;;; 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.
;;;
(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 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 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 "1.48.2")
+ (version "1.48.3")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "01yiafayl1m5704xdd2cn3zjc78rs10dqyz66lr3qkf6d8w66938"))))
+ "1rxvwikqivsgxjjcazlszy8xgz346lfh5rw4llxw6fz38fjgb0k5"))))
(properties
`((upstream-name . "biocViews")))
(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 "0.6.1")
+ (version "0.6.5")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DelayedArray" version))
(sha256
(base32
- "0sjwszxdi0vkj2i2di5i46gh9chc660yr3gs5nk9qnqp77713zds"))))
+ "10b03zrnvz5isfh4z55hasya2m71lrfx10l5lm2sdmqs0gwkanrd"))))
(properties
`((upstream-name . "DelayedArray")))
(build-system r-build-system)
(define-public r-rtracklayer
(package
(name "r-rtracklayer")
- (version "1.40.3")
+ (version "1.40.6")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "rtracklayer" version))
(sha256
(base32
- "0kvsjdaypn1jnxbnsxpycildwdyxwnjkigfq8qm8mlyfc4ahdgy3"))))
+ "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-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 "2.3.2")
+ (version "2.3.4")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
- "1sjpy5rrpvlpm6hs7qy7qpglgbp7zrgfybcsalpmjb51rhxhgcg1"))
- ;; 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-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)
;; 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