
+ ("bzip2" ,bzip2)
+ ("cityhash" ,cityhash)))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)))
+ (synopsis "Sequence search tools for metagenomics")
+ (description
+ "VSEARCH supports DNA sequence searching, clustering, chimera detection,
+dereplication, pairwise alignment, shuffling, subsampling, sorting and
+masking. The tool takes advantage of parallelism in the form of SIMD
+vectorization as well as multiple threads to perform accurate alignments at
+high speed. VSEARCH uses an optimal global aligner (full dynamic programming
+Needleman-Wunsch).")
+ (home-page "https://github.com/torognes/vsearch")
+ ;; vsearch uses non-portable SSE intrinsics so building fails on other
+ ;; platforms.
+ (supported-systems '("x86_64-linux"))
+ ;; Dual licensed; also includes public domain source.
+ (license (list license:gpl3 license:bsd-2))))
+
+(define-public bio-locus
+ (package
+ (name "bio-locus")
+ (version "0.0.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "bio-locus" version))
+ (sha256
+ (base32
+ "02vmrxyimkj9sahsp4zhfhnmbvz6dbbqz1y01vglf8cbwvkajfl0"))))
+ (build-system ruby-build-system)
+ (native-inputs
+ `(("ruby-rspec" ,ruby-rspec)))
+ (synopsis "Tool for fast querying of genome locations")
+ (description
+ "Bio-locus is a tabix-like tool for fast querying of genome
+locations. Many file formats in bioinformatics contain records that
+start with a chromosome name and a position for a SNP, or a start-end
+position for indels. Bio-locus allows users to store this chr+pos or
+chr+pos+alt information in a database.")
+ (home-page "https://github.com/pjotrp/bio-locus")
+ (license license:expat)))
+
+(define-public bio-blastxmlparser
+ (package
+ (name "bio-blastxmlparser")
+ (version "2.0.4")
+ (source (origin
+ (method url-fetch)
+ (uri (rubygems-uri "bio-blastxmlparser" version))
+ (sha256
+ (base32
+ "1wf4qygcmdjgcqm6flmvsagfr1gs9lf63mj32qv3z1f481zc5692"))))
+ (build-system ruby-build-system)
+ (propagated-inputs
+ `(("ruby-bio-logger" ,ruby-bio-logger)
+ ("ruby-nokogiri" ,ruby-nokogiri)))
+ (inputs
+ `(("ruby-rspec" ,ruby-rspec)))
+ (synopsis "Fast big data BLAST XML parser and library")
+ (description
+ "Very fast parallel big-data BLAST XML file parser which can be used as
+command line utility. Use blastxmlparser to: Parse BLAST XML; filter output;
+generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.")
+ (home-page "http://github.com/pjotrp/blastxmlparser")
+ (license license:expat)))
+
+(define-public bioruby
+ (package
+ (name "bioruby")
+ (version "1.5.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "bio" version))
+ (sha256
+ (base32
+ "01k2fyjl5fpx4zn8g6gqiqvsg2j1fgixrs9p03vzxckynxdq3wmc"))))
+ (build-system ruby-build-system)
+ (propagated-inputs
+ `(("ruby-libxml" ,ruby-libxml)))
+ (native-inputs
+ `(("which" ,which))) ; required for test phase
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'build 'patch-test-command
+ (lambda _
+ (substitute* '("test/functional/bio/test_command.rb")
+ (("/bin/sh") (which "sh")))
+ (substitute* '("test/functional/bio/test_command.rb")
+ (("/bin/ls") (which "ls")))
+ (substitute* '("test/functional/bio/test_command.rb")
+ (("which") (which "which")))
+ (substitute* '("test/functional/bio/test_command.rb",
+ "test/data/command/echoarg2.sh")
+ (("/bin/echo") (which "echo")))
+ #t)))))
+ (synopsis "Ruby library, shell and utilities for bioinformatics")
+ (description "BioRuby comes with a comprehensive set of Ruby development
+tools and libraries for bioinformatics and molecular biology. BioRuby has
+components for sequence analysis, pathway analysis, protein modelling and
+phylogenetic analysis; it supports many widely used data formats and provides
+easy access to databases, external programs and public web services, including
+BLAST, KEGG, GenBank, MEDLINE and GO.")
+ (home-page "http://bioruby.org/")
+ ;; Code is released under Ruby license, except for setup
+ ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
+ (license (list license:ruby license:lgpl2.1+ license:gpl2+ ))))
+
+(define-public r-qtl
+ (package
+ (name "r-qtl")
+ (version "1.37-11")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://cran/src/contrib/qtl_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0h20d36mww7ljp51pfs66xq33yq4b4fwq9nsh02dpmfhlaxgx1xi"))))
+ (build-system r-build-system)
+ (home-page "http://rqtl.org/")
+ (synopsis "R package for analyzing QTL experiments in genetics")
+ (description "R/qtl is an extension library for the R statistics
+system. It is used to analyze experimental crosses for identifying
+genes contributing to variation in quantitative traits (so-called
+quantitative trait loci, QTLs).
+
+Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
+identify genotyping errors, and to perform single-QTL and two-QTL,
+two-dimensional genome scans.")
+ (license license:gpl3)))
HCoop / jackhill / guix / guix.git / blobdiff