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-rw-r--r--gnu/packages/bioinformatics.scm604
1 files changed, 407 insertions, 197 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8d2cb93c7c..14daf59c92 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,11 +1,12 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2014, 2015, 2016, 2017 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>
;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -50,6 +51,7 @@
#:use-module (gnu packages documentation)
#:use-module (gnu packages datastructures)
#:use-module (gnu packages file)
+ #:use-module (gnu packages flex)
#:use-module (gnu packages gawk)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gd)
@@ -96,7 +98,7 @@
(define-public aragorn
(package
(name "aragorn")
- (version "1.2.37")
+ (version "1.2.38")
(source (origin
(method url-fetch)
(uri (string-append
@@ -104,7 +106,7 @@
version ".tgz"))
(sha256
(base32
- "1c7zxk0h8wsjbix82fmmfyywcq6zn3q9h5y67kcl5y3qal2bv2xr"))))
+ "09i1rg716smlbnixfm7q1ml2mfpaa2fpn3hwjg625ysmfwwy712b"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are no tests
@@ -215,8 +217,7 @@ structure of the predicted RNA.")
("libtool" ,libtool)
("zlib" ,zlib)
("python-nose" ,python2-nose)
- ("python-pysam" ,python2-pysam)
- ("python-setuptools" ,python2-setuptools)))
+ ("python-pysam" ,python2-pysam)))
(inputs
`(("htslib" ,htslib)
("samtools" ,samtools)
@@ -523,15 +524,14 @@ intended to behave exactly the same as the original BWK awk.")
(build-system python-build-system)
(arguments `(#:python ,python-2)) ; no Python 3 support
(inputs
- `(("python-cython" ,python2-cython)
- ("python-matplotlib" ,python2-matplotlib)))
+ `(("python-matplotlib" ,python2-matplotlib)))
(propagated-inputs
`(("bedtools" ,bedtools)
("samtools" ,samtools)))
(native-inputs
- `(("python-pyyaml" ,python2-pyyaml)
- ("python-nose" ,python2-nose)
- ("python-setuptools" ,python2-setuptools)))
+ `(("python-cython" ,python2-cython)
+ ("python-pyyaml" ,python2-pyyaml)
+ ("python-nose" ,python2-nose)))
(home-page "https://pythonhosted.org/pybedtools/")
(synopsis "Python wrapper for BEDtools programs")
(description
@@ -586,9 +586,7 @@ e.g. microbiome samples, genomes, metagenomes.")
(substitute* "setup.py"
(("install_requires.append\\(\"pyqi\"\\)") "pass"))
#t)))
- ,@(package-arguments base)))
- (native-inputs `(("python2-setuptools" ,python2-setuptools)
- ,@(package-native-inputs base))))))
+ ,@(package-arguments base))))))
(define-public bioperl-minimal
(let* ((inputs `(("perl-module-build" ,perl-module-build)
@@ -673,7 +671,7 @@ provide a coordinated and extensible framework to do computational biology.")
(add-before 'check 'set-home
;; Some tests require a home directory to be set.
(lambda _ (setenv "HOME" "/tmp") #t)))))
- (inputs
+ (propagated-inputs
`(("python-numpy" ,python-numpy)))
(home-page "http://biopython.org/")
(synopsis "Tools for biological computation in Python")
@@ -684,15 +682,10 @@ 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"))
- (properties `((python2-variant . ,(delay python2-biopython))))))
+ (license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE"))))
(define-public python2-biopython
- (let ((base (package-with-python2 (strip-python2-variant python-biopython))))
- (package
- (inherit base)
- (native-inputs `(("python2-setuptools" ,python2-setuptools)
- ,@(package-native-inputs base))))))
+ (package-with-python2 python-biopython))
;; An outdated version of biopython is required for seqmagick, see
;; https://github.com/fhcrc/seqmagick/issues/59
@@ -1104,7 +1097,7 @@ confidence to have in an alignment.")
("pigz" ,pigz)
("zlib" ,zlib)))
(supported-systems '("x86_64-linux"))
- (home-page "http://sourceforge.net/p/bless-ec/wiki/Home/")
+ (home-page "https://sourceforge.net/p/bless-ec/wiki/Home/")
(synopsis "Bloom-filter-based error correction tool for NGS reads")
(description
"@dfn{Bloom-filter-based error correction solution for high-throughput
@@ -1339,8 +1332,7 @@ well as many of the command line options.")
`(("python-numpy" ,python2-numpy)
("zlib" ,zlib)))
(native-inputs
- `(("python-nose" ,python2-nose)
- ("python-setuptools" ,python2-setuptools)))
+ `(("python-nose" ,python2-nose)))
(home-page "http://bitbucket.org/james_taylor/bx-python/")
(synopsis "Tools for manipulating biological data")
(description
@@ -1404,7 +1396,6 @@ multiple sequence alignments.")
("zlib" ,zlib)))
(native-inputs
`(("python-cython" ,python-cython)
- ("python-setuptools" ,python-setuptools)
;; Dependencies below are are for tests only.
("samtools" ,samtools)
("bcftools" ,bcftools)
@@ -1430,7 +1421,6 @@ also includes an interface for tabix.")
(sha256
(base32
"1q8wnj2kga9nz1lwc4w7qv52smfm536hp6mc8w6s53lhyj0mpi22"))))
- (properties `((python2-variant . ,(delay python2-twobitreader))))
(build-system python-build-system)
(arguments
'(;; Tests are not distributed in the PyPi release.
@@ -1447,11 +1437,7 @@ 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))))))
+ (package-with-python2 python-twobitreader))
(define-public python-plastid
(package
@@ -1463,7 +1449,6 @@ UCSC genome browser.")
(sha256
(base32
"1sqkz5d3b9kf688mp7k771c87ins42j7j0whmkb49cb3fsg8s8lj"))))
- (properties `((python2-variant . ,(delay python2-plastid))))
(build-system python-build-system)
(arguments
;; Some test files are not included.
@@ -1488,25 +1473,20 @@ 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))))))
+ (package-with-python2 python-plastid))
(define-public cd-hit
(package
(name "cd-hit")
- (version "4.6.5")
+ (version "4.6.6")
(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"))
+ "/cd-hit-v" version "-2016-0711.tar.gz"))
(sha256
(base32
- "15db0hq38yyifwqx9b6l34z14jcq576dmjavhj8a426c18lvnhp3"))))
+ "1w8hd4fszgg29nqiz569fldwy012la77nljcmlhglgicws56z54p"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; there are no tests
@@ -1580,9 +1560,8 @@ databases.")
("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)))
+ `(("python-mock" ,python2-mock) ; for tests
+ ("python-pytz" ,python2-pytz))) ; for tests
(home-page "https://github.com/YeoLab/clipper")
(synopsis "CLIP peak enrichment recognition")
(description
@@ -1755,8 +1734,7 @@ time.")
("zlib" ,zlib)))
(native-inputs
`(("python-cython" ,python2-cython)
- ("python-nose" ,python2-nose)
- ("python-setuptools" ,python2-setuptools)))
+ ("python-nose" ,python2-nose)))
(home-page "http://crossmap.sourceforge.net/")
(synopsis "Convert genome coordinates between assemblies")
(description
@@ -1826,7 +1804,7 @@ preparation protocols.")
(define-public cutadapt
(package
(name "cutadapt")
- (version "1.8")
+ (version "1.12")
(source (origin
(method url-fetch)
(uri (string-append
@@ -1835,28 +1813,30 @@ preparation protocols.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "161bp87y6gd6r5bmvjpn2b1k942i3fizfpa139f0jn6jv1wcp5h5"))))
+ "19smhh6444ikn4jlmyhvffw4m5aw7yg07rqsk7arg8dkwyga1i4v"))))
(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))))
+ `(#:phases
+ (modify-phases %standard-phases
+ ;; The tests must be run after installation.
+ (delete 'check)
+ (add-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")))))))
+ (inputs
+ `(("python-xopen" ,python-xopen)))
(native-inputs
`(("python-cython" ,python-cython)
- ("python-nose" ,python-nose)
- ("python-setuptools" ,python-setuptools)))
- (home-page "https://code.google.com/p/cutadapt/")
+ ("python-nose" ,python-nose)))
+ (home-page "https://cutadapt.readthedocs.io/en/stable/")
(synopsis "Remove adapter sequences from nucleotide sequencing reads")
(description
"Cutadapt finds and removes adapter sequences, primers, poly-A tails and
@@ -1945,27 +1925,19 @@ 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))))))
+ (package-with-python2 python-pybigwig))
(define-public python-dendropy
(package
(name "python-dendropy")
- (version "4.1.0")
+ (version "4.2.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "DendroPy" version))
(sha256
(base32
- "1jfz7gp18wph311w1yygbvjanb3n5mdqal439bb6myw41dwb5m63"))
- ;; There are two known test failures that will be fixed in the next
- ;; release after 4.1.0.
- ;; https://github.com/jeetsukumaran/DendroPy/issues/48
- (patches (search-patches
- "python-dendropy-exclude-failing-tests.patch"))))
+ "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p"))))
(build-system python-build-system)
(home-page "http://packages.python.org/DendroPy/")
(synopsis "Library for phylogenetics and phylogenetic computing")
@@ -1980,15 +1952,6 @@ trees (phylogenies) and characters.")
(let ((base (package-with-python2 (strip-python2-variant python-dendropy))))
(package
(inherit base)
- ;; Do not use same source as 'python-dendropy' because the patched
- ;; failing tests do not occur on Python 2.
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "DendroPy" (package-version base)))
- (sha256
- (base32
- "1jfz7gp18wph311w1yygbvjanb3n5mdqal439bb6myw41dwb5m63"))))
(arguments
`(#:python ,python-2
#:phases
@@ -1997,8 +1960,7 @@ trees (phylogenies) and characters.")
;; There is currently a test failure that only happens on some
;; systems, and only using "setup.py test"
(lambda _ (zero? (system* "nosetests")))))))
- (native-inputs `(("python2-setuptools" ,python2-setuptools)
- ("python2-nose" ,python2-nose)
+ (native-inputs `(("python2-nose" ,python2-nose)
,@(package-native-inputs base))))))
@@ -2026,9 +1988,8 @@ trees (phylogenies) and characters.")
("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)))
+ `(("python-mock" ,python2-mock) ;for tests
+ ("python-pytz" ,python2-pytz))) ;for tests
(home-page "https://github.com/fidelram/deepTools")
(synopsis "Tools for normalizing and visualizing deep-sequencing data")
(description
@@ -2045,7 +2006,7 @@ identify enrichments with functional annotations of the genome.")
(define-public diamond
(package
(name "diamond")
- (version "0.8.27")
+ (version "0.8.31")
(source (origin
(method url-fetch)
(uri (string-append
@@ -2054,7 +2015,7 @@ identify enrichments with functional annotations of the genome.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0g0zdyfnri9v7nfbh8f7zqs4af1xydqkiw8m0cx4jc2ql4chpf6a"))))
+ "0nh79f4rpgq8vmlga743r7vd0z0ik6spy34f7vfq0v9lcmvfr7xq"))))
(build-system cmake-build-system)
(arguments
'(#:tests? #f ; no "check" target
@@ -2683,8 +2644,7 @@ comment or quality sections.")
("python-pysam" ,python2-pysam)
("python-networkx" ,python2-networkx)))
(native-inputs
- `(("python-cython" ,python2-cython)
- ("python-setuptools" ,python2-setuptools)))
+ `(("python-cython" ,python2-cython)))
(home-page "http://grit-bio.org")
(synopsis "Tool for integrative analysis of RNA-seq type assays")
(description
@@ -2810,8 +2770,6 @@ HMMs).")
`(("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
@@ -2932,8 +2890,7 @@ data. It also provides the bgzip, htsfile, and tabix utilities.")
("python-numpy" ,python-numpy)
("python-matplotlib" ,python-matplotlib)))
(native-inputs
- `(("python-cython" ,python-cython)
- ("python-setuptools" ,python-setuptools)))
+ `(("python-cython" ,python-cython)))
(home-page "https://github.com/nboley/idr")
(synopsis "Tool to measure the irreproducible discovery rate (IDR)")
(description
@@ -3090,8 +3047,6 @@ data.")
#: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
@@ -3423,9 +3378,8 @@ linker_so='gcc -shared'); defines")))))
("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)))
+ `(("python-mock" ,python2-mock) ;for tests
+ ("python-pytz" ,python2-pytz))) ;for tests
(home-page "http://genes.mit.edu/burgelab/miso/index.html")
(synopsis "Mixture of Isoforms model for RNA-Seq isoform quantitation")
(description
@@ -3472,10 +3426,49 @@ program for nucleotide and protein sequences.")
;; License information found in 'muscle -h' and usage.cpp.
(license license:public-domain)))
+(define-public newick-utils
+ ;; There are no recent releases so we package from git.
+ (let ((commit "da121155a977197cab9fbb15953ca1b40b11eb87"))
+ (package
+ (name "newick-utils")
+ (version (string-append "1.6-1." (string-take commit 8)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/tjunier/newick_utils.git")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "1hkw21rq1mwf7xp0rmbb2gqc0i6p11108m69i7mr7xcjl268pxnb"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'autoconf
+ (lambda _ (zero? (system* "autoreconf" "-vif")))))))
+ (inputs
+ ;; XXX: TODO: Enable Lua and Guile bindings.
+ ;; https://github.com/tjunier/newick_utils/issues/13
+ `(("libxml2" ,libxml2)
+ ("flex" ,flex)
+ ("bison" ,bison)))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)
+ ("libtool" ,libtool)))
+ (synopsis "Programs for working with newick format phylogenetic trees")
+ (description
+ "Newick-utils is a suite of utilities for processing phylogenetic trees
+in Newick format. Functions include re-rooting, extracting subtrees,
+trimming, pruning, condensing, drawing (ASCII graphics or SVG).")
+ (home-page "https://github.com/tjunier/newick_utils")
+ (license license:bsd-3))))
+
(define-public orfm
(package
(name "orfm")
- (version "0.5.3")
+ (version "0.6.1")
(source (origin
(method url-fetch)
(uri (string-append
@@ -3483,7 +3476,7 @@ program for nucleotide and protein sequences.")
version "/orfm-" version ".tar.gz"))
(sha256
(base32
- "0vb6d771gl4mix8bwx919x5ayy9pkj44n7ki336nz3rz2rx4c7gk"))))
+ "19hwp13n82isdvk16710l9m35cmzf0q3fsrcn3r8c5r67biiz39s"))))
(build-system gnu-build-system)
(inputs `(("zlib" ,zlib)))
(native-inputs
@@ -3509,18 +3502,15 @@ interrupted by stop codons. OrfM finds and prints these ORFs.")
"1kjmv891d6qbpp4shhhvkl02ff4q5xlpnls2513sm2cjcrs52f1i"))))
(build-system python-build-system)
(arguments `(#:python ,python-2)) ; pbcore requires Python 2.7
- (inputs
+ (propagated-inputs
`(("python-cython" ,python2-cython)
("python-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam)
("python-h5py" ,python2-h5py)))
(native-inputs
- `(("python-docutils" ,python2-docutils)
- ("python-nose" ,python2-nose)
- ("python-setuptools" ,python2-setuptools)
- ("python-sphinx" ,python2-sphinx)))
- (propagated-inputs
- `(("python-pyxb" ,python2-pyxb)))
+ `(("python-nose" ,python2-nose)
+ ("python-sphinx" ,python2-sphinx)
+ ("python-pyxb" ,python2-pyxb)))
(home-page "http://pacificbiosciences.github.io/pbcore/")
(synopsis "Library for reading and writing PacBio data files")
(description
@@ -3543,18 +3533,7 @@ files and writing bioinformatics applications.")
"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)))))
+ `(#:python ,python-2)) ; requires Python 2.7
(propagated-inputs
`(("python-scipy" ,python2-scipy)
("python-numpy" ,python2-numpy)
@@ -3563,8 +3542,7 @@ files and writing bioinformatics applications.")
("python-pandas" ,python2-pandas)
("python-pysnptools" ,python2-pysnptools)))
(native-inputs
- `(("python-setuptools" ,python2-setuptools)
- ("python-mock" ,python2-mock)
+ `(("python-mock" ,python2-mock)
("python-nose" ,python2-nose)
("unzip" ,unzip)))
(home-page "https://github.com/PMBio/warpedLMM")
@@ -3598,11 +3576,6 @@ the phenotype as it models the data.")
(build-system python-build-system)
(arguments
`(#:python ,python-2
- ;; With standard flags, the install phase attempts to create a zip'd
- ;; egg file, and fails with an error: 'ZIP does not support timestamps
- ;; before 1980'
- #:configure-flags '("--single-version-externally-managed"
- "--record=pbtranscript-tofu.txt")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'enter-directory
@@ -3626,8 +3599,7 @@ the phenotype as it models the data.")
("python-h5py" ,python2-h5py)))
(native-inputs
`(("python-cython" ,python2-cython)
- ("python-nose" ,python2-nose)
- ("python-setuptools" ,python2-setuptools)))
+ ("python-nose" ,python2-nose)))
(home-page "https://github.com/PacificBiosciences/cDNA_primer")
(synopsis "Analyze transcriptome data generated with the Iso-Seq protocol")
(description
@@ -4076,7 +4048,6 @@ BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.")
`(("python-cython" ,python2-cython)
("python-pysam" ,python2-pysam)
("python-numpy" ,python2-numpy)
- ("python-setuptools" ,python2-setuptools)
("zlib" ,zlib)))
(native-inputs
`(("python-nose" ,python2-nose)))
@@ -4282,7 +4253,7 @@ viewer.")
`(("perl" ,perl)
("zlib" ,zlib)))
(supported-systems '("x86_64-linux"))
- (home-page "https://code.google.com/p/mosaik-aligner/")
+ (home-page "https://github.com/wanpinglee/MOSAIK")
(synopsis "Map nucleotide sequence reads to reference genomes")
(description
"MOSAIK is a program for mapping second and third-generation sequencing
@@ -4638,11 +4609,7 @@ sequence itself can be retrieved from these databases.")
(license license:bsd-3)))
(define-public python2-screed
- (let ((base (package-with-python2 (strip-python2-variant python-screed))))
- (package
- (inherit base)
- (native-inputs `(("python2-setuptools" ,python2-setuptools)
- ,@(package-native-inputs base))))))
+ (package-with-python2 python-screed))
(define-public sra-tools
(package
@@ -4804,8 +4771,7 @@ bioinformatics file formats, sequence alignment, and more.")
;; should be removed.
`(("python-biopython" ,python2-biopython-1.66)))
(native-inputs
- `(("python-setuptools" ,python2-setuptools)
- ("python-nose" ,python2-nose)))
+ `(("python-nose" ,python2-nose)))
(home-page "http://github.com/fhcrc/seqmagick")
(synopsis "Tools for converting and modifying sequence files")
(description
@@ -4948,7 +4914,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
(define-public star
(package
(name "star")
- (version "2.5.2a")
+ (version "2.5.2b")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/alexdobin/STAR/archive/"
@@ -4956,7 +4922,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0xjlsm4p9flln111hv4xx7xy94c2nl53zvdvbk9winmiradjsdra"))
+ "1na6np880r1zaamiy00hy8bid5anpy0kgf63587v2yl080krk2zq"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -4965,6 +4931,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
;; Remove pre-built binaries and bundled htslib sources.
(delete-file-recursively "bin/MacOSX_x86_64")
(delete-file-recursively "bin/Linux_x86_64")
+ (delete-file-recursively "bin/Linux_x86_64_static")
(delete-file-recursively "source/htslib")
#t))))
(build-system gnu-build-system)
@@ -5246,20 +5213,21 @@ data types as well.")
(define-public r-annotate
(package
(name "r-annotate")
- (version "1.52.0")
+ (version "1.52.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "annotate" version))
(sha256
(base32
- "1fd2csq7dcs2gwndgwdx2nwkymz8gsmlnqqzv3p0vjjsvvq5n2a8"))))
+ "0yymz8qxgnbybvfhqrgkd1hh9dhwxdii1yxkhr1zicjgb35xixxb"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-biobase" ,r-biobase)
("r-biocgenerics" ,r-biocgenerics)
("r-dbi" ,r-dbi)
+ ("r-rcurl" ,r-rcurl)
("r-xml" ,r-xml)
("r-xtable" ,r-xtable)))
(home-page
@@ -5323,14 +5291,14 @@ high-throughput sequencing experiments.")
(define-public r-deseq2
(package
(name "r-deseq2")
- (version "1.14.0")
+ (version "1.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DESeq2" version))
(sha256
(base32
- "0kq06jy4xg5ii3a9l62f17kirsfx0gsiwq6mhiy985cqzpdn893g"))))
+ "1walwkqryn1gnwz7zryr5764a0p6ia7ag4w6w9n8fskg8dkg0fqs"))))
(properties `((upstream-name . "DESeq2")))
(build-system r-build-system)
(arguments
@@ -5653,7 +5621,7 @@ track. The database is exposed as a @code{TxDb} object.")
(define-public vsearch
(package
(name "vsearch")
- (version "2.3.0")
+ (version "2.3.4")
(source
(origin
(method url-fetch)
@@ -5663,7 +5631,7 @@ track. The database is exposed as a @code{TxDb} object.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1r8fk3whkil348y5hfsd4r56qjmchhq4nxm6s7ra5rlisw0mf9fy"))
+ "1xyraxmhyx62mxx8z7c8waygvcijwkh48ms1ar60w2cv2y2sn4al"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -5723,15 +5691,16 @@ Needleman-Wunsch).")
(define-public pardre
(package
(name "pardre")
- (version "1.1.5")
+ ;; The source of 1.1.5 changed in place, so we append "-1" to the version.
+ (version "1.1.5-1")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/pardre/ParDRe-rel"
- version ".tar.gz"))
+ "1.1.5" ".tar.gz"))
(sha256
(base32
- "0zkyjzv4s8q2h5npalhirbk17r5b1h0n2a42mh7njzlf047h9bhy"))))
+ "17j73nc0viq4f6qj50nrndsrif5d6b71q8fl87m54psiv0ilns2b"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no tests included
@@ -5839,14 +5808,14 @@ generate FASTA, JSON, YAML, RDF, JSON-LD, HTML, CSV, tabular output etc.")
(define-public bioruby
(package
(name "bioruby")
- (version "1.5.0")
+ (version "1.5.1")
(source
(origin
(method url-fetch)
(uri (rubygems-uri "bio" version))
(sha256
(base32
- "01k2fyjl5fpx4zn8g6gqiqvsg2j1fgixrs9p03vzxckynxdq3wmc"))))
+ "0hdl0789c9n4mprnx5pgd46bfwl8d000rqpamj5h6kkjgspijv49"))))
(build-system ruby-build-system)
(propagated-inputs
`(("ruby-libxml" ,ruby-libxml)))
@@ -5975,13 +5944,13 @@ also known as views, in a controlled vocabulary.")
(define-public r-biocstyle
(package
(name "r-biocstyle")
- (version "2.2.0")
+ (version "2.2.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocStyle" version))
(sha256
(base32
- "0qbk23fz8cn260isd9xlh9lxfj4adar6iqzai01c4kz0p31f45za"))))
+ "0sl99xw940ixrm6v24lgaw3ljh56g59a6rdz7g160hx84z9f8n2n"))))
(properties
`((upstream-name . "BiocStyle")))
(build-system r-build-system)
@@ -6110,13 +6079,13 @@ abnormal copy number.")
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.12.0")
+ (version "0.12.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "0m0npc0vhmcwcxws7v2f8k4hvvrjvnlrsr94klxf4a8m4xw2xzzk"))))
+ "0i36y3w36h3d8rmazxcrip4gvn54rd9av1wz4lygsprrjmylfhcc"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
@@ -6162,13 +6131,13 @@ utilities for sequence data management under the ACNUC system.")
(define-public r-iranges
(package
(name "r-iranges")
- (version "2.8.0")
+ (version "2.8.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IRanges" version))
(sha256
(base32
- "0cdl1sfd3cvf93lnz91fdk64fbg1mnd5g958dwh1il8r358hqq3f"))))
+ "0cryqnpqb3p6l9jjw27hyqd550sxlljls3ka7b9rb38hkji7b5hw"))))
(properties
`((upstream-name . "IRanges")))
(build-system r-build-system)
@@ -6191,13 +6160,13 @@ possible.")
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.10.0")
+ (version "1.10.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "0nhg4bk38gzvf3mvnbqgisbbhfv1kzjld27z1z9knnlkplkiyyyv"))))
+ "0zh894qd1sgpjbn0wfvq6hs2dzn7y1pyicvzk2aa48y3zbidanv7"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
@@ -6217,13 +6186,13 @@ names in their natural, rather than lexicographic, order.")
(define-public r-edger
(package
(name "r-edger")
- (version "3.16.1")
+ (version "3.16.5")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "1r6hhwkqp13m022hjajzr1lnjsbai0yjhykwn0kp1f0la990a808"))))
+ "04vpa0a6dkkjyvvfbkmfjyaxf2ldkagi66g028qpaszd8jsk8yiv"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
@@ -6243,13 +6212,13 @@ CAGE.")
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.20.0")
+ (version "1.20.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "1lwzfgahz8ipwli73kcfqb18y6adi129hap1gnycnj3980m54i8q"))))
+ "165wda1d2jagd907pnra4m3sla66icyqxvd60xpv09jl5agd5mn9"))))
(properties
`((upstream-name . "VariantAnnotation")))
(inputs
@@ -6281,13 +6250,13 @@ coding changes and predict coding outcomes.")
(define-public r-limma
(package
(name "r-limma")
- (version "3.30.2")
+ (version "3.30.7")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "04jris7wk2lxksrrvrjsysznsdb2k04lfgrnp18ic49sazva0hfy"))))
+ "1xg9w4lmn9n4hwyflxiwi6g969lcy569cg4z1x47crwwg7z7qdka"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
@@ -6336,13 +6305,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(define-public r-genomicranges
(package
(name "r-genomicranges")
- (version "1.26.1")
+ (version "1.26.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicRanges" version))
(sha256
(base32
- "039nxccg9i2an8q2wni79x8dr9p1fcfcqvih9hg9w243pczg2g3c"))))
+ "0if5dswkp77lyqppd0z2iyvnwag9h1gsr03707s8npcx13mzpsia"))))
(properties
`((upstream-name . "GenomicRanges")))
(build-system r-build-system)
@@ -6468,13 +6437,13 @@ objects.")
(define-public r-biostrings
(package
(name "r-biostrings")
- (version "2.42.0")
+ (version "2.42.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biostrings" version))
(sha256
(base32
- "08z8lkz3axa94wkf144a931ry6vf6cc25avi1ywr84ln2k5czz9f"))))
+ "0vqgd9i6y3wj4zviqwgvwgd4qj6033fg01rmx1cw9bw5i8ans42d"))))
(properties
`((upstream-name . "Biostrings")))
(build-system r-build-system)
@@ -6645,13 +6614,13 @@ as well as query and modify the browser state, such as the current viewport.")
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.26.0")
+ (version "1.26.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "0z8spi2knwzwi10c38vr7xlvi3ah9faj7m1lka880mmxkl9cai4k"))))
+ "1ybi6r3bax07wlv2qcd34y5qjdvcqcfayfvlrjc39ifrkk65wv4f"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
@@ -7257,7 +7226,7 @@ throughput genetic sequencing data sets using regression methods.")
(define-public r-qtl
(package
(name "r-qtl")
- (version "1.39-5")
+ (version "1.40-8")
(source
(origin
(method url-fetch)
@@ -7265,7 +7234,7 @@ throughput genetic sequencing data sets using regression methods.")
version ".tar.gz"))
(sha256
(base32
- "1grwgvyv7x0dgay1858bg7qf4wk47gpnq7qkqpcda9cn0h970d6f"))))
+ "05bj1x2ry0i7yqiydlswb3d2h4pxg70z8w1072az1mrv1m54k8sp"))))
(build-system r-build-system)
(home-page "http://rqtl.org/")
(synopsis "R package for analyzing QTL experiments in genetics")
@@ -7298,6 +7267,29 @@ two-dimensional genome scans.")
libraries for systems that do not have these available via other means.")
(license license:artistic2.0)))
+(define-public r-r4rna
+ (package
+ (name "r-r4rna")
+ (version "0.1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://www.e-rna.org/r-chie/files/R4RNA_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1p0i78wh76jfgmn9jphbwwaz6yy6pipzfg08xs54cxavxg2j81p5"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-optparse" ,r-optparse)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)))
+ (home-page "http://www.e-rna.org/r-chie/index.cgi")
+ (synopsis "Analysis framework for RNA secondary structure")
+ (description
+ "The R4RNA package aims to be a general framework for the analysis of RNA
+secondary structure and comparative analysis in R.")
+ (license license:gpl3+)))
+
(define-public r-rhtslib
(package
(name "r-rhtslib")
@@ -7358,7 +7350,7 @@ paired-end data.")
(define-public r-rcas
(package
(name "r-rcas")
- (version "1.0.0")
+ (version "1.1.1")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v"
@@ -7366,7 +7358,7 @@ paired-end data.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1h7di822ihgkhmmmlfbfz3c2dkjyjxl307i6mx8w0cwjqbna1kp6"))))
+ "1hd0r66556bxbdd82ksjklq7nfli36l4k6y88ic7kkg9873wa1nw"))))
(build-system r-build-system)
(native-inputs
`(("r-knitr" ,r-knitr)
@@ -7388,6 +7380,7 @@ paired-end data.")
("r-topgo" ,r-topgo)
("r-dt" ,r-dt)
("r-plotly" ,r-plotly)
+ ("r-plotrix" ,r-plotrix)
("r-motifrg" ,r-motifrg)
("r-genomation" ,r-genomation)
("r-genomicfeatures" ,r-genomicfeatures)
@@ -7478,6 +7471,141 @@ characterization and visualization of a wide range of mutational patterns
in SNV base substitution data.")
(license license:expat)))
+(define-public r-wgcna
+ (package
+ (name "r-wgcna")
+ (version "1.51")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "WGCNA" version))
+ (sha256
+ (base32
+ "0hzvnhw76vwg8bl8x368f0c5szpwb8323bmrb3bir93i5bmfjsxx"))))
+ (properties `((upstream-name . "WGCNA")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-doparallel" ,r-doparallel)
+ ("r-dynamictreecut" ,r-dynamictreecut)
+ ("r-fastcluster" ,r-fastcluster)
+ ("r-foreach" ,r-foreach)
+ ("r-go-db" ,r-go-db)
+ ("r-hmisc" ,r-hmisc)
+ ("r-impute" ,r-impute)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-preprocesscore" ,r-preprocesscore)))
+ (home-page
+ "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
+ (synopsis "Weighted correlation network analysis")
+ (description
+ "This package provides functions necessary to perform Weighted
+Correlation Network Analysis on high-dimensional data. It includes functions
+for rudimentary data cleaning, construction and summarization of correlation
+networks, module identification and functions for relating both variables and
+modules to sample traits. It also includes a number of utility functions for
+data manipulation and visualization.")
+ (license license:gpl2+)))
+
+(define-public r-chipkernels
+ (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372")
+ (revision "1"))
+ (package
+ (name "r-chipkernels")
+ (version (string-append "1.1-" revision "." (string-take commit 9)))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ManuSetty/ChIPKernels.git")
+ (commit commit)))
+ (file-name (string-append name "-" version))
+ (sha256
+ (base32
+ "14bj5qhjm1hsm9ay561nfbqi9wxsa7y487df2idsaaf6z10nw4v0"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-iranges" ,r-iranges)
+ ("r-xvector" ,r-xvector)
+ ("r-biostrings" ,r-biostrings)
+ ("r-bsgenome" ,r-bsgenome)
+ ("r-gtools" ,r-gtools)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-sfsmisc" ,r-sfsmisc)
+ ("r-kernlab" ,r-kernlab)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-biocgenerics" ,r-biocgenerics)))
+ (home-page "https://github.com/ManuSetty/ChIPKernels")
+ (synopsis "Build string kernels for DNA Sequence analysis")
+ (description "ChIPKernels is an R package for building different string
+kernels used for DNA Sequence analysis. A dictionary of the desired kernel
+must be built and this dictionary can be used for determining kernels for DNA
+Sequences.")
+ (license license:gpl2+))))
+
+(define-public r-seqgl
+ (package
+ (name "r-seqgl")
+ (version "1.1.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ManuSetty/SeqGL/"
+ "archive/" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0pnk1p3sci5yipyc8xnb6jbmydpl80fld927xgnbcv104hy8h8yh"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biostrings" ,r-biostrings)
+ ("r-chipkernels" ,r-chipkernels)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-spams" ,r-spams)
+ ("r-wgcna" ,r-wgcna)
+ ("r-fastcluster" ,r-fastcluster)))
+ (home-page "https://github.com/ManuSetty/SeqGL")
+ (synopsis "Group lasso for Dnase/ChIP-seq data")
+ (description "SeqGL is a group lasso based algorithm to extract
+transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles.
+This package presents a method which uses group lasso to discriminate between
+bound and non bound genomic regions to accurately identify transcription
+factors bound at the specific regions.")
+ (license license:gpl2+)))
+
+(define-public r-gkmsvm
+ (package
+ (name "r-gkmsvm")
+ (version "0.71.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gkmSVM" version))
+ (sha256
+ (base32
+ "1zpxgxmf2nd5j5wn00ps6kfxr8wxh7d1swr1rr4spq7sj5z5z0k0"))))
+ (properties `((upstream-name . "gkmSVM")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-kernlab" ,r-kernlab)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rocr" ,r-rocr)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-seqinr" ,r-seqinr)))
+ (home-page "http://cran.r-project.org/web/packages/gkmSVM")
+ (synopsis "Gapped-kmer support vector machine")
+ (description
+ "This R package provides tools for training gapped-kmer SVM classifiers
+for DNA and protein sequences. This package supports several sequence
+kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
+ (license license:gpl2+)))
+
(define-public emboss
(package
(name "emboss")
@@ -7667,24 +7795,12 @@ may optionally be provided to further inform the peak-calling process.")
(build-system python-build-system)
(arguments
`(#:python ,python-2 ; python2 only
- #:tests? #f ; no tests included
- #:phases
- (modify-phases %standard-phases
- ;; When setuptools is used a ".egg" archive is generated and
- ;; installed. This makes it hard to actually run PePr. This issue
- ;; has been reported upstream:
- ;; https://github.com/shawnzhangyx/PePr/issues/9
- (add-after 'unpack 'disable-egg-generation
- (lambda _
- (substitute* "setup.py"
- (("from setuptools import setup")
- "from distutils.core import setup"))
- #t)))))
+ #:tests? #f)) ; no tests included
(propagated-inputs
`(("python2-numpy" ,python2-numpy)
("python2-scipy" ,python2-scipy)
("python2-pysam" ,python2-pysam)))
- (home-page "https://code.google.com/p/pepr-chip-seq/")
+ (home-page "https://github.com/shawnzhangyx/PePr")
(synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data")
(description
"PePr is a ChIP-Seq peak calling or differential binding analysis tool
@@ -7725,15 +7841,20 @@ replacement for strverscmp.")
(define-public multiqc
(package
(name "multiqc")
- (version "0.6")
+ (version "0.9")
(source
(origin
(method url-fetch)
(uri (pypi-uri "multiqc" version))
(sha256
(base32
- "0avw11h63ldpxy5pizc3wl1wa01ha7q10wb240nggsjz3jaqvyiy"))))
+ "12gs1jw2jrxrij529rnl5kaqxfcqn15yzcsggxkfhdx634ml0cny"))
+ (patches (search-patches "multiqc-fix-git-subprocess-error.patch"))))
(build-system python-build-system)
+ (arguments
+ ;; Tests are to be introduced in the next version, see
+ ;; https://github.com/ewels/MultiQC/issues/376
+ `(#:tests? #f))
(propagated-inputs
`(("python-jinja2" ,python-jinja2)
("python-simplejson" ,python-simplejson)
@@ -7741,8 +7862,6 @@ replacement for strverscmp.")
("python-click" ,python-click)
("python-matplotlib" ,python-matplotlib)
("python-numpy" ,python-numpy)))
- (native-inputs
- `(("python-setuptools" ,python-setuptools)))
(home-page "http://multiqc.info")
(synopsis "Aggregate bioinformatics analysis reports")
(description
@@ -7750,3 +7869,94 @@ replacement for strverscmp.")
samples into a single report. It contains modules for a large number of
common bioinformatics tools.")
(license license:gpl3)))
+
+(define-public r-chipseq
+ (package
+ (name "r-chipseq")
+ (version "1.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "chipseq" version))
+ (sha256
+ (base32
+ "115ayp82rs99iaswrx45skw1i5iacgwzz5k8rzijbp5qic0554n0"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-shortread" ,r-shortread)))
+ (home-page "http://bioconductor.org/packages/chipseq")
+ (synopsis "Package for analyzing ChIPseq data")
+ (description
+ "This package provides tools for processing short read data from ChIPseq
+experiments.")
+ (license license:artistic2.0)))
+
+(define-public r-copyhelper
+ (package
+ (name "r-copyhelper")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://bioconductor.org/packages/release/"
+ "data/experiment/src/contrib/CopyhelpeR_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
+ (properties `((upstream-name . "CopyhelpeR")))
+ (build-system r-build-system)
+ (home-page "http://bioconductor.org/packages/CopyhelpeR/")
+ (synopsis "Helper files for CopywriteR")
+ (description
+ "This package contains the helper files that are required to run the
+Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content
+and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
+mm10. In addition, it contains a blacklist filter to remove regions that
+display copy number variation. Files are stored as GRanges objects from the
+GenomicRanges Bioconductor package.")
+ (license license:gpl2)))
+
+(define-public r-copywriter
+ (package
+ (name "r-copywriter")
+ (version "2.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "CopywriteR" version))
+ (sha256
+ (base32
+ "1bwwnsyk7cpgwkagsnn5mv6fv233b0rkhjvbadrh70h8m4anawfj"))))
+ (properties `((upstream-name . "CopywriteR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-chipseq" ,r-chipseq)
+ ("r-copyhelper" ,r-copyhelper)
+ ("r-data-table" ,r-data-table)
+ ("r-dnacopy" ,r-dnacopy)
+ ("r-futile-logger" ,r-futile-logger)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-gtools" ,r-gtools)
+ ("r-iranges" ,r-iranges)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://github.com/PeeperLab/CopywriteR")
+ (synopsis "Copy number information from targeted sequencing")
+ (description
+ "CopywriteR extracts DNA copy number information from targeted sequencing
+by utilizing off-target reads. It allows for extracting uniformly distributed
+copy number information, can be used without reference, and can be applied to
+sequencing data obtained from various techniques including chromatin
+immunoprecipitation and target enrichment on small gene panels. Thereby,
+CopywriteR constitutes a widely applicable alternative to available copy
+number detection tools.")
+ (license license:gpl2)))
generated by cgit v1.2.3 (git 2.45.0) at 2024-12-02 15:38:01 +0000