diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 102 |
1 files changed, 55 insertions, 47 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5af4947b68..61e5d8bc34 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -252,7 +252,7 @@ instance, it implements several methods to assess contig-wise read coverage.") (define-public bamtools (package (name "bamtools") - (version "2.4.1") + (version "2.5.1") (source (origin (method url-fetch) (uri (string-append @@ -261,7 +261,7 @@ instance, it implements several methods to assess contig-wise read coverage.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0jr024kcrhjb82cm69i7p5fcg5375zlc1h3qh2n1v368hcd0qflk")))) + "1z3kg24qrwq13a88n9d86izngrar4fll7gr6phddb2faw75pdgaa")))) (build-system cmake-build-system) (arguments `(#:tests? #f ;no "check" target @@ -285,7 +285,7 @@ BAM files.") (define-public bcftools (package (name "bcftools") - (version "1.5") + (version "1.8") (source (origin (method url-fetch) (uri (string-append @@ -293,12 +293,11 @@ BAM files.") version "/bcftools-" version ".tar.bz2")) (sha256 (base32 - "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz")) - (patches (search-patches "bcftools-regidx-unsigned-char.patch")) + "1vgw2mwngq20c530zim52zvgmw1lci8rzl33pvh44xqk3xlzvjsa")) (modules '((guix build utils))) (snippet '(begin ;; Delete bundled htslib. - (delete-file-recursively "htslib-1.5") + (delete-file-recursively "htslib-1.8") #t)))) (build-system gnu-build-system) (arguments @@ -339,7 +338,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") (define-public bedops (package (name "bedops") - (version "2.4.14") + (version "2.4.33") (source (origin (method url-fetch) (uri (string-append "https://github.com/bedops/bedops/archive/v" @@ -347,7 +346,7 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1kqbac547wyqma81cyky9n7mkgikjpsfd3nnmcm6hpqwanqgh10v")))) + "0kx4awrwby8f33wqyx8w7ms7v25xhf0d421csgf96a3hfzn2mb0m")))) (build-system gnu-build-system) (arguments '(#:tests? #f @@ -2089,7 +2088,7 @@ accurately delineate genomic rearrangements throughout the genome.") (define-public diamond (package (name "diamond") - (version "0.9.19") + (version "0.9.21") (source (origin (method url-fetch) (uri (string-append @@ -2098,7 +2097,7 @@ accurately delineate genomic rearrangements throughout the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0c4y8l90vdxmglb0w37y0413v11qzcwg8sdmy9k0c0gr3bsq7dzs")))) + "1cf98vcsiwcv3c4apg50w1240v1mpw0zln1sdw3g692dqa4y041z")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -2349,7 +2348,8 @@ dynamic programming or a variety of heuristics.") (string-append (assoc-ref inputs "bamtools") "/include/bamtools"))) (substitute* "src/CMakeLists.txt" (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib") - (string-append (assoc-ref inputs "bamtools") "/lib/bamtools"))) + (string-append (assoc-ref inputs "bamtools") "/lib")) + (("libprotobuf.a") "libprotobuf.so")) #t))))) (inputs `(("boost" ,boost) @@ -3462,7 +3462,7 @@ The main functions of FastQC are: (define-public htslib (package (name "htslib") - (version "1.7") + (version "1.8") (source (origin (method url-fetch) (uri (string-append @@ -3470,7 +3470,7 @@ The main functions of FastQC are: version "/htslib-" version ".tar.bz2")) (sha256 (base32 - "1il6i2p84b0y9c93dhvzzki1ifw9bvapm2mvpr0xvb2nq8jlwgdy")))) + "18bw0mn9pj5wgarnlaxmf1bb8pdqgl1zd6czirqcr62ajpn1xvy0")))) (build-system gnu-build-system) (inputs `(("openssl" ,openssl) @@ -4587,7 +4587,7 @@ partial genes, and identifies translation initiation sites.") (define-public roary (package (name "roary") - (version "3.11.0") + (version "3.12.0") (source (origin (method url-fetch) @@ -4596,7 +4596,7 @@ partial genes, and identifies translation initiation sites.") version ".tar.gz")) (sha256 (base32 - "10lw78x1xzvn7xzvnmh4bm3cak3ah5cssapl0yidvhaj1f44h29i")))) + "0qxrds9wx7cfhlkihrp6697kx0flhhxymap9fwan0b3rbdhcnmff")))) (build-system perl-build-system) (arguments `(#:phases @@ -4934,7 +4934,7 @@ to the user's query of interest.") (define-public samtools (package (name "samtools") - (version "1.7") + (version "1.8") (source (origin (method url-fetch) @@ -4943,7 +4943,7 @@ to the user's query of interest.") version "/samtools-" version ".tar.bz2")) (sha256 (base32 - "18acyqysbxpydlc44lqv2hpp57l06bs9a3yqmcvjk8va2xrrdc77")))) + "05myg7bs90i68qbqab9cdg9rqj2xh39azibrx82ipzc5kcfvqhn9")))) (build-system gnu-build-system) (arguments `(#:modules ((ice-9 ftw) @@ -5784,7 +5784,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (define-public star (package (name "star") - (version "2.5.3a") + (version "2.6.0a") (source (origin (method url-fetch) (uri (string-append "https://github.com/alexdobin/STAR/archive/" @@ -5792,7 +5792,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "013wirlz8lllgjyagl48l75n1isxyabqb3sj7qlsl0x1rmvqw99a")) + "0yci4ymy4407kjh0lqp021nzccp6r31wgrkixkmix5p130cxvc56")) (modules '((guix build utils))) (snippet '(begin @@ -5979,13 +5979,13 @@ Cuffdiff or Ballgown programs.") (define-public taxtastic (package (name "taxtastic") - (version "0.6.4") + (version "0.8.5") (source (origin (method url-fetch) (uri (pypi-uri "taxtastic" version)) (sha256 (base32 - "0s79z8kfl853x7l4h8ms05k31q87aw62nrchlk20w9n227j35929")))) + "03pysw79lsrvz4lwzis88j15067ffqbi4cid5pqhrlxmd6bh8rrk")))) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -6098,19 +6098,20 @@ information as possible.") (define-public r-vegan (package (name "r-vegan") - (version "2.4-6") + (version "2.5-1") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "175mqr42mmxy98gpf3rky8alnkw3w1k90ggdw3cispl36841p76w")))) + "0pynr02d1xngda6c3va8fc4nxpgfkawhzcnz1ws4dnarp9b1w90r")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) (propagated-inputs `(("r-cluster" ,r-cluster) + ("r-knitr" ,r-knitr) ("r-lattice" ,r-lattice) ("r-mass" ,r-mass) ("r-mgcv" ,r-mgcv) @@ -6266,14 +6267,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.24.3") + (version "1.24.4") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "0xip73hlbr3zry9d7ly9vvvsbb3xjcmfa09lr9fdy528dwjrf084")))) + "1a80yv742fx5c7qav7imsdybphf0d5bixsqyf8w5zng7fk8j16d5")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -6619,7 +6620,7 @@ SELECT or UPDATE queries to an end-point.") (define-public vsearch (package (name "vsearch") - (version "2.7.1") + (version "2.8.0") (source (origin (method url-fetch) @@ -6629,7 +6630,7 @@ SELECT or UPDATE queries to an end-point.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0jlzfgh79fzmb4g7sngzdjjsjyc37icvs1k7vmc2ksxglj6x5i7f")) + "15pbirgzhvflj4pi5n82vybbzjy9mlb0lv5l3qhrmdkfzpbyahw3")) (patches (search-patches "vsearch-unbundle-cityhash.patch")) (snippet '(begin @@ -7604,13 +7605,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.14.1") + (version "1.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "033p6fw46sn7w2yyn14nb9qcnkf30cl0nv6zh014ixflm3iifz39")))) + "1659nj1xps7vliy5955i51x6hvrf16n1z0dfh10mmpaaswn2d2mv")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -9077,14 +9078,14 @@ replacement for strverscmp.") (define-public multiqc (package (name "multiqc") - (version "1.4") + (version "1.5") (source (origin (method url-fetch) (uri (pypi-uri "multiqc" version)) (sha256 (base32 - "0ihx4rzmsfphv4byn05qv6f1y95g2dxs6viwziipl4wjk96acgm8")))) + "02iihfl0w0hpnr4pa0sbd1y9qxrg3ycyhjp5lidkcrqh1lmzs3zy")))) (build-system python-build-system) (propagated-inputs `(("python-jinja2" ,python-jinja2) @@ -9652,13 +9653,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "2.2.1") + (version "2.3.0") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "1sr82nf38hq07avrfn8vlrzjq7dfm4pcr8l1nh6mnglcql2bk9z2")) + "0kp3lw1s896zkjd6x2wp8qcg7wnm5b40g8vihps13f1m7j4nx7r0")) ;; Delete pre-built jar. (snippet '(begin (delete-file "inst/java/ModularityOptimizer.jar") @@ -9688,11 +9689,15 @@ Main-Class: ModularityOptimizer\n"))) (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) @@ -9704,13 +9709,16 @@ Main-Class: ModularityOptimizer\n"))) ("r-igraph" ,r-igraph) ("r-irlba" ,r-irlba) ("r-lars" ,r-lars) + ("r-lmtest" ,r-lmtest) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) ("r-metap" ,r-metap) ("r-mixtools" ,r-mixtools) ("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-rcppeigen" ,r-rcppeigen) @@ -10185,14 +10193,14 @@ effort and encourages consistency.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.26.0") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "1bqxfqy0hff87ax92z4lfbjz01ndrz7x8pzm6dlkdmi52p30krm9")))) + "1xlmlngn27iwnr21s9di4059kav1a7c1sajx08wja8yn8f7j06hp")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10237,14 +10245,14 @@ interval to data view, mismatch pileup, and several splicing summaries.") (define-public r-gprofiler (package (name "r-gprofiler") - (version "0.6.4") + (version "0.6.6") (source (origin (method url-fetch) (uri (cran-uri "gProfileR" version)) (sha256 (base32 - "1cka02zbz1rbppm782qpxk1xn9qxbrv2gp5rgf970j906hxm2y0b")))) + "1n6cj12j102b4x9vhyl4dljp1i0r43p23cnhqbx4als2xfxdlqgi")))) (properties `((upstream-name . "gProfileR"))) (build-system r-build-system) (propagated-inputs @@ -10355,14 +10363,14 @@ several related annotation packages.") (define-public r-erma (package (name "r-erma") - (version "0.10.0") + (version "0.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "0gcfs9g8vvdv5vmq9b21kd8sq5mizjj49nfzd4in9zvp4b9v7x1g")))) + "1fi8nc6fbd7i4p9i9hli31xplmdpsxqcdrb8v3nf8fx9klllbdav")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10391,14 +10399,14 @@ by Ernst and Kellis.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "18nfsixh6d2wfrb9laqsgly5w1frzihhak683k0p8fdf51h4aqba")))) + "1q8dz8wcq1r7kr635s9q21g36sxkdybk8khhpa4p57qv8r0gppl0")))) (build-system r-build-system) (propagated-inputs `(("r-erma" ,r-erma) @@ -10608,13 +10616,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.22.0") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "0288xa1jy6nzvz2ha07csmp6dirjw5r7p9vy69q2wsbyzr02ymkp")))) + "0da1jw9my2n2gihs31zyn14wwr23d8v2vij39ll7rm6fma3ydfbl")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -10856,14 +10864,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.6.8") + (version "1.6.9") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "07wniyrh2fhhkz28v0bfgpvpi1hkkn2cvhacrvvvck142j79944x")))) + "0cs64cnf0xjcgmawr210y99j3gxs6aqgh8081n9827kkqnx2y5dm")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -12826,7 +12834,7 @@ expression report comparing samples in an easily configurable manner.") (define-public pigx-chipseq (package (name "pigx-chipseq") - (version "0.0.10") + (version "0.0.15") (source (origin (method url-fetch) (uri (string-append "https://github.com/BIMSBbioinfo/pigx_chipseq/" @@ -12834,7 +12842,7 @@ expression report comparing samples in an easily configurable manner.") "/pigx_chipseq-" version ".tar.gz")) (sha256 (base32 - "13w99bkr0w4j28ms0yzpl1x6fkpdqay0vh495q3x20bcilsjwnf1")))) + "11v9v3vyda0sv4cl45nki7mm4v4bjfcdq7a70kcvi9h465nq66wg")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; parts of the tests rely on access to the network |