diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 856 |
1 files changed, 495 insertions, 361 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 019c46adbd..e93eeb5069 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -295,9 +295,10 @@ BAM files.") (base32 "1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa")) (modules '((guix build utils))) - (snippet - ;; Delete bundled htslib. - '(delete-file-recursively "htslib-1.8")))) + (snippet '(begin + ;; Delete bundled htslib. + (delete-file-recursively "htslib-1.8") + #t)))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -1194,10 +1195,12 @@ errors at the end of reads.") "0hwa5r9qbglppb7sz5z79rlmmddr3n51n468jb3wh8rwjgn3yr90")) (modules '((guix build utils))) (snippet - '(substitute* "Makefile" - ;; replace BUILD_HOST and BUILD_TIME for deterministic build - (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") - (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))) + '(begin + (substitute* "Makefile" + ;; replace BUILD_HOST and BUILD_TIME for deterministic build + (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") + (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\"")) + #t)))) (build-system gnu-build-system) (inputs `(("perl" ,perl) @@ -1391,10 +1394,12 @@ well as many of the command line options.") "15z2w3bvnc0n4qmb9bd6d8ylc2h2nj883x2w9iixf4x3vki9b22i")) (modules '((guix build utils))) (snippet - '(substitute* "setup.py" - ;; remove dependency on outdated "distribute" module - (("^from distribute_setup import use_setuptools") "") - (("^use_setuptools\\(\\)") ""))))) + '(begin + (substitute* "setup.py" + ;; remove dependency on outdated "distribute" module + (("^from distribute_setup import use_setuptools") "") + (("^use_setuptools\\(\\)") "")) + #t)))) (build-system python-build-system) (arguments `(#:tests? #f ;tests fail because test data are not included @@ -1426,9 +1431,11 @@ multiple sequence alignments.") (base32 "0dzap2axin9cbbl0d825w294bpn00zagfm1sigamm4v2pm5bj9lp")) (modules '((guix build utils))) - (snippet - ;; Drop bundled htslib. TODO: Also remove samtools and bcftools. - '(delete-file-recursively "htslib")))) + (snippet '(begin + ;; Drop bundled htslib. TODO: Also remove samtools + ;; and bcftools. + (delete-file-recursively "htslib") + #t)))) (build-system python-build-system) (arguments `(#:modules ((ice-9 ftw) @@ -1800,9 +1807,10 @@ time.") ;; for download from Sourceforge, but it has not been merged. (patches (search-patches "crossmap-allow-system-pysam.patch")) (modules '((guix build utils))) - ;; remove bundled copy of pysam - (snippet - '(delete-file-recursively "lib/pysam")))) + (snippet '(begin + ;; remove bundled copy of pysam + (delete-file-recursively "lib/pysam") + #t)))) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -1911,7 +1919,8 @@ files.") (snippet '(begin ;; Delete bundled libBigWig sources - (delete-file-recursively "libBigWig"))))) + (delete-file-recursively "libBigWig") + #t)))) (build-system python-build-system) (arguments `(#:phases @@ -2079,7 +2088,7 @@ accurately delineate genomic rearrangements throughout the genome.") (define-public diamond (package (name "diamond") - (version "0.9.21") + (version "0.9.22") (source (origin (method url-fetch) (uri (string-append @@ -2088,7 +2097,7 @@ accurately delineate genomic rearrangements throughout the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1cf98vcsiwcv3c4apg50w1240v1mpw0zln1sdw3g692dqa4y041z")))) + "0adp87r9ak63frdrdmrdfhsn6g0jnnyq1lr2wibvqbxcl37iir9m")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -3145,6 +3154,8 @@ manipulating HTS data.") #: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" @@ -3202,6 +3213,8 @@ VCF.") (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 @@ -3292,6 +3305,8 @@ VCF.") (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) @@ -3450,6 +3465,42 @@ The main functions of FastQC are: @end itemize\n") (license license:gpl3+))) +(define-public fastp + (package + (name "fastp") + (version "0.14.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/OpenGene/fastp.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1r6ms5zbf5rps4rgp4z73nczadl00b5rqylw8f684isfz27dp0xh")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are none + #:make-flags + (list (string-append "BINDIR=" (assoc-ref %outputs "out") "/bin")) + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'install 'create-target-dir + (lambda* (#:key outputs #:allow-other-keys) + (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) + #t))))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/OpenGene/fastp/") + (synopsis "All-in-one FastQ preprocessor") + (description + "Fastp is a tool designed to provide fast all-in-one preprocessing for +FastQ files. This tool has multi-threading support to afford high +performance.") + (license license:expat))) + (define-public htslib (package (name "htslib") @@ -3834,9 +3885,11 @@ sequences).") "00fx14vpmgsijwxd1xql3if934l82v8ckqgjjyyhnr36qb9qrskv")) (modules '((guix build utils))) (snippet - ;; Delete bundled kseq. - ;; TODO: Also delete bundled murmurhash and open bloom filter. - '(delete-file "src/mash/kseq.h")))) + '(begin + ;; Delete bundled kseq. + ;; TODO: Also delete bundled murmurhash and open bloom filter. + (delete-file "src/mash/kseq.h") + #t)))) (build-system gnu-build-system) (arguments `(#:tests? #f ; No tests. @@ -4016,18 +4069,19 @@ assembled metagenomic sequence.") (base32 "1z3x0vd8ma7pdrnywj7i3kgwl89sdkwrrn62zl7r5calqaq2hyip")) (modules '((guix build utils))) - (snippet - '(substitute* "setup.py" - ;; Use setuptools, or else the executables are not - ;; installed. - (("distutils.core") "setuptools") - ;; use "gcc" instead of "cc" for compilation - (("^defines") - "cc.set_executables( + (snippet '(begin + (substitute* "setup.py" + ;; Use setuptools, or else the executables are not + ;; installed. + (("distutils.core") "setuptools") + ;; use "gcc" instead of "cc" for compilation + (("^defines") + "cc.set_executables( compiler='gcc', compiler_so='gcc', linker_exe='gcc', -linker_so='gcc -shared'); defines"))))) +linker_so='gcc -shared'); defines")) + #t)))) (build-system python-build-system) (arguments `(#:python ,python-2 ; only Python 2 is supported @@ -4828,7 +4882,8 @@ BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.") (("^from distribute_setup import use_setuptools") "") (("^use_setuptools\\(\\)") "") ;; do not use bundled copy of pysam - (("^have_pysam = False") "have_pysam = True")))))) + (("^have_pysam = False") "have_pysam = True")) + #t)))) (build-system python-build-system) (arguments `(#:python ,python-2)) (inputs @@ -4879,9 +4934,9 @@ distribution, coverage uniformity, strand specificity, etc.") "Data2DB" "PCL2Bin"))) (modify-phases %standard-phases - (add-before 'configure 'bootstrap + (replace 'bootstrap (lambda _ - (zero? (system* "bash" "gen_auto")))) + (invoke "bash" "gen_auto"))) (add-after 'build 'build-additional-tools (lambda* (#:key make-flags #:allow-other-keys) (every (lambda (dir) @@ -5384,9 +5439,10 @@ structures, classes for genomic regions, mapped sequencing reads, etc.") (sha256 (base32 "08r684l50pnxjpvmhzjgqq56yv9rfw90k8vx0nsrnrzk8mf9hsdq")) (modules '((guix build utils))) - (snippet - ;; Remove bundled samtools. - '(delete-file-recursively "samtools")))) + (snippet '(begin + ;; Remove bundled samtools. + (delete-file-recursively "samtools") + #t)))) (build-system gnu-build-system) (arguments `(#:tests? #f ;no "check" target @@ -5591,10 +5647,11 @@ writing files into the .sra format.") (out (assoc-ref %outputs "out")) (doc (assoc-ref %outputs "doc"))) (setenv "PATH" (string-append tar "/bin:" bzip "/bin")) - (system* "tar" "xvf" (assoc-ref %build-inputs "source")) + (invoke "tar" "xvf" (assoc-ref %build-inputs "source")) (chdir (string-append "seqan-library-" ,version)) (copy-recursively "include" (string-append out "/include")) - (copy-recursively "share" (string-append doc "/share")))))) + (copy-recursively "share" (string-append doc "/share")) + #t)))) (native-inputs `(("source" ,source) ("tar" ,tar) @@ -5769,15 +5826,16 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (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 @@ -6083,20 +6141,20 @@ information as possible.") (define-public r-vegan (package (name "r-vegan") - (version "2.5-1") + (version "2.5-2") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "0pynr02d1xngda6c3va8fc4nxpgfkawhzcnz1ws4dnarp9b1w90r")))) + "13pyqvlpz64qibi8k5d109v7q09j06mbv6ndix3n4cn21mjx391c")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (propagated-inputs `(("r-cluster" ,r-cluster) - ("r-knitr" ,r-knitr) + ("r-knitr" ,r-knitr) ; needed for vignettes ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-mgcv" ,r-mgcv) @@ -6113,14 +6171,14 @@ data types as well.") (define-public r-annotate (package (name "r-annotate") - (version "1.56.2") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "annotate" version)) (sha256 (base32 - "0ybg9k1s289h15nj1kp9821i1rsk1gkn8i8blplmk7gsgpbw1f42")))) + "1qmncyvy147a1ll3iri45p822kcs3s7583jfnq9jf6sz9ilk8cjf")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -6140,13 +6198,13 @@ microarrays.") (define-public r-copynumber (package (name "r-copynumber") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "copynumber" version)) (sha256 (base32 - "01kcwzl485yjrkgyg8117b1il957ss0v6rq4bbxf4ksd5fzcjmyx")))) + "0y9nnwb0psphp3ix88wj2f8z5gr45r5znf55w892ysm27isdpmms")))) (build-system r-build-system) (propagated-inputs `(("r-s4vectors" ,r-s4vectors) @@ -6163,14 +6221,14 @@ penalized least squares regression method.") (define-public r-geneplotter (package (name "r-geneplotter") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "geneplotter" version)) (sha256 (base32 - "1z3g7frc1iviwrsv2dlm4nqvkc0685h4va0388yfxn102ln8wwma")))) + "055g28xgiazl4l0gkg8xiamks64f5yckjjyvw1abd6d6qjavwx0g")))) (build-system r-build-system) (propagated-inputs `(("r-annotate" ,r-annotate) @@ -6188,14 +6246,14 @@ penalized least squares regression method.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.60.0") + (version "1.62.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "173swlg6gj4kdllbqvyiw5dggbcxiwlwpqmllsv4dxzn7h25i3g7")))) + "14l0ff02spmjwxj0m1czhg5vlkgwcfi73cym8m2n9vn6i7bjdaqi")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -6215,14 +6273,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "1iyimg1s0x5pdmvl8x08s8h0v019y0nhjzs50chagbpk2x91fsmv")))) + "1wjnfpb41a9mmf9a22bz4zh7r1d4id50vpdc1mn5vfzrz7li9qik")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -6252,14 +6310,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.24.4") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1a80yv742fx5c7qav7imsdybphf0d5bixsqyf8w5zng7fk8j16d5")))) + "1mqb3mdxcsi3largsl7k27bvqrgps9ixv806xvmf29pw0xn05sg1")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -6295,14 +6353,14 @@ exploration of the results.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "01vbrf76vqfvxh6vpfxkjwccxggnha3byqzj333glqz2b6kwx5q1")))) + "12ffj7h95adiya5mzyjxazqn1qgr434ajpabfcyhrj5v83s4vk65")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -6325,14 +6383,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "18jad23i3899ypv4bg3l47cvvs3qnj1pqis2p9x0135yv5y6wnv7")))) + "0hj972mmqpyi5fx1rq33kysavdyz4nspi6gcffzi3rv339m0anhf")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph))) @@ -6346,14 +6404,14 @@ the graph algorithms contained in the Boost library.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.40.1") + (version "1.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "10cmjxahg2plwacfan6g0k8cwyzya96ypc7m1r79gwqkyykxw5fz")))) + "11bv92svik399q677jv96b71i4bq68xxyxn1yijpdik2lq4hgl7a")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -6373,14 +6431,14 @@ Enrichment Analysis} (GSEA).") (define-public r-category (package (name "r-category") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "0mkav04vbla0xfa0dssxdd0rjs589sxi83xklf5iq5hj3dm8y0i8")))) + "03wfqa8d1dgwsm327zl2mpkq7dq3mzhq12598qz3ylfhrwplbgx0")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -6404,14 +6462,14 @@ analysis.") (define-public r-gostats (package (name "r-gostats") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "04gqfdlx9fxf97qf0l28x4aaqvl10n6v58qiz5fiaw05sbj1pf1i")))) + "1i5mydz5d95w2k28qr9j01hmbnl2id55jq94jvcpcyp1pvinkdq0")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -6435,14 +6493,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "1cyv47632m9ljkxfsvnvmd19sb607ys5kz8fwh6v39dnw16g0a6m")))) + "038z3z7qaw5bpgjzy91sjkybsny6jwjjsrnnq4gdqdw9ss1qy1fb")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -6477,14 +6535,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "11mj8pjq5vj25768vmagpzv74fvi3p3kdk5zdlznqyiaggri04cv")))) + "1550pd63mmky0vgkmpni7zf14kqz1741wv63nfaw29kcmhh3m5lm")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -6523,14 +6581,14 @@ annotation infrastructure.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.12.0") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "0cjkj0ypyc4dfi9s8dh88kh6q4xlpnc0wal7njg4b4gqj0l2hva7")))) + "1kjb14apyly44qdlx2ld6gr69wlazd4mbhs58l35hir12aphgrzp")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -6842,13 +6900,13 @@ barplots or heatmaps.") (define-public r-biocgenerics (package (name "r-biocgenerics") - (version "0.24.0") + (version "0.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocGenerics" version)) (sha256 (base32 - "03wxvhxyrhipbgcg83lqlfn7p9gbzzrnl48y0dq7303xgp232zai")))) + "19qxhy2cd3pykkhzbb5q3crgaxf65cpzf2mkfsz16gqhi8flj72p")))) (properties `((upstream-name . "BiocGenerics"))) (build-system r-build-system) @@ -6862,13 +6920,13 @@ packages.") (define-public r-biocinstaller (package (name "r-biocinstaller") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocInstaller" version)) (sha256 (base32 - "19fga27bv6q9v5mpil74y76lahmnwvpg2h33rdx1r79nvljkd19d")))) + "1xg1gi1hf5vflp71ji21gnmr4kcjpx8a6c47cllpc7yqnjv5nfg0")))) (properties `((upstream-name . "BiocInstaller"))) (build-system r-build-system) @@ -6881,13 +6939,13 @@ Bioconductor, CRAN, and Github.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "09zyqj1kqc089lmh9sliy0acanx9zimcasvp71dsrg2bqm08r1md")))) + "1yx2lir67ny0j150wyfqca0wsxp84byri8nscbs9qlndkh2jppq9")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -6932,13 +6990,13 @@ authoring books and technical documents with R Markdown.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.6.1") + (version "2.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "03pp04pkcq99kdv2spzr995h2cxsza7l6w3d4gp4112m06prcybm")))) + "17m901ylz00w1a3nq5f910v55zixm1nr6rb3qrsbhqd94qzr0l2p")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -6957,13 +7015,13 @@ functionality.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1nzp8kgw13z9pgf885rplj6k37jcldfhbz0adqclxr2gq0yalmyx")))) + "1srp1g809f1nn0fyqknr7r6dq89bw1xpjvmygr7cw6ffknbc671s")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -7048,13 +7106,13 @@ that accept short and long options.") (define-public r-dnacopy (package (name "r-dnacopy") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DNAcopy" version)) (sha256 (base32 - "127il5rlg1hzjlhwhs64x3nm18p00q1pd9ckb2b9ifl0rax95wai")))) + "03hfhmmc5y60r2gcgm367w2fr7qj115l74m9bp3h9qpn5yci0d8n")))) (properties `((upstream-name . "DNAcopy"))) (build-system r-build-system) @@ -7070,13 +7128,13 @@ abnormal copy number.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.16.0") + (version "0.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "03s8vz33nl6mivjb7dbvj702dkypi340lji1sjban03fyyls0hw0")))) + "0qvj2j0zl4djjl7vrwc6xak6h8dxr53iwypfbcvfb3sh7jwhdiz5")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -7122,13 +7180,13 @@ utilities for sequence data management under the ACNUC system.") (define-public r-iranges (package (name "r-iranges") - (version "2.12.0") + (version "2.14.10") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "1vqczb9wlxsmpwpqig6j1dmiblcfpq6mgnq8qwzcrvddm4cp47m5")))) + "10ccw930vfmkskkrzbps14xglqlkxf588623dr7f1a9ckx7yr2p6")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -7174,13 +7232,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "1jhm0imkac4gvchbjxj408aakk39xdv2fyh818d3lk295bz6bnyp")))) + "0yhnqhaydmmq7ihmhj3rbal4afq5p993l2qqrd0n5wmbyg7glg2d")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -7202,13 +7260,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.20.9") + (version "3.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0y52snwbz37xzdd7gihdkqczbndlfzmmypv6hri3ymjyfmlx6qaw")))) + "07py2g6vg9jbflwhc1hnzr2silbinrjwxq3mkq30nzjgf0n0hrf3")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7230,13 +7288,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.24.5") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "07ywn3c4w83l3sr76d0z3b1nv9icgdh3phsjlc6cfx7i6nfmvxw2")))) + "06bccdf57vja7m63chmgc4539lwng3q3b8zxn285fj8524l6mcn7")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -7268,13 +7326,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.34.9") + (version "3.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1y2fm61g5i0fn0j3l31xvwh9zww9bpkc4nwzb1d0yv1cag20jkdc")))) + "1982g5v35ilfgxm2vkq1p3j1bbir795pjvfzx4nzam2rlqqymbqm")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7287,13 +7345,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-xvector (package (name "r-xvector") - (version "0.18.0") + (version "0.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "1i4i3kdxr78lr1kcxq657p11ybi7kq10c8kyaqyh6gfc8i9rhvmk")))) + "1zjlhh9lsyhg0js1858csyw2389kbrzdqnqnha833wazkwxilp3f")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -7323,13 +7381,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.30.3") + (version "1.32.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "07cszc9ri94nzk4dffwnsj247ih6pchnrzrvnb0q4dkk33gwy8n1")))) + "03gmka6rlz18vd4229796l5l3l6446v5cb90sn2nb5knjbp84hni")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -7352,13 +7410,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-biobase (package (name "r-biobase") - (version "2.38.0") + (version "2.40.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "1cgm1ja1kp56zdlzyy9ggbkfn8r2vbsd4hncmz8g4hjd47fg18kg")))) + "1iwds2a5ir29k19dbpynlc7nn836cw2gamchhgpi2jf2xar9m9jz")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -7374,13 +7432,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.40.0") + (version "1.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "1dh4qs1a757n640gs34lf6z2glc96nan86x0sqaw5csadl2rhnlc")))) + "0afkbzli08vq02r2pr9phrz3rxd6ilp1w7yw8y99nbjiz14f8b1c")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -7401,13 +7459,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.34.2") + (version "2.36.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1zlgs2zg0lmnk572p55n7m34nkxka8w10x8f2ndssjkffl2csy79")))) + "0b70s350ffc74v3xz5c3jpazr9zxdb7gjmjfj7aghlsrizrspill")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) @@ -7434,13 +7492,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.12.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "13ng3n2wsgl3fh0v6jnz3vg51k5c1sh44pqdvblcrcd1qyjmmqhd")))) + "00qg1kg2l9qqpyjaw5q910cmf84vwfiw1fhsx3ig784gwinwgj6n")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -7459,13 +7517,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.46.0") + (version "2.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0vg50qdlxqcm2d6axjnzg8wh8pr4c5gz03l8bdl0llmwzp0zclzk")))) + "118b490jk87ydigm6ln25ms4kskzkw0akmh77clzznhzpqnxsi6j")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -7485,13 +7543,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "0pjny5fjvbnfdyhl3bwxin678sha2drvs00sivxh3l772cn6yams")))) + "1s65y5wn4d0x8zsljg2kmhcl6r9884h95kr041j7hp49bmxg3an6")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -7529,18 +7587,19 @@ files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.4.1") + (version "0.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0s7h2giyvz04cg6248kbbzpwhxdrpnsvl2s8k5c8ricisd9aaz4b")))) + "0n3w57cwy911q812wc8658y0v3xgpmg379sj98kfqdxa80z1mxdf")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) ("r-s4vectors" ,r-s4vectors) ("r-iranges" ,r-iranges) ("r-matrixstats" ,r-matrixstats))) @@ -7559,13 +7618,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.8.1") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "19vlwnby83fqjrilsxvnvgz0gvby7mrxvlmx18nb3p1w591ddfjh")))) + "0v3zxl9cqsv79ag5cnvzlhvgaz5cr8f4rn7flmwnwpqd508cznl1")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -7590,13 +7649,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.14.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "1659nj1xps7vliy5955i51x6hvrf16n1z0dfh10mmpaaswn2d2mv")))) + "00pi2cnkkbj2023fg2x2cmglkdalwzy1vr3glsikwz7ix9yylcaw")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -7623,13 +7682,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.38.3") + (version "1.40.3") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "1khzfczm35k5lq9h0jlqrq01192spzjyh8s6is89spj006flwn4k")))) + "0kvsjdaypn1jnxbnsxpycildwdyxwnjkigfq8qm8mlyfc4ahdgy3")))) (build-system r-build-system) (arguments `(#:phases @@ -7641,6 +7700,8 @@ alignments.") (substitute* "NAMESPACE" (("import\\(zlibbioc\\)") "")) #t))))) + (native-inputs + `(("pkg-config" ,pkg-config))) (inputs `(("zlib" ,zlib))) (propagated-inputs @@ -7668,13 +7729,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.30.3") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "010vn8hlwbnw12pd1d8pv6m12yp3xwx557gba5rbjq9p4qypnn3z")))) + "1cqcl72q0k5wylw1brn4g4h7xzys1v06piry19cvp0gjcvm5sp7a")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -7690,7 +7751,6 @@ as well as query and modify the browser state, such as the current viewport.") ("r-iranges" ,r-iranges) ("r-rcurl" ,r-rcurl) ("r-rsqlite" ,r-rsqlite) - ("r-rmysql" ,r-rmysql) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-xvector" ,r-xvector))) @@ -7734,13 +7794,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-graph (package (name "r-graph") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "graph" version)) (sha256 (base32 - "15aajjp8h2z14p80c8hyd4rrmr9vqsm7bvwb989jxjl4k6g52an1")))) + "1zx445lk36g1s6i5dbhhf00nzzazyklfjxxjfax6q8hnhvgm9759")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics))) @@ -7753,13 +7813,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-topgo (package (name "r-topgo") - (version "2.30.1") + (version "2.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "1cgz4knxr328xfqlhl6ypxl6x86rfrlqz748kn94ainxjzz55i6x")))) + "05yxnkid8bgw9lkm90if9fg63djhgvbailfa3qsfqa5c0zjmixw1")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -7786,13 +7846,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "1jbzq7lm2iajajn2bifxnkss0k9fdvgqr30mral17cbhp5f6w4lq")))) + "1rk2piqq5dppkd51ln3r872d7ng3rvq98071mnd0xdv2xwnyn5g8")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -7847,13 +7907,13 @@ genome data packages and support for efficient SNP representation.") (define-public r-impute (package (name "r-impute") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "0b8r4swvyx3cjcc2ky8yn0ncpzlbi1pgfsn3wpbjmhh7sqrffm2n")))) + "1d3cpfaqlq2gnb3hsc2yhxwkrnbd7m6ifif32yp0ya0jr5brl4hr")))) (inputs `(("gfortran" ,gfortran))) (build-system r-build-system) @@ -7867,13 +7927,13 @@ microarray data, using nearest neighbor averaging.") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "1kcm5w83q7w0v0vs7nyp4gq5z86c6n6pqy9zmyyhxcrns7f597pm")))) + "0dw0yldfcf0ibvpqxlpx1ijnjf9lma47w9w22siszzhw09i0wp3w")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -7894,13 +7954,13 @@ reference point and sorted by a user defined feature.") (define-public r-genomation (package (name "r-genomation") - (version "1.11.3") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "1d2g1v6xhrf3gm86pv8ln22df5g6v6k6i4i39v4j82zn4apany6v")))) + "1vdmdyrq0n7pf8cvy2950v7hrcrcbd9zl4fg7dcmyly3iiwdyirp")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -8072,14 +8132,14 @@ annotations for the genome of the model mouse Mus musculus.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.44.0") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "1ql4q4vx0j61a893dqc3c8zxmgs8sqhy3j1qhyfdvbd01vw9w1kq")))) + "16xvqcdknix9vjm8mrixi6nyfsr45jm844jh1x90m8044lwrsic1")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/seqLogo") @@ -8318,14 +8378,14 @@ Biostrings objects.") (define-public r-motifrg (package (name "r-motifrg") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifRG" version)) (sha256 (base32 - "193zl2rlzwxv9p9q5i7rilj3w05ndqfyp9bdpvagp5s5cin4hf44")))) + "0mxhyidkyd2zqahdbg69y20r550z78lvr1r3pbjymnwfg4hcfq1p")))) (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs @@ -8370,13 +8430,13 @@ two-dimensional genome scans.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "1zr9hbh55hglfpy15cpxwmddxblhyb0an15953l3rbhmlh2vpy92")))) + "1rwr0mci8a712q0isavi4jmhm94gwivc4nr8j7r4kw05flp4g7gz")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -8412,14 +8472,14 @@ secondary structure and comparative analysis in R.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.10.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "1dw3p44bfr0m7w39ckc2k37sjcp1zz0b9g12mr8am15jaj6v0q2j")))) + "16ywnb8cmr2xabd1i21b92rfziw7xfbv25yv16ipw617p41wa39z")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) (propagated-inputs @@ -8427,7 +8487,7 @@ secondary structure and comparative analysis in R.") (inputs `(("zlib" ,zlib))) (native-inputs - `(("autoconf" ,autoconf))) + `(("pkg-config" ,pkg-config))) (home-page "https://github.com/nhayden/Rhtslib") (synopsis "High-throughput sequencing library as an R package") (description @@ -8439,14 +8499,14 @@ of other R packages who wish to make use of HTSlib.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.10.0") + (version "1.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "15id6mkj95skb4kfafvfs2j7ylydal60c3pspcl7llhwpq6vcqvl")))) + "141q3p4lzwiqk1mfxi8q1q84axjl0gyiqg59xd3sp4viny4jqmgv")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8469,43 +8529,51 @@ paired-end data.") (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 @@ -8517,7 +8585,7 @@ library implementing most of the pipeline's features.") (define-public rcas-web (package (name "rcas-web") - (version "0.0.4") + (version "0.0.5") (source (origin (method url-fetch) @@ -8526,7 +8594,7 @@ library implementing most of the pipeline's features.") "/rcas-web-" version ".tar.gz")) (sha256 (base32 - "1p16frfys41a8yaa4gkm457nzkqhqs2pc3lkac0ds457w9w5j1gm")))) + "0igz7jpcf7cm9800zcag6p3gd1i649figrhbdba6cjkm8f4gfspr")))) (build-system gnu-build-system) (arguments `(#:phases @@ -8561,18 +8629,19 @@ library implementing most of the pipeline's features.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "1.4.3") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "0ml4gsp5dfv23xqrknxh25q8q65hly1xb1215lcwyc8hj9z8f941")))) + "1yq7351j42mjxn8fd3c5bdxzb2l5s4lvqhjdvv4rwj4f600n6wj9")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) + ;; These two packages are suggested packages ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5) ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) ("r-genomicranges" ,r-genomicranges) @@ -8736,13 +8805,13 @@ kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") (define-public r-tximport (package (name "r-tximport") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "1gyqcm91hxg1kgjqcz2qw1n56yp9pymjzs50rwcpb2893dr8sp2h")))) + "1qjc7ah9dzccpvcjrp9k4qnaz13x6kvy1c1xpdj503km6k528lip")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") @@ -8758,39 +8827,18 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.22.0") + (version "2.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "145858qg1xan6imxcbprzq3yn3mdf532aahdr6cibvdjg47hs4c1")))) + "15cmmchhk8bnp94gxg0zk9qyzdjx5kv16dzpbnb62mkq7ydmifx6")))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'unpack-smallhdf5 - (lambda* (#:key outputs #:allow-other-keys) - (system* "tar" "-xzvf" - "src/hdf5source/hdf5small.tgz" "-C" "src/" ) - (substitute* "src/hdf5/configure" - (("/bin/mv") "mv")) - ;; Remove timestamp and host system information to make - ;; the build reproducible. - (substitute* "src/hdf5/src/libhdf5.settings.in" - (("Configured on: @CONFIG_DATE@") - "Configured on: Guix") - (("Uname information:.*") - "Uname information: Linux\n") - ;; Remove unnecessary store reference. - (("C Compiler:.*") - "C Compiler: GCC\n")) - #t))))) (propagated-inputs - `(("r-zlibbioc" ,r-zlibbioc))) + `(("r-rhdf5lib" ,r-rhdf5lib))) (inputs - `(("perl" ,perl) - ("zlib" ,zlib))) + `(("zlib" ,zlib))) (home-page "https://bioconductor.org/packages/rhdf5") (synopsis "HDF5 interface to R") (description @@ -8806,13 +8854,13 @@ the available RAM.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.2.0") + (version "1.4.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "04zf864c1fvdlaay2r5cn30fc1n5i3czh31fs62qlrvs61wjiscs")))) + "1w8ypfdz4g7vnwfrvnhjcpm8waciqyq2cn883ajdwg4vv7a5mj9a")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) @@ -9085,6 +9133,19 @@ replacement for strverscmp.") ("python-numpy" ,python-numpy) ;; MultQC checks for the presence of nose at runtime. ("python-nose" ,python-nose))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "setup.py" + ;; MultiQC 1.5 ‘requires’ a version of python-matplotlib older + ;; than the one in Guix, but should work fine with 2.2.2. + ;; See <https://github.com/ewels/MultiQC/issues/725> and + ;; <https://github.com/ewels/MultiQC/issues/732> for details. + (("['\"]matplotlib.*?['\"]") + "'matplotlib'")) + #t))))) (home-page "http://multiqc.info") (synopsis "Aggregate bioinformatics analysis reports") (description @@ -9096,14 +9157,14 @@ common bioinformatics tools.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1ymcq77krwjzrkzzcw7i9909cmkqa7c0675z9wzvrrk81hgdssfq")))) + "09f8dgl5ni75qkf7nvvppwr3irpplv4xb3ks59ld7l8i2mplcrx7")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -9148,14 +9209,14 @@ GenomicRanges Bioconductor package.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "17fy2lc5yf3nh6v077kv87h53n263hqz2540lzrl0vjiqrl2plca")))) + "0b7xwq1va2zclb54f07c5ipmmq4iv2hrlph3j93jz5hmyayv50z3")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs @@ -9188,13 +9249,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.4.1") + (version "1.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "1k0nfn9318sgwm4z963bhnbp4c3zv85v3f9886vc5hgaisr0yvai")))) + "1hr2czi5ybdf7hdmqsv39d17f3mvmw94wa38bc14zzm9mgy9gfy7")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -9234,14 +9295,14 @@ TAB-Seq.") (define-public r-sva (package (name "r-sva") - (version "3.26.0") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0q5xb68wfcnchy8rkv5ma67pmz1i91lsnvmwmj8f1c3w4xan3pgw")))) + "0a3jqbz0jp1jxrnjkqfpmca840yqcdwxprdl608bzzx2zb4jl52s")))) (build-system r-build-system) (propagated-inputs `(("r-genefilter" ,r-genefilter) @@ -9344,14 +9405,14 @@ as allowing spectra with different resolutions.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "16ijp50448wnabp43klx943rhdvh7x45hvy7cnpq1s4dckxhhyni")))) + "05jbadw2aiwy8vi2ia0jxg06cmwhly2cq4dy1ag7kdxf1c5i9ccn")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -9364,14 +9425,14 @@ proteomics packages.") (define-public r-mzr (package (name "r-mzr") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1x3gp30sfxz2v3k3swih9kff9b2rvk7hzhnlkp6ywlnn2wgb0q8c")) + "190m2bq5bqxhljaj4f7vz9wj5h5laaxd8zp5jampnql6xc4zmarg")) (modules '((guix build utils))) (snippet '(begin @@ -9393,12 +9454,14 @@ proteomics packages.") #t))))) (inputs `(("boost" ,boost) ; use this instead of the bundled boost sources - ("netcdf" ,netcdf))) + ("netcdf" ,netcdf) + ("zlib" ,zlib))) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-protgenerics" ,r-protgenerics) ("r-rcpp" ,r-rcpp) + ("r-rhdf5lib" ,r-rhdf5lib) ("r-zlibbioc" ,r-zlibbioc))) (home-page "https://github.com/sneumann/mzR/") (synopsis "Parser for mass spectrometry data files") @@ -9414,14 +9477,14 @@ previously been used in XCMS.") (define-public r-affyio (package (name "r-affyio") - (version "1.48.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "1pzzp3d3dbmyf34gvivfiprkpscn36rgvhrq853a1d3avcwr5ak9")))) + "0sh5wnnchyfpq5n6rchbqmb27byn7kdzn5rgran6i39c81i5z22n")))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) @@ -9438,14 +9501,14 @@ CDF file formats.") (define-public r-affy (package (name "r-affy") - (version "1.56.0") + (version "1.58.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "0jmbkimma5ffsdkk3xp03g4lpz84gd95nkqakif2nqq6wmx0syrj")))) + "0sxq875sigm21sf3qncrfrwfdz9nqw1vldxn3d3hj6aq64jg1ki6")))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) @@ -9454,6 +9517,8 @@ CDF file formats.") ("r-biocinstaller" ,r-biocinstaller) ("r-preprocesscore" ,r-preprocesscore) ("r-zlibbioc" ,r-zlibbioc))) + (inputs + `(("zlib" ,zlib))) (home-page "https://bioconductor.org/packages/affy") (synopsis "Methods for affymetrix oligonucleotide arrays") (description @@ -9464,14 +9529,14 @@ analysis.") (define-public r-vsn (package (name "r-vsn") - (version "3.46.0") + (version "3.48.1") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "18y62phzirj75gg6v5l41jwybmk23ia6w7qhch0kxc4bl2rysw6j")))) + "0k6mah3g3zqbfap31xmvig4fn452a18xwwa5y0mfj5mj8588p57h")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -9498,14 +9563,14 @@ and specific in detecting differential transcription.") (define-public r-mzid (package (name "r-mzid") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "0yk70dka56zd8w62f03ggx3mandj91gfa767h9ajj0sd3mjmfqb9")))) + "060k0xlhg8q802c6zsb4b8ps0ccd9ybyaz0gnsvqkxb786i2vk40")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -9528,14 +9593,14 @@ specific parser.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.70.0") + (version "1.72.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "0ii235g0x0492kh8cfrf28ni0b6vd6fh7kizkqmczzqggd6b1bk8")))) + "0v99yf8m7ryh6z0r3z0ggpqfnflcq5bn1q1i1cl9b7q4p6b4sa07")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -9558,14 +9623,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.4.2") + (version "2.6.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "1ig64bf881p118dwqfr0ry41m7yhnyv165smv8fdwfv7sb6sagif")))) + "0zrpx9r93q5ca2zdak5rs2m9sjm0wjdra1xfj3d3sx6p5gzfyg6n")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -9579,6 +9644,7 @@ structure (pcaRes) to provide a common interface to the PCA results.") ("r-iranges" ,r-iranges) ("r-lattice" ,r-lattice) ("r-maldiquant" ,r-maldiquant) + ("r-mass" ,r-mass) ("r-mzid" ,r-mzid) ("r-mzr" ,r-mzr) ("r-pcamethods" ,r-pcamethods) @@ -9587,6 +9653,7 @@ structure (pcaRes) to provide a common interface to the PCA results.") ("r-protgenerics" ,r-protgenerics) ("r-rcpp" ,r-rcpp) ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) ("r-vsn" ,r-vsn) ("r-xml" ,r-xml))) (home-page "https://github.com/lgatto/MSnbase") @@ -9599,14 +9666,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.12.1") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "1zw508kk4f8brg69674wp18gqkpx2kpya5f6x9cl3qng7v4h5pxx")))) + "172q5chi44104iz4y0g42wrimfp7hlhrfa8vzybx6m0ccrkkhl17")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs @@ -9638,13 +9705,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "2.3.0") + (version "2.3.1") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "0kp3lw1s896zkjd6x2wp8qcg7wnm5b40g8vihps13f1m7j4nx7r0")) + "0hi59rgdrr2iqfvx5bq7yq02hbjxkjl1fzidqj14z0ypq0nzbjys")) ;; Delete pre-built jar. (snippet '(begin (delete-file "inst/java/ModularityOptimizer.jar") @@ -9688,7 +9755,6 @@ Main-Class: ModularityOptimizer\n"))) ("r-ggplot2" ,r-ggplot2) ("r-ggridges" ,r-ggridges) ("r-gplots" ,r-gplots) - ("r-gridextra" ,r-gridextra) ("r-hmisc" ,r-hmisc) ("r-ica" ,r-ica) ("r-igraph" ,r-igraph) @@ -9709,6 +9775,7 @@ Main-Class: ModularityOptimizer\n"))) ("r-rcppeigen" ,r-rcppeigen) ("r-rcppprogress" ,r-rcppprogress) ("r-reshape2" ,r-reshape2) + ("r-reticulate" ,r-reticulate) ("r-rocr" ,r-rocr) ("r-rtsne" ,r-rtsne) ("r-sdmtools" ,r-sdmtools) @@ -9731,14 +9798,14 @@ discovery of differentially expressed genes and markers.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.8.0") + (version "3.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "0crnk6851jwypqr5l5jcbbay0vi5vvdjyisaf6z2d69c39wmr6sc")))) + "1dxsiwsrwcq9mj573f9vpdzrhagdqzal328ma8076px4gg6khxkn")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -9758,14 +9825,14 @@ classes.") (define-public r-deseq (package (name "r-deseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq" version)) (sha256 (base32 - "0mn5w3cy16iwwk8zxs7za6aa6cnrca75z0g45zd5zh1py5d7nfv9")))) + "0ykxw8ksif026xy25wx50j2sdsrp156aqkmhcgfjkpgcw699glnm")))) (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs @@ -9789,14 +9856,14 @@ distribution.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.12.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "07zm89zcivyn2261aq9grqmly8ji482kr9h9dyfknfdfrpv7jpwv")))) + "1832pb3jkim4vrqzb8lajwx9r482bhww5n9nz3s6crvyamlp2dj0")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -9827,14 +9894,14 @@ global-scaling and full-quantile normalization.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "01yb945jqqimwjgriza6yy4dnp303cdirxrhl4hjyprfdlmnz5p5")))) + "05w58z3i9vkma4jd6rhjaxls4yiq4kwrppgcdq9xrr1pxp99k575")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) @@ -9851,14 +9918,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.10.1") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "14v8g44a6zg9j2rwn9x9y8509k0wr2cw8yccliz24glplb40wva4")))) + "11gh7qkgazs90czdqgv74gh2hz26xrmdp6wsz9x5pygbxls8xdw3")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -9886,14 +9953,14 @@ by the user, helping with quick and reproducible access.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "0dd7nr3klwz9ailwshnbynhd62lwb8zbbpj6jf3igpb94yi6x2jp")))) + "1yw6hai6hb8qy7akdm4frfp6h4zy93zb68kdj094sanm7kgqmgik")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -9916,14 +9983,14 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "02gwmm79djj55a90dzc80hlgwc6bafl7xd7fnx2q59pk945k3z9c")))) + "1349vidgl9m10l1rbrp3pkwwgi2xcbsw9h9z2xqbvg97lmqc4r8j")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -9940,14 +10007,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.28.2") + (version "2.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "0h0mlhns9j7cpfksvdlvx9jb7szm3r1dwqb3s4s8p8hmkb9byyii")))) + "0j3cqxy97lpf146wkmdfaq9680gicmzxvhp6w5pxq3j7ipiy7262")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -9969,14 +10036,14 @@ analysis using other methods.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.14.0") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "0r0wmrs5jycf1kckhnc2sgjmp336srlcjdkpbb1ymm7kazdd0s9n")))) + "0bhsq5czigrjyl9gkb2kpkpl367b3ac5g8s280adkcxggn9g7sxq")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -10002,14 +10069,14 @@ provide added flexibility for data combination and manipulation.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "1.17.1") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "1x6kp55iqqsd8bhdl3qch95nfiy2y46ldbbsx1sj1v8f0b0ywwcy")))) + "0z57mrginzd40niy51dvnyqgbrij05ji0dbwqs3x2as80sq28i3q")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -10032,14 +10099,14 @@ self-defined annotation graphics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "1c4s6x0qm20556grcd1xys9kkpnlzpasaai474malwcg6qvgi4x1")))) + "0vcyp81b90in4ls5nbadc66cw2g9aydr94aqifq5j4b7diq74yfs")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -10061,19 +10128,18 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.2.2") + (version "2.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "1yngndkf3588z91z0a2fvkg423p26ajm6xv1p27x0l9mzhhaqq3k")))) + "1l2b4cxiycv05mz4z4f3dhx57r9ksha02psc114h30ldm5rxz8w6")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-annotationfilter" ,r-annotationfilter) - ("r-annotationhub" ,r-annotationhub) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-biostrings" ,r-biostrings) @@ -10105,14 +10171,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "0yxvhwn0m53wfwp0zi81x96argdf7cf1lpymc2as51apvfcnjdl8")))) + "0hb9ni41bjfy5s5ryw2qmqs2sx3i7j47w1g0l8g1pvn7ppnxb6cv")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs @@ -10137,14 +10203,14 @@ the fact that each of these packages implements a select methods.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "14l4vhj0a4ssr9m9zdzz3qpd4qw1mhgq5bmxq7jhrq3j9kmd6i2f")))) + "0lkiqdr3ics6hgv47lwkykcy761823bbkhffbn4ykyfzyqwl4p67")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -10178,14 +10244,14 @@ effort and encourages consistency.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.26.1") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "1xlmlngn27iwnr21s9di4059kav1a7c1sajx08wja8yn8f7j06hp")))) + "0wszh3w8yia5zw758h837i1q35k99sn444y2hahcxqbdmmlbf7in")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10254,14 +10320,14 @@ organisms via the @code{g:Profiler} toolkit.") (define-public r-gqtlbase (package (name "r-gqtlbase") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLBase" version)) (sha256 (base32 - "1756vfcj2dkkgcmfkkg7qdaig36dv9gfvpypn9rbrky56wm1p035")))) + "1m3ajpqjhw1nwwsn372r44xfxq0a9a0pzsnrprzdjp6mh52p9b5m")))) (properties `((upstream-name . "gQTLBase"))) (build-system r-build-system) (propagated-inputs @@ -10289,14 +10355,14 @@ and more.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "1x9qwynh2hwl24vq02naf4mchpch7xi2pkdrlgw896k28kx0lvir")))) + "0iydgfnm053iw860qa1bbh4f6nwzlsf3vhgq92gvl2v4xsz1jbbs")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -10348,24 +10414,26 @@ several related annotation packages.") (define-public r-erma (package (name "r-erma") - (version "0.10.1") + (version "0.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "1fi8nc6fbd7i4p9i9hli31xplmdpsxqcdrb8v3nf8fx9klllbdav")))) + "1ka68n18yizlyvb8bpwwcl4hqbsasg8hw8jb3vgy3cd4szji87hh")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) - ("r-foreach" ,r-foreach) + ("r-biocparallel" ,r-biocparallel) + ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfiles" ,r-genomicfiles) ("r-genomicranges" ,r-genomicranges) ("r-ggplot2" ,r-ggplot2) ("r-homo-sapiens" ,r-homo-sapiens) + ("r-iranges" ,r-iranges) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors) ("r-shiny" ,r-shiny) @@ -10384,17 +10452,18 @@ by Ernst and Kellis.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.8.1") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "1q8dz8wcq1r7kr635s9q21g36sxkdybk8khhpa4p57qv8r0gppl0")))) + "0c24zvnwsp39d3q0bps13sc441jj9ms2zi34xsb8c392lqmbypvd")))) (build-system r-build-system) (propagated-inputs - `(("r-erma" ,r-erma) + `(("r-biocgenerics" ,r-biocgenerics) + ("r-erma" ,r-erma) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfiles" ,r-genomicfiles) ("r-go-db" ,r-go-db) @@ -10415,14 +10484,14 @@ defining LD blocks.") (define-public r-gqtlstats (package (name "r-gqtlstats") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLstats" version)) (sha256 (base32 - "0gvq1sf2zjbkk431x40z6wql3c1rpclnnwa2f1hvykb8mmw70kmq")))) + "19g8qhfgngdc14cw9k4i44cxhs3qva87x56gjzmn25k1yj8qgsp1")))) (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) (propagated-inputs @@ -10445,8 +10514,8 @@ defining LD blocks.") ("r-ggplot2" ,r-ggplot2) ("r-gqtlbase" ,r-gqtlbase) ("r-hardyweinberg" ,r-hardyweinberg) + ("r-homo-sapiens" ,r-homo-sapiens) ("r-iranges" ,r-iranges) - ("r-ldblock" ,r-ldblock) ("r-limma" ,r-limma) ("r-mgcv" ,r-mgcv) ("r-plotly" ,r-plotly) @@ -10469,14 +10538,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.22.3") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "1grjzrjpzkw572pbvpsvdnfkfgwybl0cnjd7nnk2xdr26wnbsi9a")))) + "1fhli7ahkl5r43j0hc89ib41mfadj6qyrg36i03ncz8zs6iqwpx4")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -10515,14 +10584,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "0n5x5i5v6a8wpn5mxmlpkl34b4kyypmymiwww6g61zch7xqrgywi")))) + "08ba9il4vbjjwlbwmqg4ai6ya1p09js9agn95sw0dhc9gqln42hx")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10555,13 +10624,13 @@ EMBL-EBI GWAS catalog.") (define-public r-sushi (package (name "r-sushi") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "0axaqm480z8d0b2ldgxwm0swava1p4irc62bpl17p2k8k78g687g")))) + "1m15hmg4k0qhshyn65xfj5hx7xbaf0kxqw70lxisak6pj1w00l41")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs @@ -10577,13 +10646,13 @@ visualizations for publication-quality multi-panel figures.") (define-public r-fithic (package (name "r-fithic") - (version "1.4.0") + (version "1.6.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "12ylhrppi051m7nqsgq95kzd9g9wmp34i0zzfi55cjqawlpx7c6n")))) + "06w4q836bi1mvkbl1saghv4r5p4hxpjg8cp7kgad13ls450kqmyd")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs @@ -10601,13 +10670,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.22.1") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "0da1jw9my2n2gihs31zyn14wwr23d8v2vij39ll7rm6fma3ydfbl")))) + "0qkk5139f51lwwy1yh7nbkflh5d69prirmhniwam34nlg9rzjm2z")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -10630,14 +10699,14 @@ provided.") (define-public r-qvalue (package (name "r-qvalue") - (version "2.10.0") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "1rd9rnf16kh8wc076kahd9hsb9rfwsbzmz3kjmp0pj6rbiq0051i")))) + "1ndwkj0hh7v4lwylq1v0fkxqs7mfmbcj8kxbdpj1wkvf131z2ns8")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -10659,14 +10728,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "0kcdza41saqv6vlpvqd841awbiwkg84lh0plx6c7fmfgbqv7a0jh")))) + "1l0276qxkhgdxsfck3jmi8jvnsr20g10gjki53g0mqa45wnhm3ck")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (propagated-inputs @@ -10685,14 +10754,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.0.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0kkc4rprjbqn2wvbx4d49kk9l91vihccxbl4843qr1wqk6v33r1w")))) + "1y59acac6v8hrhv84gghn9ifsni9xxxacaj177rrl4frmkrz4x3c")))) (properties `((upstream-name . "Rhdf5lib"))) (build-system r-build-system) (arguments @@ -10703,10 +10772,10 @@ block processing.") (for-each delete-file '("configure" "configure.ac")) ;; Do not make other packages link with the proprietary libsz. (substitute* "R/zzz.R" - (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a'") - "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a'") - (("'%s/libhdf5.a %s/libsz.a'") - "'%s/libhdf5.a %s/libhdf5.a'")) + (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'") + "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'") + (("'%s/libhdf5.a %s/libsz.a -lz'") + "'%s/libhdf5.a %s/libhdf5.a -lz'")) (with-directory-excursion "src" (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) (rename-file (string-append "hdf5-" ,(package-version hdf5)) @@ -10733,8 +10802,7 @@ block processing.") (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") ;; szip is non-free software (("cp \\$\\{SZIP_LIB\\}.*") "") - (("PKG_LIBS = \\$\\{HDF5_LIB\\} \\$\\{SZIP_LIB\\}") - "PKG_LIBS = ${HDF5_LIB}\n"))) + (("\\$\\{USER_LIB_DIR\\}libsz.a") ""))) #t))))) (inputs `(("zlib" ,zlib))) @@ -10751,17 +10819,18 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "1.0.2") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "0b6dzja5fbx4dawb7ixj67mlhw4fy62pfp20mfp918fy96zmdwqz")))) + "1w90v0jx1zgrfxzx99gdkk0dz2vi25hr51jml1bvq33i64rj7996")))) (build-system r-build-system) (inputs - `(("hdf5" ,hdf5))) + `(("hdf5" ,hdf5) + ("zlib" ,zlib))) (propagated-inputs `(("r-delayedarray" ,r-delayedarray) ("r-hdf5array" ,r-hdf5array) @@ -10778,14 +10847,14 @@ matrices.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "1r276i97w64a5vdlg6952gkj7bls909p42zl8fn8yz87cdwyaars")))) + "0mz3chia250v8v6q8r5cqv5fc4bpcw1hhrfr3p7l5i4xi85scpka")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -10805,27 +10874,27 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.6.3") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0q3s96gf8saa1dq2fvmpl0jyj7bx3wrdfck3hanb8pxkcir2p7dn")))) + "0bhpikgz3b9f510dawsay4zry9rlp8vjx5n6zvwbcpwrd94p3903")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) - ("r-biomart" ,r-biomart) ("r-data-table" ,r-data-table) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dplyr" ,r-dplyr) ("r-edger" ,r-edger) ("r-ggbeeswarm" ,r-ggbeeswarm) ("r-ggplot2" ,r-ggplot2) ("r-limma" ,r-limma) ("r-matrix" ,r-matrix) - ("r-matrixstats" ,r-matrixstats) ("r-plyr" ,r-plyr) ("r-rcpp" ,r-rcpp) ("r-reshape2" ,r-reshape2) @@ -10849,19 +10918,21 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.6.9") + (version "1.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "0cs64cnf0xjcgmawr210y99j3gxs6aqgh8081n9827kkqnx2y5dm")))) + "0nbn5x75gf9d0p18w7vpkbv30cpdqvp5bz8xvila0h7jla7xdyih")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) ("r-biocgenerics" ,r-biocgenerics) ("r-biocparallel" ,r-biocparallel) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dt" ,r-dt) ("r-dynamictreecut" ,r-dynamictreecut) ("r-edger" ,r-edger) @@ -10878,8 +10949,7 @@ quality control.") ("r-singlecellexperiment" ,r-singlecellexperiment) ("r-statmod" ,r-statmod) ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-viridis" ,r-viridis) - ("r-zoo" ,r-zoo))) + ("r-viridis" ,r-viridis))) (home-page "https://bioconductor.org/packages/scran") (synopsis "Methods for single-cell RNA-Seq data analysis") (description "This package implements a variety of low-level analyses of @@ -10891,14 +10961,14 @@ variable and significantly correlated genes.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.0.3") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1cxjbjdq9hg9cm95rci0al7a4pk2h73ym276ahw9q4977zbg6381")))) + "1dasghfy8x27zzmd0igag4mc1gxxxbchsl4hpc1050dj3wnw9w3y")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -10994,11 +11064,6 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (sha256 (base32 "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9")))) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'bootstrap - (lambda _ (invoke "autoreconf" "-vif")))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -11141,25 +11206,22 @@ with narrow binding events such as transcription factor ChIP-seq.") (define-public trim-galore (package (name "trim-galore") - (version "0.4.2") + (version "0.4.5") (source (origin - (method url-fetch) - (uri (string-append "http://www.bioinformatics.babraham.ac.uk/" - "projects/trim_galore/trim_galore_v" - version ".zip")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/FelixKrueger/TrimGalore.git") + (commit version))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0b9qdxi4521gsrjvbhgky8g7kry9b5nx3byzaxkgxz7p4k8bn1mn")))) + "0x5892l48c816pf00wmnz5vq0zq6170d3xc8zrxncd4jcz7h1p71")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no tests #:phases (modify-phases %standard-phases - ;; The archive contains plain files. - (replace 'unpack - (lambda* (#:key source #:allow-other-keys) - (zero? (system* "unzip" source)))) (delete 'configure) (delete 'build) (add-after 'unpack 'hardcode-tool-references @@ -11540,7 +11602,9 @@ browser.") (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((target (assoc-ref outputs "out")) - (doc (string-append target "/share/doc/f-seq/"))) + (bin (string-append target "/bin")) + (doc (string-append target "/share/doc/f-seq")) + (lib (string-append target "/lib"))) (mkdir-p target) (mkdir-p doc) (substitute* "bin/linux/fseq" @@ -11549,11 +11613,11 @@ browser.") (string-append (assoc-ref inputs "java-commons-cli") "/share/java/commons-cli.jar")) (("REALDIR=.*") - (string-append "REALDIR=" target "/bin\n"))) + (string-append "REALDIR=" bin "\n"))) (install-file "README.txt" doc) - (install-file "bin/linux/fseq" (string-append target "/bin")) - (install-file "build~/fseq.jar" (string-append target "/lib")) - (copy-recursively "lib" (string-append target "/lib")) + (install-file "bin/linux/fseq" bin) + (install-file "build~/fseq.jar" lib) + (copy-recursively "lib" lib) #t)))))) (inputs `(("perl" ,perl) @@ -11571,47 +11635,61 @@ Browser.") (define-public bismark (package (name "bismark") - (version "0.16.3") + (version "0.19.1") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/FelixKrueger/Bismark/" - "archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/FelixKrueger/Bismark.git") + (commit version))) + (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "1204i0pa02ll2jn5pnxypkclnskvv7a2nwh5nxhagmhxk9wfv9sq")))) + "0yb5l36slwg02fp4b1jdlplgljcsxgqfzvzihzdnphd87dghcc84")) + (snippet + '(begin + ;; highcharts.js is non-free software. The code is available under + ;; CC-BY-NC or proprietary licenses only. + (delete-file "bismark_sitrep/highcharts.js") + #t)))) (build-system perl-build-system) (arguments - `(#:tests? #f ; there are no tests + `(#:tests? #f ; there are no tests #:phases (modify-phases %standard-phases (delete 'configure) (delete 'build) (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") - "/bin")) - (docdir (string-append (assoc-ref outputs "out") - "/share/doc/bismark")) - (docs '("Bismark_User_Guide.pdf" - "RELEASE_NOTES.txt")) - (scripts '("bismark" - "bismark_genome_preparation" - "bismark_methylation_extractor" - "bismark2bedGraph" - "bismark2report" - "coverage2cytosine" - "deduplicate_bismark" - "bismark_sitrep.tpl" - "bam2nuc" - "bismark2summary"))) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (share (string-append out "/share/bismark")) + (docdir (string-append out "/share/doc/bismark")) + (docs '("Docs/Bismark_User_Guide.html")) + (scripts '("bismark" + "bismark_genome_preparation" + "bismark_methylation_extractor" + "bismark2bedGraph" + "bismark2report" + "coverage2cytosine" + "deduplicate_bismark" + "filter_non_conversion" + "bam2nuc" + "bismark2summary"))) + (substitute* "bismark2report" + (("\\$RealBin/bismark_sitrep") + (string-append share "/bismark_sitrep"))) + (mkdir-p share) (mkdir-p docdir) (mkdir-p bin) (for-each (lambda (file) (install-file file bin)) scripts) (for-each (lambda (file) (install-file file docdir)) docs) + (copy-recursively "Docs/Images" (string-append docdir "/Images")) + (copy-recursively "bismark_sitrep" + (string-append share "/bismark_sitrep")) + ;; Fix references to gunzip (substitute* (map (lambda (file) (string-append bin "/" file)) @@ -11738,7 +11816,7 @@ accurate as existing quantification tools.") code that is used in the Cufflinks codebase. The goal of this library is to provide this functionality without the necessity of drawing in a heavy-weight dependency like SeqAn.") - (license (license:x11-style "http://www.boost.org/LICENSE_1_0.txt")))) + (license (license:x11-style "https://www.boost.org/LICENSE_1_0.txt")))) (define-public libdivsufsort (package @@ -11899,7 +11977,8 @@ bytes of memory space, where n is the length of the string.") (snippet '(begin (delete-file-recursively "include/spdlog") (for-each delete-file '("include/xxhash.h" - "src/xxhash.c")))))) + "src/xxhash.c")) + #t)))) ("libdivsufsort" ,libdivsufsort) ("libgff" ,libgff) ("tbb" ,tbb) @@ -12624,7 +12703,8 @@ contains (snippet '(begin (for-each delete-file (find-files "jar/lib" "\\.jar$")) - (delete-file-recursively "3rdParty"))))) + (delete-file-recursively "3rdParty") + #t)))) (build-system ant-build-system) (arguments `(#:tests? #f ; test data are not included @@ -12643,6 +12723,9 @@ contains (guix build ant-build-system)) #:phases (modify-phases %standard-phases + ;; FIXME: fails with "java.io.FileNotFoundException: + ;; /gnu/store/q76y0ximcziplgfpbn26kbw4h3s14f33-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. @@ -12969,7 +13052,7 @@ methylation and segmentation.") (define-public pigx-scrnaseq (package (name "pigx-scrnaseq") - (version "0.0.3") + (version "0.0.4") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_scrnaseq/" @@ -12977,7 +13060,7 @@ methylation and segmentation.") "/pigx_scrnaseq-" version ".tar.gz")) (sha256 (base32 - "12qdq0nj1wdkyighdxj6924bmbpd1a0b3gam6w64l4hiqrv5sijz")))) + "1pvjm6f3mascprs65vflggwwg5v925knvgal7k7a6nnlmw5qndrf")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -13000,7 +13083,7 @@ methylation and segmentation.") ("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) @@ -13111,3 +13194,54 @@ Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods 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+)))) |