diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 230 |
1 files changed, 105 insertions, 125 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6ec378c0d9..c71e70bc63 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2084,7 +2084,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.8.36") + (version "0.8.37") (source (origin (method url-fetch) (uri (string-append @@ -2093,7 +2093,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "092smzzjcg51n3x4h84k52ijpz9m40ri838j9k2i463ribc3c8rh")))) + "1zn7q8m41ayfnjvf9snrsnq00mm68alf9rhdadx5q1sk23lyvp2l")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -3196,7 +3196,7 @@ sequencing tag position and orientation.") (define-public mafft (package (name "mafft") - (version "7.305") + (version "7.310") (source (origin (method url-fetch) (uri (string-append @@ -3205,7 +3205,7 @@ sequencing tag position and orientation.") (file-name (string-append name "-" version ".tgz")) (sha256 (base32 - "0ziim7g58n3z8gppsa713f5fxprl60ldj3xck186z0n9dpp06i8r")))) + "0gbsaz6z2qa307kd7wfb06c3y4ikmv1hsdvlns11f6zq4w1z9pwc")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no automated tests, though there are tests in the read me @@ -4041,7 +4041,7 @@ extremely diverse sets of genomes.") (define-public raxml (package (name "raxml") - (version "8.2.9") + (version "8.2.10") (source (origin (method url-fetch) @@ -4052,7 +4052,7 @@ extremely diverse sets of genomes.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1pv8p2fy67y21a9y4cm7xpvxqjwz2v4201flfjshdq1p8j52rqf7")))) + "13s7aspfdcfr6asynwdg1x6vznys6pzap5f8wsffbnnwpkkg9ya8")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; There are no tests. @@ -4790,50 +4790,61 @@ sequence itself can be retrieved from these databases.") "/lib64" "/lib32"))) #:phases - (alist-replace - 'configure - (lambda* (#:key inputs outputs #:allow-other-keys) - ;; The build system expects a directory containing the sources and - ;; raw build output of ncbi-vdb, including files that are not - ;; installed. Since we are building against an installed version of - ;; ncbi-vdb, the following modifications are needed. - (substitute* "setup/konfigure.perl" - ;; Make the configure script look for the "ilib" directory of - ;; "ncbi-vdb" without first checking for the existence of a - ;; matching library in its "lib" directory. - (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);") - "my $f = File::Spec->catdir($ilibdir, $ilib);") - ;; Look for interface libraries in ncbi-vdb's "ilib" directory. - (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);") - "my $ilibdir = File::Spec->catdir($dir, 'ilib');")) - - ;; Dynamic linking - (substitute* "tools/copycat/Makefile" - (("smagic-static") "lmagic")) - - ;; The 'configure' script doesn't recognize things like - ;; '--enable-fast-install'. - (zero? (system* - "./configure" - (string-append "--build-prefix=" (getcwd) "/build") - (string-append "--prefix=" (assoc-ref outputs "out")) - (string-append "--debug") - (string-append "--with-fuse-prefix=" - (assoc-ref inputs "fuse")) - (string-append "--with-magic-prefix=" - (assoc-ref inputs "libmagic")) - ;; TODO: building with libxml2 fails with linker errors - ;; (string-append "--with-xml2-prefix=" - ;; (assoc-ref inputs "libxml2")) - (string-append "--with-ncbi-vdb-sources=" - (assoc-ref inputs "ncbi-vdb")) - (string-append "--with-ncbi-vdb-build=" - (assoc-ref inputs "ncbi-vdb")) - (string-append "--with-ngs-sdk-prefix=" - (assoc-ref inputs "ngs-sdk")) - (string-append "--with-hdf5-prefix=" - (assoc-ref inputs "hdf5"))))) - %standard-phases))) + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; The build system expects a directory containing the sources and + ;; raw build output of ncbi-vdb, including files that are not + ;; installed. Since we are building against an installed version of + ;; ncbi-vdb, the following modifications are needed. + (substitute* "setup/konfigure.perl" + ;; Make the configure script look for the "ilib" directory of + ;; "ncbi-vdb" without first checking for the existence of a + ;; matching library in its "lib" directory. + (("^ my \\$f = File::Spec->catdir\\(\\$libdir, \\$lib\\);") + "my $f = File::Spec->catdir($ilibdir, $ilib);") + ;; Look for interface libraries in ncbi-vdb's "ilib" directory. + (("my \\$ilibdir = File::Spec->catdir\\(\\$builddir, 'ilib'\\);") + "my $ilibdir = File::Spec->catdir($dir, 'ilib');")) + + ;; Dynamic linking + (substitute* "tools/copycat/Makefile" + (("smagic-static") "lmagic")) + + ;; The 'configure' script doesn't recognize things like + ;; '--enable-fast-install'. + (zero? (system* + "./configure" + (string-append "--build-prefix=" (getcwd) "/build") + (string-append "--prefix=" (assoc-ref outputs "out")) + (string-append "--debug") + (string-append "--with-fuse-prefix=" + (assoc-ref inputs "fuse")) + (string-append "--with-magic-prefix=" + (assoc-ref inputs "libmagic")) + ;; TODO: building with libxml2 fails with linker errors + ;; (string-append "--with-xml2-prefix=" + ;; (assoc-ref inputs "libxml2")) + (string-append "--with-ncbi-vdb-sources=" + (assoc-ref inputs "ncbi-vdb")) + (string-append "--with-ncbi-vdb-build=" + (assoc-ref inputs "ncbi-vdb")) + (string-append "--with-ngs-sdk-prefix=" + (assoc-ref inputs "ngs-sdk")) + (string-append "--with-hdf5-prefix=" + (assoc-ref inputs "hdf5")))))) + ;; This version of sra-tools fails to build with glibc because of a + ;; naming conflict. glibc-2.25/include/bits/mathcalls.h already + ;; contains a definition of "canonicalize", so we rename it. + ;; + ;; See upstream bug report: + ;; https://github.com/ncbi/sra-tools/issues/67 + (add-after 'unpack 'patch-away-glibc-conflict + (lambda _ + (substitute* "tools/bam-loader/bam.c" + (("canonicalize\\(" line) + (string-append "sra_tools_" line))) + #t))))) (native-inputs `(("perl" ,perl))) (inputs `(("ngs-sdk" ,ngs-sdk) @@ -5345,40 +5356,18 @@ information as possible.") (define-public r-vegan (package (name "r-vegan") - (version "2.4-2") + (version "2.4-3") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "12wf64izrpq9z3ix7mgm5421mq0xsm8dw5qblvcrz452nfhjf5w9")))) + "15zcxfix2d854897k1lr0sfmj2n00339nlsppcr3zrb238lb2mi5")))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'revert-test-deletion - ;; The distributed sources do not include tests with the CRAN - ;; package. Here we revert the commit - ;; `591d0e8ba1deaaf82445474ec6619c0b43db4e63' which deletes these - ;; tests. There are plans to not delete tests in future as - ;; documented at https://github.com/vegandevs/vegan/issues/181. - (lambda* (#:key inputs #:allow-other-keys) - (zero? - (system* "patch" "-R" "-p1" "-i" - (assoc-ref inputs "r-vegan-delete-tests-patch")))))))) (native-inputs `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr) - ("r-vegan-delete-tests-patch" - ,(origin - (method url-fetch) - (uri (string-append - "https://github.com/vegandevs/vegan/commit/" - "591d0e8ba1deaaf82445474ec6619c0b43db4e63.patch")) - (sha256 - (base32 - "0b1bi7y4jjdl3ph721vm9apm51dr2z9piwvhy4355sf2b4kyyj5a")))))) + ("r-knitr" ,r-knitr))) (propagated-inputs `(("r-cluster" ,r-cluster) ("r-lattice" ,r-lattice) @@ -5486,14 +5475,6 @@ high-throughput sequencing experiments.") "1walwkqryn1gnwz7zryr5764a0p6ia7ag4w6w9n8fskg8dkg0fqs")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'link-against-armadillo - (lambda _ - (substitute* "src/Makevars" - (("PKG_LIBS =" prefix) - (string-append prefix "-larmadillo")))))))) (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) @@ -5521,14 +5502,14 @@ distribution.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "02msyb9p3hywrryx00zpjkjl126mrv827i1ah1092s0cplm6xxvf")))) + "0l1g9hy88sh5g567svyfd8pnjvkyklkn6a3gjn8zalvh62qqjjq1")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -5660,14 +5641,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.32.0") + (version "1.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "0mjdlg92x5qw4x2djc4dv5lxwl7ai6ix56nnf86zr07jk8vc7yls")))) + "1m7lbfxs7xwcy9xs76zy5rky2mb96anvh457xfw60lh3kygwfpxc")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -5807,7 +5788,7 @@ track. The database is exposed as a @code{TxDb} object.") (define-public vsearch (package (name "vsearch") - (version "2.4.2") + (version "2.4.3") (source (origin (method url-fetch) @@ -5817,7 +5798,7 @@ track. The database is exposed as a @code{TxDb} object.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "15zy2d9xvgbgdjlxvrhj8s5ga42p13k7a3xv015ingn0bi1p3n6w")) + "0hc110ycqpa54nr6x173qg7190hk08qp7yz7zzqxlsypqnpc5zzp")) (patches (search-patches "vsearch-unbundle-cityhash.patch")) (snippet '(begin @@ -6131,13 +6112,13 @@ functionality.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1rfy37xg1nc2cmgbclvzsi7sgmdcdjiahsx9crgx3yaw7kxgiack")))) + "197kpiycyl3qawm6801fxyxj81d2g57a00qxaqprapsf1d140l52")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -6165,10 +6146,8 @@ functionality.") (propagated-inputs `(("r-codetools" ,r-codetools) ("r-graph" ,r-graph) - ("r-knitr" ,r-knitr) ("r-httr" ,r-httr) ("r-optparse" ,r-optparse) - ("r-devtools" ,r-devtools) ("r-biocinstaller" ,r-biocinstaller) ("r-biocviews" ,r-biocviews))) (home-page "http://bioconductor.org/packages/BiocCheck") @@ -6247,13 +6226,13 @@ abnormal copy number.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.12.1") + (version "0.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0i36y3w36h3d8rmazxcrip4gvn54rd9av1wz4lygsprrjmylfhcc")))) + "0syx0qgipx97zsp3b8afhzamsr30835a2a99yb9wnq7b50g3v3p1")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -6274,14 +6253,14 @@ S4Vectors package itself.") (define-public r-seqinr (package (name "r-seqinr") - (version "3.3-3") + (version "3.3-6") (source (origin (method url-fetch) (uri (cran-uri "seqinr" version)) (sha256 (base32 - "0rk4yba8km26c0rh1f4h474zsb5n6kjmqsi55bnzr6p8pymp18hj")))) + "13d0qxm2244wgdl2dy2s8vnrnf5fx4n47if9gkb49dqx6c0sx8s2")))) (build-system r-build-system) (propagated-inputs `(("r-ade4" ,r-ade4) @@ -6299,13 +6278,13 @@ utilities for sequence data management under the ACNUC system.") (define-public r-iranges (package (name "r-iranges") - (version "2.8.1") + (version "2.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "0cryqnpqb3p6l9jjw27hyqd550sxlljls3ka7b9rb38hkji7b5hw")))) + "0x8h74ik3xwdnwrkn89hq5ll0qa1lp9jgzlbmpa02dpws7snfwyr")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -6328,19 +6307,20 @@ possible.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.10.2") + (version "1.10.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0zh894qd1sgpjbn0wfvq6hs2dzn7y1pyicvzk2aa48y3zbidanv7")))) + "18g24cf6b3vi13w85ki2mam6i2gl4yxr1zchyga34xc3dkdngzrw")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) ("r-s4vectors" ,r-s4vectors))) (home-page "http://bioconductor.org/packages/GenomeInfoDb") (synopsis "Utilities for manipulating chromosome identifiers") @@ -6381,13 +6361,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.20.2") + (version "1.20.3") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "165wda1d2jagd907pnra4m3sla66icyqxvd60xpv09jl5agd5mn9")))) + "10v8apgfw57nd4dxmdxdrijxpw135jpp2p8wrk3wjpb3hhfjp1qj")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -6419,13 +6399,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.30.7") + (version "3.30.13") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1xg9w4lmn9n4hwyflxiwi6g969lcy569cg4z1x47crwwg7z7qdka")))) + "1ji8kb19anwq2505zii2kzqlrnk75mk1mpz8vy4s1mckzs1cz4m0")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -6438,13 +6418,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-xvector (package (name "r-xvector") - (version "0.14.0") + (version "0.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "09lbqxpqr80g0kw77mpz0p1a8cq706j33kz8194wp71il67cdzi7")))) + "1j14ip4c260kdp3zcmgfa2v8ky88csa0gfdg6a1xsb64s03hdbm6")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -6474,13 +6454,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.26.2") + (version "1.26.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "0if5dswkp77lyqppd0z2iyvnwag9h1gsr03707s8npcx13mzpsia")))) + "1789ycqzv20d8p1axkxrhsz9v0ww6w1dk2mfvm85p8j53zd1f67c")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -6525,13 +6505,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.36.0") + (version "1.36.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "0ydrqw1k1j5p6w76bwc753cx545c055x88q87wzya93858synj6r")))) + "0574lmyisn3nv9aicz9x3iivx990da4q2j4i0f1jz0mpj9v3vc2w")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -6582,13 +6562,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.8.1") + (version "1.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "123i928rwi4h4sy4fpysv6pinw5nns0sm3myxi2ghqhm34ws8gyl")))) + "18zpa0vl375n9pvxsgbid1k96m17nqqgv1g1sfnlmm7kj34jxg6v")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -6632,13 +6612,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "1.26.1") + (version "1.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "0pf4f6brf4bl5zgjrah0f38qslazrs49ayqgyh0xfqgrh63yx4ck")))) + "118nsajgghi4cy3h0wi7777kc70a5j1fdyxv5n1dy01glix2z4qk")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -6706,13 +6686,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "11vb0a0zd36i4yhg4mfijv787v0nihn6pkjj6q7rfy19gwy61xlc")))) + "1dilghbsyf64iz5c0kib2c7if72x7almd5w3ali09a2b2ff2mcjk")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -6739,13 +6719,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.34.1") + (version "1.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0x59k2fd0iaqi93gy6bm58p2j2z90z1b7a6w5b4c098y98n096rc")))) + "1j3cyvg1wg1d9l0lkcjk3jn7pb96zi17nd1qsa5lglsimja19mpl")))) (build-system r-build-system) (arguments `(#:phases @@ -6784,13 +6764,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.26.2") + (version "1.26.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1ybi6r3bax07wlv2qcd34y5qjdvcqcfayfvlrjc39ifrkk65wv4f")))) + "1y16lqach0v3ym5zhdhj4r2imfi0kpa0djlb51hj85yf7xkzwdlb")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -8295,14 +8275,14 @@ unmodeled, or latent sources of noise.") (define-public r-seqminer (package (name "r-seqminer") - (version "5.3") + (version "5.7") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 - "0y0gc5lws3hdxasjb84m532ics6imb7qg9sl1zy62h503jh4j9gw")))) + "0p75wyl70cvp36mwg5y74nv573j1gdqi15ac2a7xf61jmsq7ycpy")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -8349,14 +8329,14 @@ trait.") (define-public r-maldiquant (package (name "r-maldiquant") - (version "1.16") + (version "1.16.2") (source (origin (method url-fetch) (uri (cran-uri "MALDIquant" version)) (sha256 (base32 - "067xbmy10mpsvmv77g62chd7wwhdhcfn5hmp5fisbnz2h5rq0q60")))) + "0z5srzsfgsgi4bssr4chls4ry6d18y2g9143znqmraylppwrrqzr")))) (properties `((upstream-name . "MALDIquant"))) (build-system r-build-system) (home-page "http://cran.r-project.org/web/packages/MALDIquant") |