;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
+;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
+;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;;
;;; This file is part of GNU Guix.
;;;
(inputs inputs)
(native-inputs
`(("perl-test-most" ,perl-test-most)))
- (home-page "http://search.cpan.org/dist/BioPerl")
+ (home-page "https://metacpan.org/release/BioPerl")
(synopsis "Bioinformatics toolkit")
(description
"BioPerl is the product of a community effort to produce Perl code which
(define-public python2-biopython
(package-with-python2 python-biopython))
+(define-public python-fastalite
+ (package
+ (name "python-fastalite")
+ (version "0.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "fastalite" version))
+ (sha256
+ (base32
+ "1qli6pxp77i9xn2wfciq2zaxhl82bdxb33cpzqzj1z25yd036wqj"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f)) ; Test data is not distributed.
+ (home-page "https://github.com/nhoffman/fastalite")
+ (synopsis "Simplest possible FASTA parser")
+ (description "This library implements a FASTA and a FASTQ parser without
+relying on a complex dependency tree.")
+ (license license:expat)))
+
+(define-public python2-fastalite
+ (package-with-python2 python-fastalite))
+
(define-public bpp-core
;; The last release was in 2014 and the recommended way to install from source
;; is to clone the git repository, so we do this.
(define-public libbigwig
(package
(name "libbigwig")
- (version "0.1.4")
+ (version "0.4.2")
(source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/dpryan79/libBigWig/"
- "archive/" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/dpryan79/libBigWig.git")
+ (commit version)))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "098rjh35pi4a9q83n8wiwvyzykjqj6l8q189p1xgfw4ghywdlvw1"))))
+ "0h2smg24v5srdcqzrmz2g23cmlp4va465mgx8r2z571sfz8pv454"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
+ #:tests? #f ; tests require access to the web
#:make-flags
(list "CC=gcc"
(string-append "prefix=" (assoc-ref %outputs "out")))
#:phases
(modify-phases %standard-phases
- (delete 'configure)
- (add-before 'check 'disable-curl-test
- (lambda _
- (substitute* "Makefile"
- (("./test/testRemote.*") ""))
- #t))
- ;; This has been fixed with the upstream commit 4ff6959cd8a0, but
- ;; there has not yet been a release containing this change.
- (add-before 'install 'create-target-dirs
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (mkdir-p (string-append out "/lib"))
- (mkdir-p (string-append out "/include"))
- #t))))))
+ (delete 'configure))))
(inputs
`(("zlib" ,zlib)
("curl" ,curl)))
(native-inputs
- `(("doxygen" ,doxygen)))
+ `(("doxygen" ,doxygen)
+ ;; Need for tests
+ ("python" ,python-2)))
(home-page "https://github.com/dpryan79/libBigWig")
(synopsis "C library for handling bigWig files")
(description
(define-public python-pybigwig
(package
(name "python-pybigwig")
- (version "0.2.5")
+ (version "0.3.12")
(source (origin
(method url-fetch)
(uri (pypi-uri "pyBigWig" version))
(sha256
(base32
- "0yrpdxg3y0sny25x4w22lv1k47jzccqjmg7j4bp0hywklvp0hg7d"))
+ "00w4kfnm2c5l7wdwr2nj1z5djv8kzgf7h1zhsgv6njff1rwr26g0"))
(modules '((guix build utils)))
(snippet
'(begin
(substitute* "setup.py"
(("libs=\\[") "libs=[\"BigWig\", "))
#t)))))
+ (propagated-inputs
+ `(("python-numpy" ,python-numpy)))
(inputs
`(("libbigwig" ,libbigwig)
("zlib" ,zlib)
(define-public python-dendropy
(package
(name "python-dendropy")
- (version "4.2.0")
+ (version "4.4.0")
(source
(origin
(method url-fetch)
- (uri (pypi-uri "DendroPy" version))
+ ;; Source from GitHub so that tests are included.
+ (uri
+ (string-append "https://github.com/jeetsukumaran/DendroPy/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "15c7s3d5gf19ljsxvq5advaa752wfi7pwrdjyhzmg85hccyvp47p"))
- (patches (search-patches "python-dendropy-fix-tests.patch"))))
+ "0v2fccny5xjaah546bsch1mw4kh61qq5frz2ibllxs9mp6ih9bsn"))))
(build-system python-build-system)
(home-page "http://packages.python.org/DendroPy/")
(synopsis "Library for phylogenetics and phylogenetic computing")
"DendroPy is a library for phylogenetics and phylogenetic computing: reading,
writing, simulation, processing and manipulation of phylogenetic
trees (phylogenies) and characters.")
- (license license:bsd-3)
- (properties `((python2-variant . ,(delay python2-dendropy))))))
+ (license license:bsd-3)))
(define-public python2-dendropy
- (let ((base (package-with-python2 (strip-python2-variant python-dendropy))))
- (package
- (inherit base)
- (arguments
- `(#:python ,python-2
- #:phases
- (modify-phases %standard-phases
- (replace 'check
- ;; 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-nose" ,python2-nose)
- ,@(package-native-inputs base))))))
+ (package-with-python2 python-dendropy))
(define-public python-py2bit
(package
#:jdk ,icedtea-8
#:phases
(modify-phases %standard-phases
+ ;; FIXME: this phase fails with "duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class"
+ (delete 'generate-jar-indices)
(add-after 'unpack 'use-our-htsjdk
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "build.xml"
(sxml xpath))
#:phases
(modify-phases %standard-phases
+ ;; FIXME: this phase fails with "duplicate entry: htsjdk/samtools/AbstractBAMFileIndex$1.class"
+ (delete 'generate-jar-indices)
(add-after 'unpack 'remove-useless-build.xml
(lambda _ (delete-file "build.xml") #t))
;; This is necessary to ensure that htsjdk is found when using
(msg (format #f
"\
Class-Path: /~a \
- ~a/share/java/htsjdk.jar${line.separator}"
+ ~a/share/java/htsjdk.jar${line.separator}${line.separator}"
;; maximum line length is 70
(string-tabulate (const #\b) 57)
(assoc-ref inputs "java-htsjdk"))))
(if (member "manifest" name)
`(,tag ,@kids
+ (replaceregexp
+ (@ (file "${manifest.file}")
+ (match "\\r\\n\\r\\n")
+ (replace "${line.separator}")))
(echo
(@ (message ,msg)
(file "${manifest.file}")
(list "-Dsamjdk.intel_deflater_so_path=lib/jni/libIntelDeflater.so")
#:phases
(modify-phases %standard-phases
+ ;; FIXME: This phase fails.
+ (delete 'generate-jar-indices)
;; Do not use bundled ant bzip2.
(add-after 'unpack 'use-ant-bzip
(lambda* (#:key inputs #:allow-other-keys)
(define-public jellyfish
(package
(name "jellyfish")
- (version "2.2.7")
+ (version "2.2.10")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/gmarcais/Jellyfish/"
"/jellyfish-" version ".tar.gz"))
(sha256
(base32
- "1a1iwq9pq54k2m9ypvwl5s0bqfl64gwh9dx5af9i382ajas2016q"))))
+ "1k4pc3fvv6w1km2yph4m5sd78fbxp21d6xyzgmy0gjihzc6mb249"))))
(build-system gnu-build-system)
(outputs '("out" ;for library
"ruby" ;for Ruby bindings
translated into a human-readable text format using the @code{jellyfish dump}
command, or queried for specific k-mers with @code{jellyfish query}.")
(home-page "http://www.genome.umd.edu/jellyfish.html")
- ;; From their website: JELLYFISH runs on 64-bit Intel-compatible processors
- (supported-systems '("x86_64-linux"))
+ ;; JELLYFISH seems to be 64-bit only.
+ (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
;; The combined work is published under the GPLv3 or later. Individual
;; files such as lib/jsoncpp.cpp are released under the Expat license.
(license (list license:gpl3+ license:expat))))
(define-public macs
(package
(name "macs")
- (version "2.1.0.20151222")
+ (version "2.1.1.20160309")
(source (origin
(method url-fetch)
(uri (pypi-uri "MACS2" version))
(sha256
(base32
- "1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5"))))
+ "09ixspd1vcqmz1c81ih70xs4m7qml2iy5vyx1y74zww3iy1vl210"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2 ; only compatible with Python 2.7
(define-public star
(package
(name "star")
- (version "2.6.0a")
+ (version "2.6.0c")
(source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/alexdobin/STAR/archive/"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/alexdobin/STAR.git")
+ (commit version)))
+ (file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "0yci4ymy4407kjh0lqp021nzccp6r31wgrkixkmix5p130cxvc56"))
+ "04cj6jw8d9q6lk9c78wa4fky6jdlicf1d13plq7182h8vqiz8p59"))
(modules '((guix build utils)))
(snippet
'(begin
`(("python-sqlalchemy" ,python2-sqlalchemy)
("python-decorator" ,python2-decorator)
("python-biopython" ,python2-biopython)
- ("python-pandas" ,python2-pandas)))
+ ("python-pandas" ,python2-pandas)
+ ("python-psycopg2" ,python2-psycopg2)
+ ("python-fastalite" ,python2-fastalite)
+ ("python-pyyaml" ,python2-pyyaml)
+ ("python-six" ,python2-six)
+ ("python-jinja2" ,python2-jinja2)
+ ("python-dendropy" ,python2-dendropy)))
(home-page "https://github.com/fhcrc/taxtastic")
(synopsis "Tools for taxonomic naming and annotation")
(description
(define-public r-annotationforge
(package
(name "r-annotationforge")
- (version "1.22.0")
+ (version "1.22.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationForge" version))
(sha256
(base32
- "12ffj7h95adiya5mzyjxazqn1qgr434ajpabfcyhrj5v83s4vk65"))))
+ "17kmy7nvpyyj6w5jyrjciw87rydmmmc8q6cnwqjv1j7li9bp09gr"))))
(properties
`((upstream-name . "AnnotationForge")))
(build-system r-build-system)
(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.48.0")
+ (version "1.48.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "1yx2lir67ny0j150wyfqca0wsxp84byri8nscbs9qlndkh2jppq9"))))
+ "1rxvwikqivsgxjjcazlszy8xgz346lfh5rw4llxw6fz38fjgb0k5"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
checks on R packages that are to be submitted to the Bioconductor repository.")
(license license:artistic2.0)))
-(define-public r-getopt
- (package
- (name "r-getopt")
- (version "1.20.2")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "getopt" version))
- (sha256
- (base32
- "13p35lbpy7i578752fa71sbfvcsqw5qfa9p6kf8b5m3c5p9i4v1x"))))
- (build-system r-build-system)
- (home-page "https://github.com/trevorld/getopt")
- (synopsis "Command-line option processor for R")
- (description
- "This package is designed to be used with Rscript to write shebang
-scripts that accept short and long options. Many users will prefer to
-use the packages @code{optparse} or @code{argparse} which add extra
-features like automatically generated help options and usage texts,
-support for default values, positional argument support, etc.")
- (license license:gpl2+)))
-
(define-public r-optparse
(package
(name "r-optparse")
- (version "1.4.4")
+ (version "1.6.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "optparse" version))
(sha256
(base32
- "1ff4wmsszrb3spwfp7ynfs8w11qpy1sdzfxm1wk8dqqvdwris7qb"))))
+ "1d7v5gl45x4amsfmzn5zyyffyqlc7a82h01szlnda22viyxids0h"))))
(build-system r-build-system)
(propagated-inputs
`(("r-getopt" ,r-getopt)))
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.18.2")
+ (version "0.18.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "0qvj2j0zl4djjl7vrwc6xak6h8dxr53iwypfbcvfb3sh7jwhdiz5"))))
+ "02bps2rpjqx2npwxq3x62ncwi9ggr165cwi56h6hld28bw2gddy8"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
(define-public r-iranges
(package
(name "r-iranges")
- (version "2.14.10")
+ (version "2.14.11")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IRanges" version))
(sha256
(base32
- "10ccw930vfmkskkrzbps14xglqlkxf588623dr7f1a9ckx7yr2p6"))))
+ "0wz63hysspyjihqadg91dbvllc5a61zzjrsz0b9498lihqc6m1la"))))
(properties
`((upstream-name . "IRanges")))
(build-system r-build-system)
(define-public r-edger
(package
(name "r-edger")
- (version "3.22.2")
+ (version "3.22.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "07py2g6vg9jbflwhc1hnzr2silbinrjwxq3mkq30nzjgf0n0hrf3"))))
+ "0w3jv29n0kkaiig8dbbdqy2dkng8xfaihch82mj9ci5hphrx3nng"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.26.0")
+ (version "1.26.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "06bccdf57vja7m63chmgc4539lwng3q3b8zxn285fj8524l6mcn7"))))
+ "1r55ki951dj81qvy73knfcy69ik5vzkd56wnk3f6vvf9vngqb8jr"))))
(properties
`((upstream-name . "VariantAnnotation")))
(inputs
(define-public r-limma
(package
(name "r-limma")
- (version "3.36.1")
+ (version "3.36.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "1982g5v35ilfgxm2vkq1p3j1bbir795pjvfzx4nzam2rlqqymbqm"))))
+ "0iiifszr6hcqih6kszdsbkx3gacfg3d7v8hdx0lbjqnjqgqz7pwk"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
(define-public r-genomicranges
(package
(name "r-genomicranges")
- (version "1.32.3")
+ (version "1.32.6")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicRanges" version))
(sha256
(base32
- "03gmka6rlz18vd4229796l5l3l6446v5cb90sn2nb5knjbp84hni"))))
+ "0p58yk2i5gqvjlkx548mnrr49wvs0xfcl06l9rqj2hi6hkkbvnp3"))))
(properties
`((upstream-name . "GenomicRanges")))
(build-system r-build-system)
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.14.1")
+ (version "1.14.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "00qg1kg2l9qqpyjaw5q910cmf84vwfiw1fhsx3ig784gwinwgj6n"))))
+ "1llb5a62hn4yxpdgqdh2l7i5zd06mjkk8hagsna69cq65wv6iifm"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
(define-public r-rsamtools
(package
(name "r-rsamtools")
- (version "1.32.0")
+ (version "1.32.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Rsamtools" version))
(sha256
(base32
- "1s65y5wn4d0x8zsljg2kmhcl6r9884h95kr041j7hp49bmxg3an6"))))
+ "1hpjr22h33pf4fgv0sj83rqzv6l5l7s6fpmmqvchh45ikks1mnhq"))))
(properties
`((upstream-name . "Rsamtools")))
(build-system r-build-system)
(define-public r-delayedarray
(package
(name "r-delayedarray")
- (version "0.6.0")
+ (version "0.6.5")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DelayedArray" version))
(sha256
(base32
- "0n3w57cwy911q812wc8658y0v3xgpmg379sj98kfqdxa80z1mxdf"))))
+ "10b03zrnvz5isfh4z55hasya2m71lrfx10l5lm2sdmqs0gwkanrd"))))
(properties
`((upstream-name . "DelayedArray")))
(build-system r-build-system)
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.40.2")
+ (version "1.40.6")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "0l90jn4df3akxl0n1i9wvnbjqrzjc0d15r8vqr7b15q2117mrn5r"))))
+ "1wxxxlyps19dw3i0pw4mlm3kinnswsc35rgvlnbwvpnpjbca6w4l"))))
(build-system r-build-system)
(arguments
`(#:phases
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.32.0")
+ (version "1.32.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "1cqcl72q0k5wylw1brn4g4h7xzys1v06piry19cvp0gjcvm5sp7a"))))
+ "0kfyyg1ib8fkq2hxraal10z4bx3rg8figdskw4yhn1mbh6l42q5f"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
(define-public r-bamsignals
(package
(name "r-bamsignals")
- (version "1.12.0")
+ (version "1.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "bamsignals" version))
(sha256
(base32
- "09l4v414ijkjpkvcv2580v13v18ky196f0lv27ldblpa8bddvmns"))))
+ "141q3p4lzwiqk1mfxi8q1q84axjl0gyiqg59xd3sp4viny4jqmgv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
(define-public r-rcas
(package
(name "r-rcas")
- (version "1.3.4")
+ (version "1.6.0")
(source (origin
(method url-fetch)
- (uri (string-append "https://github.com/BIMSBbioinfo/RCAS/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (uri (bioconductor-uri "RCAS" version))
(sha256
(base32
- "1qgc7vi6fpzl440yg7jhiycg5q336kd4pxqzx10yx2zcq3bq3msg"))))
+ "0vmn7a0rm2ban0kaxrf5danhss2r4hfhnwh5889fjcgqy300fdd5"))))
(build-system r-build-system)
(native-inputs
- `(("r-knitr" ,r-knitr)
- ("r-testthat" ,r-testthat)
+ `(("r-testthat" ,r-testthat)
;; During vignette building knitr checks that "pandoc-citeproc"
;; is in the PATH.
("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)))
(propagated-inputs
- `(("r-data-table" ,r-data-table)
+ `(("r-biocgenerics" ,r-biocgenerics)
("r-biomart" ,r-biomart)
- ("r-org-hs-eg-db" ,r-org-hs-eg-db)
- ("r-org-ce-eg-db" ,r-org-ce-eg-db)
- ("r-org-dm-eg-db" ,r-org-dm-eg-db)
- ("r-org-mm-eg-db" ,r-org-mm-eg-db)
+ ("r-biostrings" ,r-biostrings)
("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
("r-bsgenome-celegans-ucsc-ce10" ,r-bsgenome-celegans-ucsc-ce10)
("r-bsgenome-dmelanogaster-ucsc-dm3" ,r-bsgenome-dmelanogaster-ucsc-dm3)
- ("r-topgo" ,r-topgo)
+ ("r-cowplot" ,r-cowplot)
+ ("r-data-table" ,r-data-table)
+ ("r-dbi" ,r-dbi)
("r-dt" ,r-dt)
+ ("r-genomation" ,r-genomation)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggseqlogo" ,r-ggseqlogo)
+ ("r-knitr" ,r-knitr)
+ ("r-motifrg" ,r-motifrg)
+ ("r-org-hs-eg-db" ,r-org-hs-eg-db)
+ ("r-org-ce-eg-db" ,r-org-ce-eg-db)
+ ("r-org-dm-eg-db" ,r-org-dm-eg-db)
+ ("r-org-mm-eg-db" ,r-org-mm-eg-db)
("r-pbapply" ,r-pbapply)
+ ("r-pheatmap" ,r-pheatmap)
("r-plotly" ,r-plotly)
("r-plotrix" ,r-plotrix)
- ("r-motifrg" ,r-motifrg)
- ("r-genomation" ,r-genomation)
- ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-proxy" ,r-proxy)
+ ("r-rsqlite" ,r-rsqlite)
("r-rtracklayer" ,r-rtracklayer)
- ("r-rmarkdown" ,r-rmarkdown)))
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-topgo" ,r-topgo)))
(synopsis "RNA-centric annotation system")
(description
"RCAS aims to be a standalone RNA-centric annotation system that provides
(define-public rcas-web
(package
(name "rcas-web")
- (version "0.0.4")
+ (version "0.0.5")
(source
(origin
(method url-fetch)
"/rcas-web-" version ".tar.gz"))
(sha256
(base32
- "1p16frfys41a8yaa4gkm457nzkqhqs2pc3lkac0ds457w9w5j1gm"))))
+ "0igz7jpcf7cm9800zcag6p3gd1i649figrhbdba6cjkm8f4gfspr"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(define-public r-methylkit
(package
(name "r-methylkit")
- (version "1.6.0")
+ (version "1.6.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "methylKit" version))
(sha256
(base32
- "01qmndm5z21p78w7xfp8ynan6jpfg54rnkpj8b86rc081qh0sgjj"))))
+ "1hr2czi5ybdf7hdmqsv39d17f3mvmw94wa38bc14zzm9mgy9gfy7"))))
(properties `((upstream-name . "methylKit")))
(build-system r-build-system)
(propagated-inputs
(define-public r-seqminer
(package
(name "r-seqminer")
- (version "6.0")
+ (version "6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "seqminer" version))
(sha256
(base32
- "057j1l6dip35l1aivilapl2zv9db677b3di2pb3sfgq2sxg0ps3l"))))
+ "15yhg4vfc7jg1jnqb3371j00pgbmbyc9l1xx63hq1l3p34lazq2l"))))
(build-system r-build-system)
(inputs
`(("zlib" ,zlib)))
(define-public r-maldiquant
(package
(name "r-maldiquant")
- (version "1.17")
+ (version "1.18")
(source
(origin
(method url-fetch)
(uri (cran-uri "MALDIquant" version))
(sha256
(base32
- "047s6007ydc38x8wm027mlb4mngz15n0d4238fr8h43wyll5zy0z"))))
+ "18nl214xjsxkcpbg79jkmw0yznwm5szyh2qb84n7ip46mm779ha6"))))
(properties `((upstream-name . "MALDIquant")))
(build-system r-build-system)
(home-page "https://cran.r-project.org/web/packages/MALDIquant")
(define-public r-msnbase
(package
(name "r-msnbase")
- (version "2.6.1")
+ (version "2.6.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "MSnbase" version))
(sha256
(base32
- "0zrpx9r93q5ca2zdak5rs2m9sjm0wjdra1xfj3d3sx6p5gzfyg6n"))))
+ "15jhqg02ypmznc0wxksw56yij02csy678vqy531fdv86fsmypwa0"))))
(properties `((upstream-name . "MSnbase")))
(build-system r-build-system)
(propagated-inputs
(define-public r-seurat
(package
(name "r-seurat")
- (version "2.3.1")
+ (version "2.3.4")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
- "0hi59rgdrr2iqfvx5bq7yq02hbjxkjl1fzidqj14z0ypq0nzbjys"))
- ;; Delete pre-built jar.
- (snippet
- '(begin (delete-file "inst/java/ModularityOptimizer.jar")
- #t))))
+ "0l8bv4i9nzz26mirnva10mq6pimibj24vk7vpvfypgn7xk4942hd"))))
(properties `((upstream-name . "Seurat")))
(build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'build-jar
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((classesdir "tmp-classes"))
- (setenv "JAVA_HOME" (assoc-ref inputs "jdk"))
- (mkdir classesdir)
- (with-output-to-file "manifest"
- (lambda _
- (display "Manifest-Version: 1.0
-Main-Class: ModularityOptimizer\n")))
- (and (zero? (apply system* `("javac" "-d" ,classesdir
- ,@(find-files "java" "\\.java$"))))
- (zero? (system* "jar"
- "-cmf" "manifest"
- "inst/java/ModularityOptimizer.jar"
- "-C" classesdir ".")))))))))
- (native-inputs
- `(("jdk" ,icedtea "jdk")))
(propagated-inputs
`(("r-ape" ,r-ape)
- ("r-caret" ,r-caret)
("r-cluster" ,r-cluster)
("r-cowplot" ,r-cowplot)
- ("r-diffusionmap" ,r-diffusionmap)
("r-dosnow" ,r-dosnow)
("r-dplyr" ,r-dplyr)
("r-dtw" ,r-dtw)
("r-fitdistrplus" ,r-fitdistrplus)
- ("r-fnn" ,r-fnn)
("r-foreach" ,r-foreach)
("r-fpc" ,r-fpc)
- ("r-gdata" ,r-gdata)
("r-ggplot2" ,r-ggplot2)
("r-ggridges" ,r-ggridges)
("r-gplots" ,r-gplots)
+ ("r-hdf5r" ,r-hdf5r)
("r-hmisc" ,r-hmisc)
+ ("r-httr" ,r-httr)
("r-ica" ,r-ica)
("r-igraph" ,r-igraph)
("r-irlba" ,r-irlba)
("r-pbapply" ,r-pbapply)
("r-plotly" ,r-plotly)
("r-png" ,r-png)
- ("r-ranger" ,r-ranger)
("r-rann" ,r-rann)
("r-rcolorbrewer" ,r-rcolorbrewer)
("r-rcpp" ,r-rcpp)
("r-rocr" ,r-rocr)
("r-rtsne" ,r-rtsne)
("r-sdmtools" ,r-sdmtools)
- ("r-stringr" ,r-stringr)
- ("r-tclust" ,r-tclust)
("r-tidyr" ,r-tidyr)
- ("r-tsne" ,r-tsne)
- ("r-vgam" ,r-vgam)))
+ ("r-tsne" ,r-tsne)))
(home-page "http://www.satijalab.org/seurat")
(synopsis "Seurat is an R toolkit for single cell genomics")
(description
(define-public r-edaseq
(package
(name "r-edaseq")
- (version "2.14.0")
+ (version "2.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "EDASeq" version))
(sha256
(base32
- "1832pb3jkim4vrqzb8lajwx9r482bhww5n9nz3s6crvyamlp2dj0"))))
+ "0970w9d5ddqw1qxqqafdidkxh6hmcv9j5djwgnpz3fgl05kmysg8"))))
(properties `((upstream-name . "EDASeq")))
(build-system r-build-system)
(propagated-inputs
(define-public r-keggrest
(package
(name "r-keggrest")
- (version "1.20.0")
+ (version "1.20.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "KEGGREST" version))
(sha256
(base32
- "1349vidgl9m10l1rbrp3pkwwgi2xcbsw9h9z2xqbvg97lmqc4r8j"))))
+ "1ss0xd5570x570v01r6lp64rr1apjrzp0j62520pvm3g8knjhfvs"))))
(properties `((upstream-name . "KEGGREST")))
(build-system r-build-system)
(propagated-inputs
(define-public r-complexheatmap
(package
(name "r-complexheatmap")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ComplexHeatmap" version))
(sha256
(base32
- "0z57mrginzd40niy51dvnyqgbrij05ji0dbwqs3x2as80sq28i3q"))))
+ "0qjwz1hzpjnc90jiinjkikfnr0shi72q3zfdjjz7pxydy0mglq8n"))))
(properties
`((upstream-name . "ComplexHeatmap")))
(build-system r-build-system)
(define-public r-biovizbase
(package
(name "r-biovizbase")
- (version "1.28.0")
+ (version "1.28.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biovizBase" version))
(sha256
(base32
- "0lkiqdr3ics6hgv47lwkykcy761823bbkhffbn4ykyfzyqwl4p67"))))
+ "0wc45j3hfn01i44bkkxjj3n8b8xzbkkcdv35mrkzb1f9yprkf8gq"))))
(properties `((upstream-name . "biovizBase")))
(build-system r-build-system)
(propagated-inputs
("r-hmisc" ,r-hmisc)
("r-iranges" ,r-iranges)
("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rlang" ,r-rlang)
("r-rsamtools" ,r-rsamtools)
("r-s4vectors" ,r-s4vectors)
("r-scales" ,r-scales)
(define-public r-ggbio
(package
(name "r-ggbio")
- (version "1.28.0")
+ (version "1.28.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggbio" version))
(sha256
(base32
- "0wszh3w8yia5zw758h837i1q35k99sn444y2hahcxqbdmmlbf7in"))))
+ "19s2v40fycwf44fl3lm791y635xzw67b30sq2g0qq4a6phjik42d"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-iranges" ,r-iranges)
("r-organismdbi" ,r-organismdbi)
("r-reshape2" ,r-reshape2)
+ ("r-rlang" ,r-rlang)
("r-rsamtools" ,r-rsamtools)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
(define-public r-hdf5array
(package
(name "r-hdf5array")
- (version "1.8.0")
+ (version "1.8.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HDF5Array" version))
(sha256
(base32
- "1l0276qxkhgdxsfck3jmi8jvnsr20g10gjki53g0mqa45wnhm3ck"))))
+ "1s44zgm9jg82bk4b8k3dh7xw7mxychlfm3grs8516mxnw91zpvy5"))))
(properties `((upstream-name . "HDF5Array")))
(build-system r-build-system)
(propagated-inputs
(define-public r-scater
(package
(name "r-scater")
- (version "1.8.0")
+ (version "1.8.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "scater" version))
(sha256
(base32
- "0bhpikgz3b9f510dawsay4zry9rlp8vjx5n6zvwbcpwrd94p3903"))))
+ "173lfpas2fqsp4xxsw01wkxd4496c5p8himw9b4r9z4npxkfyv16"))))
(build-system r-build-system)
(propagated-inputs
`(("r-beachmat" ,r-beachmat)
("python2-numpy" ,python2-numpy)
("python2-matplotlib" ,python2-matplotlib)
("python2-pysam" ,python2-pysam)))
- (home-page "http://3dgenomes.github.io/TADbit/")
+ (home-page "https://3dgenomes.github.io/TADbit/")
(synopsis "Analyze, model, and explore 3C-based data")
(description
"TADbit is a complete Python library to deal with all steps to analyze,
(guix build ant-build-system))
#:phases
(modify-phases %standard-phases
+ ;; FIXME: fails with "java.io.FileNotFoundException:
+ ;; /gnu/store/…-dropseq-tools-1.13/share/java/lib/biojava-alignment.jar"
+ (delete 'generate-jar-indices)
;; All dependencies must be linked to "lib", because that's where
;; they will be searched for when the Class-Path property of the
;; manifest is computed.
(define-public pigx-rnaseq
(package
(name "pigx-rnaseq")
- (version "0.0.3")
+ (version "0.0.4")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
"/pigx_rnaseq-" version ".tar.gz"))
(sha256
(base32
- "0pz080k4ajlc4rlznkn3najy2a6874gb56rf9g4ag9wqz31q174j"))))
+ "16gla23rmziimqan7w494q0nr7vfbp42zzkrl9fracmr4k7b1kzr"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-tests? #f ; not supported
(lambda _
(substitute* "Makefile.in"
(("(^ tests/test_trim_galore/test.sh).*" _ m) m)
+ (("^ tests/test_multiqc/test.sh") "")
(("^ test.sh") ""))
- #t))
- (add-after 'install 'wrap-executable
- ;; Make sure the executable finds all R modules.
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (wrap-program (string-append out "/bin/pigx-rnaseq")
- `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
- `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
#t)))))
(inputs
`(("gzip" ,gzip)
- ("snakemake" ,snakemake)
+ ("snakemake" ,snakemake-4)
("fastqc" ,fastqc)
("multiqc" ,multiqc)
("star" ,star)
(define-public pigx-chipseq
(package
(name "pigx-chipseq")
- (version "0.0.15")
+ (version "0.0.20")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/"
"/pigx_chipseq-" version ".tar.gz"))
(sha256
(base32
- "11v9v3vyda0sv4cl45nki7mm4v4bjfcdq7a70kcvi9h465nq66wg"))))
+ "19a7dclqq0b4kqg3phiz4d4arlwfp34nm3z0rf1gkqdpsy7gghp3"))))
(build-system gnu-build-system)
- (arguments
- `(#:tests? #f ; parts of the tests rely on access to the network
- #:phases
- (modify-phases %standard-phases
- (add-after 'install 'wrap-executable
- ;; Make sure the executable finds all R modules.
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (wrap-program (string-append out "/bin/pigx-chipseq")
- `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
- `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
- #t)))))
+ ;; parts of the tests rely on access to the network
+ (arguments '(#:tests? #f))
(inputs
`(("grep" ,grep)
("coreutils" ,coreutils)
("fastqc" ,fastqc)
("bowtie" ,bowtie)
("idr" ,idr)
- ("snakemake" ,snakemake)
+ ("snakemake" ,snakemake-4)
("samtools" ,samtools)
("bedtools" ,bedtools)
("kentutils" ,kentutils)))
(define-public pigx-bsseq
(package
(name "pigx-bsseq")
- (version "0.0.8")
+ (version "0.0.10")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_bsseq/"
"/pigx_bsseq-" version ".tar.gz"))
(sha256
(base32
- "0irlnlhhw9fd4ha7hksrxn3y7j76mz5qq1wjswbs9p364laqg69y"))))
+ "0l97wvkq4diq8lcarraj33bby1zzf0w804jwi8mlc5qddp8idwhy"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(setenv "TZDIR"
(string-append (assoc-ref inputs "tzdata")
"/share/zoneinfo"))
- #t))
- (add-after 'install 'wrap-executable
- ;; Make sure the executable finds all R modules.
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (wrap-program (string-append out "/bin/pigx-bsseq")
- `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
- `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
#t)))))
(native-inputs
`(("tzdata" ,tzdata)))
("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
("python-wrapper" ,python-wrapper)
("python-pyyaml" ,python-pyyaml)
- ("snakemake" ,snakemake)
+ ("snakemake" ,snakemake-4)
("bismark" ,bismark)
("fastqc" ,fastqc)
("bowtie" ,bowtie)
(define-public pigx-scrnaseq
(package
(name "pigx-scrnaseq")
- (version "0.0.4")
+ (version "0.0.7")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/"
"/pigx_scrnaseq-" version ".tar.gz"))
(sha256
(base32
- "1pvjm6f3mascprs65vflggwwg5v925knvgal7k7a6nnlmw5qndrf"))))
+ "131zarirv16w8653m0d66jgjnwqfsxqc0hix0rypssz4d83bl51j"))))
(build-system gnu-build-system)
(arguments
`(#:configure-flags
(list (string-append "PICARDJAR=" (assoc-ref %build-inputs "java-picard")
"/share/java/picard.jar")
(string-append "DROPSEQJAR=" (assoc-ref %build-inputs "dropseq-tools")
- "/share/java/dropseq.jar"))
- #:phases
- (modify-phases %standard-phases
- (add-after 'install 'wrap-executable
- ;; Make sure the executable finds all R modules.
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (wrap-program (string-append out "/bin/pigx-scrnaseq")
- `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))
- `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH")))))
- #t)))))
+ "/share/java/dropseq.jar"))))
(inputs
`(("coreutils" ,coreutils)
("perl" ,perl)
("dropseq-tools" ,dropseq-tools)
("fastqc" ,fastqc)
- ("java-picard" ,java-picard)
+ ("java-picard" ,java-picard-2.10.3) ; same as for dropseq
("java" ,icedtea-8)
("python-wrapper" ,python-wrapper)
("python-pyyaml" ,python-pyyaml)
("python-pandas" ,python-pandas)
+ ("python-magic" ,python-magic)
("python-numpy" ,python-numpy)
("python-loompy" ,python-loompy)
("ghc-pandoc" ,ghc-pandoc-1)
("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1)
- ("snakemake" ,snakemake)
+ ("samtools" ,samtools)
+ ("snakemake" ,snakemake-4)
("star" ,star)
("r-minimal" ,r-minimal)
("r-argparser" ,r-argparser)
(define-public pigx
(package
(name "pigx")
- (version "0.0.2")
+ (version "0.0.3")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx/"
"/pigx-" version ".tar.gz"))
(sha256
(base32
- "0sb708sl42h3s5z872jb1w70bbqplwapnsc1wm27zcsvi7li4gw8"))))
+ "1i5njdy1clj5ncw45d16p7mwmqvb1ilikl9n797pxklc3f4s7mq7"))))
(build-system gnu-build-system)
(inputs
`(("python" ,python)
include Markov models of discrete and continuous trait evolution and constant
rate speciation and extinction.")
(license license:gpl2+)))
+
+(define-public sjcount
+ ;; There is no tag for version 3.2, nor is there a release archive.
+ (let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5")
+ (revision "1"))
+ (package
+ (name "sjcount")
+ (version (git-version "3.2" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pervouchine/sjcount-full.git")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "0gdgj35j249f04rqgq8ymcc1xg1vi9kzbajnjqpaq2wpbh8bl234"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; requires a 1.4G test file
+ #:make-flags
+ (list (string-append "SAMTOOLS_DIR="
+ (assoc-ref %build-inputs "samtools")
+ "/lib/"))
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "makefile"
+ (("-I \\$\\{SAMTOOLS_DIR\\}")
+ (string-append "-I" (assoc-ref inputs "samtools")
+ "/include/samtools"))
+ (("-lz ") "-lz -lpthread "))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (for-each (lambda (tool)
+ (install-file tool
+ (string-append (assoc-ref outputs "out")
+ "/bin")))
+ '("j_count" "b_count" "sjcount"))
+ #t)))))
+ (inputs
+ `(("samtools" ,samtools-0.1)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/pervouchine/sjcount-full/")
+ (synopsis "Annotation-agnostic splice junction counting pipeline")
+ (description "Sjcount is a utility for fast quantification of splice
+junctions in RNA-seq data. It is annotation-agnostic and offset-aware. This
+version does count multisplits.")
+ (license license:gpl3+))))
+
+(define-public minimap2
+ (package
+ (name "minimap2")
+ (version "2.10")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/lh3/minimap2/"
+ "releases/download/v" version "/"
+ "minimap2-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "080w9066irkbhbyr4nmf19pzkdd2s4v31hpzlajgq2y0drr6zcsj"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are none
+ #:make-flags
+ (list "CC=gcc"
+ (let ((system ,(or (%current-target-system)
+ (%current-system))))
+ (cond
+ ((string-prefix? "x86_64" system)
+ "all")
+ ((or (string-prefix? "armhf" system)
+ (string-prefix? "aarch64" system))
+ "arm_neon=1")
+ (_ "sse2only=1"))))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (man (string-append out "/share/man/man1")))
+ (install-file "minimap2" bin)
+ (mkdir-p man)
+ (install-file "minimap2.1" man))
+ #t)))))
+ (inputs
+ `(("zlib" ,zlib)))
+ (home-page "https://lh3.github.io/minimap2/")
+ (synopsis "Pairwise aligner for genomic and spliced nucleotide sequences")
+ (description "Minimap2 is a versatile sequence alignment program that
+aligns DNA or mRNA sequences against a large reference database. Typical use
+cases include:
+
+@enumerate
+@item mapping PacBio or Oxford Nanopore genomic reads to the human genome;
+@item finding overlaps between long reads with error rate up to ~15%;
+@item splice-aware alignment of PacBio Iso-Seq or Nanopore cDNA or Direct RNA
+ reads against a reference genome;
+@item aligning Illumina single- or paired-end reads;
+@item assembly-to-assembly alignment;
+@item full-genome alignment between two closely related species with
+ divergence below ~15%.
+@end enumerate\n")
+ (license license:expat)))
+
+(define-public r-circus
+ (package
+ (name "r-circus")
+ (version "0.1.5")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/BIMSBbioinfo/ciRcus.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0jhjn3ilb057hbf6yzrihj13ifxxs32y7nkby8l3lkm28dg4p97h"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-annotationhub" ,r-annotationhub)
+ ("r-biomart" ,r-biomart)
+ ("r-data-table" ,r-data-table)
+ ("r-dbi" ,r-dbi)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-hash" ,r-hash)
+ ("r-iranges" ,r-iranges)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rmysql" ,r-rmysql)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-stringr" ,r-stringr)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page "https://github.com/BIMSBbioinfo/ciRcus")
+ (synopsis "Annotation, analysis and visualization of circRNA data")
+ (description "Circus is an R package for annotation, analysis and
+visualization of circRNA data. Users can annotate their circRNA candidates
+with host genes, gene featrues they are spliced from, and discriminate between
+known and yet unknown splice junctions. Circular-to-linear ratios of circRNAs
+can be calculated, and a number of descriptive plots easily generated.")
+ (license license:artistic2.0)))
+
+(define-public r-loomr
+ (let ((commit "df0144bd2bbceca6fadef9edc1bbc5ca672d4739")
+ (revision "1"))
+ (package
+ (name "r-loomr")
+ (version (git-version "0.2.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/mojaveazure/loomR.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1b1g4dlmfdyhn56bz1mkh9ymirri43wiz7rjhs7py3y7bdw1s3yr"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-r6" ,r-r6)
+ ("r-hdf5r" ,r-hdf5r)
+ ("r-iterators" ,r-iterators)
+ ("r-itertools" ,r-itertools)
+ ("r-matrix" ,r-matrix)))
+ (home-page "https://github.com/mojaveazure/loomR")
+ (synopsis "R interface for loom files")
+ (description "This package provides an R interface to access, create,
+and modify loom files. loomR aims to be completely compatible with loompy.")
+ (license license:gpl3))))
+
+(define-public gffread
+ ;; We cannot use the tagged release because it is not in sync with gclib.
+ ;; See https://github.com/gpertea/gffread/issues/26
+ (let ((commit "ba7535fcb3cea55a6e5a491d916e93b454e87fd0")
+ (revision "1"))
+ (package
+ (name "gffread")
+ (version (git-version "0.9.12" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/gpertea/gffread.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1dl2nbcg96lxpd0drg48ssa8343nf7pw9s9mkrc4mjjmfwsin3ki"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no check target
+ #:make-flags
+ (list "GCLDIR=gclib")
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'unpack 'copy-gclib-source
+ (lambda* (#:key inputs #:allow-other-keys)
+ (mkdir-p "gclib")
+ (copy-recursively (assoc-ref inputs "gclib-source") "gclib")
+ #t))
+ ;; There is no install target
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (install-file "gffread" bin))
+ #t)))))
+ (native-inputs
+ `(("gclib-source"
+ ,(let ((version "0.10.3")
+ (commit "54917d0849c1e83cfb057b5f712e5cb6a35d948f")
+ (revision "1"))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/gpertea/gclib.git")
+ (commit commit)))
+ (file-name (git-file-name "gclib" version))
+ (sha256
+ (base32
+ "0b51lc0b8syrv7186fd7n8f15rwnf264qgfmm2palrwks1px24mr")))))))
+ (home-page "https://github.com/gpertea/gffread/")
+ (synopsis "Parse and convert GFF/GTF files")
+ (description
+ "This package provides a GFF/GTF file parsing utility providing format
+conversions, region filtering, FASTA sequence extraction and more.")
+ ;; gffread is under Expat, but gclib is under Artistic 2.0
+ (license (list license:expat
+ license:artistic2.0)))))
+
+(define-public find-circ
+ ;; The last release was in 2015. The license was clarified in 2017, so we
+ ;; take the latest commit.
+ (let ((commit "8655dca54970fcf7e92e22fbf57e1188724dda7d")
+ (revision "1"))
+ (package
+ (name "find-circ")
+ (version (git-version "1.2" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/marvin-jens/find_circ.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0p77pbqbclqr4srms34y1b9b4njybfpjiknc11ki84f3p8skb3cg"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; there are none
+ #:phases
+ ;; There is no actual build system.
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (path (getenv "PYTHONPATH")))
+ (for-each (lambda (script)
+ (install-file script bin)
+ (wrap-program (string-append bin "/" script)
+ `("PYTHONPATH" ":" prefix (,path))))
+ '("cmp_bed.py"
+ "find_circ.py"
+ "maxlength.py"
+ "merge_bed.py"
+ "unmapped2anchors.py")))
+ #t)))))
+ (inputs
+ `(("python2" ,python-2)
+ ("python2-pysam" ,python2-pysam)
+ ("python2-numpy" ,python2-numpy)))
+ (home-page "https://github.com/marvin-jens/find_circ")
+ (synopsis "circRNA detection from RNA-seq reads")
+ (description "This package provides tools to detect head-to-tail
+spliced (back-spliced) sequencing reads, indicative of circular RNA (circRNA)
+in RNA-seq data.")
+ (license license:gpl3))))
+
+(define-public python-scanpy
+ (package
+ (name "python-scanpy")
+ (version "1.2.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "scanpy" version))
+ (sha256
+ (base32
+ "1ak7bxms5a0yvf65prppq2g38clkv7c7jnjbnfpkh3xxv7q512jz"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-anndata" ,python-anndata)
+ ("python-igraph" ,python-igraph)
+ ("python-numba" ,python-numba)
+ ("python-joblib" ,python-joblib)
+ ("python-natsort" ,python-natsort)
+ ("python-networkx" ,python-networkx)
+ ("python-statsmodels" ,python-statsmodels)
+ ("python-scikit-learn" ,python-scikit-learn)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-pandas" ,python-pandas)
+ ("python-scipy" ,python-scipy)
+ ("python-seaborn" ,python-seaborn)
+ ("python-h5py" ,python-h5py)
+ ("python-tables" ,python-tables)))
+ (home-page "http://github.com/theislab/scanpy")
+ (synopsis "Single-Cell Analysis in Python.")
+ (description "Scanpy is a scalable toolkit for analyzing single-cell gene
+expression data. It includes preprocessing, visualization, clustering,
+pseudotime and trajectory inference and differential expression testing. The
+Python-based implementation efficiently deals with datasets of more than one
+million cells.")
+ (license license:bsd-3)))
+
+(define-public gffcompare
+ (let ((commit "be56ef4349ea3966c12c6397f85e49e047361c41")
+ (revision "1"))
+ (package
+ (name "gffcompare")
+ (version (git-version "0.10.15" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/gpertea/gffcompare/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0cp5qpxdhw4mxpya5dld8wi3jk00zyklm6rcri426wydinrnfmkg"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no check target
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'build 'copy-gclib-source
+ (lambda* (#:key inputs #:allow-other-keys)
+ (mkdir "../gclib")
+ (copy-recursively
+ (assoc-ref inputs "gclib-source") "../gclib")
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "gffcompare" bin)
+ #t))))))
+ (native-inputs
+ `(("gclib-source" ; see 'README.md' of gffcompare
+ ,(let ((commit "54917d0849c1e83cfb057b5f712e5cb6a35d948f")
+ (revision "1")
+ (name "gclib")
+ (version (git-version "0.10.3" revision commit)))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/gpertea/gclib/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0b51lc0b8syrv7186fd7n8f15rwnf264qgfmm2palrwks1px24mr")))))))
+ (home-page "https://github.com/gpertea/gffcompare/")
+ (synopsis "Tool for comparing or classifing transcripts of RNA-Seq")
+ (description
+ "@code{gffcompare} is a tool that can:
+@enumerate
+@item compare and evaluate the accuracy of RNA-Seq transcript assemblers
+(Cufflinks, Stringtie);
+@item collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g.
+resulted from assembly of different samples);
+@item classify transcripts from one or multiple GTF/GFF3 files as they relate to
+reference transcripts provided in a annotation file (also in GTF/GFF3 format).
+@end enumerate")
+ (license
+ (list
+ license:expat ;license for gffcompare
+ license:artistic2.0))))) ;license for gclib
HCoop / jackhill / guix / guix.git / blobdiff