diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 102 |
1 files changed, 70 insertions, 32 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9f5d8141d8..9b4afbfcfb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -614,7 +614,7 @@ Python.") (define-public python-biom-format (package (name "python-biom-format") - (version "2.1.5") + (version "2.1.6") (source (origin (method url-fetch) @@ -625,14 +625,15 @@ Python.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1n25w3p1rixbpac8iysmzcja6m4ip5r6sz19l8y6wlwi49hxn278")))) + "08cr7wpahk6zb31h4bs7jmzpvxcqv9s13xz40h6y2h656jvdvnpj")))) (build-system python-build-system) (propagated-inputs `(("python-numpy" ,python-numpy) ("python-scipy" ,python-scipy) ("python-future" ,python-future) ("python-click" ,python-click) - ("python-h5py" ,python-h5py))) + ("python-h5py" ,python-h5py) + ("python-pandas" ,python-pandas))) (native-inputs `(("python-nose" ,python-nose))) (home-page "http://www.biom-format.org") @@ -2092,7 +2093,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.8.38") + (version "0.9.0") (source (origin (method url-fetch) (uri (string-append @@ -2101,7 +2102,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0q2z6z5f7c0kbbzpjamkcyqg0rc6h5rxfp97qbmb0wxaycr7jajq")))) + "19lvz661mmgikbry0nvnsjc01fdxqbw9rl2868dvjfraxbcx9ras")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -2121,8 +2122,7 @@ translated DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings.") - (license (license:non-copyleft "file://src/COPYING" - "See src/COPYING in the distribution.")))) + (license license:agpl3+))) (define-public discrover (package @@ -2417,7 +2417,7 @@ similarity of community members.") (define-public fasttree (package (name "fasttree") - (version "2.1.9") + (version "2.1.10") (source (origin (method url-fetch) (uri (string-append @@ -2425,7 +2425,7 @@ similarity of community members.") version ".c")) (sha256 (base32 - "0ljvvw8i1als1wbfzvrf15c3ii2vw9db20a259g6pzg34xyyb97k")))) + "0vcjdvy1j4m702vmak4svbfkrpcw63k7wymfksjp9a982zy8kjsl")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no "check" target @@ -2551,7 +2551,7 @@ Illumina, Roche 454, and the SOLiD platform.") (define-public fraggenescan (package (name "fraggenescan") - (version "1.20") + (version "1.30") (source (origin (method url-fetch) @@ -2559,7 +2559,7 @@ Illumina, Roche 454, and the SOLiD platform.") (string-append "mirror://sourceforge/fraggenescan/" "FragGeneScan" version ".tar.gz")) (sha256 - (base32 "1zzigqmvqvjyqv4945kv6nc5ah2xxm1nxgrlsnbzav3f5c0n0pyj")))) + (base32 "158dcnwczgcyhwm4qlx19sanrwgdpzf6bn2y57mbpx55lkgz1mzj")))) (build-system gnu-build-system) (arguments `(#:phases @@ -2574,6 +2574,7 @@ Illumina, Roche 454, and the SOLiD platform.") (string-append "system(\"" (which "rm"))) (("system\\(\"mv") (string-append "system(\"" (which "mv"))) + (("\\\"awk") (string-append "\"" (which "awk"))) ;; This script and other programs expect the training files ;; to be in the non-standard location bin/train/XXX. Change ;; this to be share/fraggenescan/train/XXX instead. @@ -2583,10 +2584,7 @@ Illumina, Roche 454, and the SOLiD platform.") "train/\".$FGS_train_file;"))) (substitute* "run_hmm.c" (("^ strcat\\(train_dir, \\\"train/\\\"\\);") - (string-append " strcpy(train_dir, \"" share "/train/\");"))) - (substitute* "post_process.pl" - (("^my \\$dir = substr.*") - (string-append "my $dir = \"" share "\";")))) + (string-append " strcpy(train_dir, \"" share "/train/\");")))) #t)) (replace 'build (lambda _ (and (zero? (system* "make" "clean")) @@ -2598,8 +2596,6 @@ Illumina, Roche 454, and the SOLiD platform.") (share (string-append out "/share/fraggenescan/train"))) (install-file "run_FragGeneScan.pl" bin) (install-file "FragGeneScan" bin) - (install-file "FGS_gff.py" bin) - (install-file "post_process.pl" bin) (copy-recursively "train" share)))) (delete 'check) (add-after 'install 'post-install-check @@ -2607,8 +2603,9 @@ Illumina, Roche 454, and the SOLiD platform.") ;; output files gets created. (lambda* (#:key outputs #:allow-other-keys) (let* ((out (string-append (assoc-ref outputs "out"))) - (bin (string-append out "/bin/"))) - (and (zero? (system* (string-append bin "run_FragGeneScan.pl") + (bin (string-append out "/bin/")) + (frag (string-append bin "run_FragGeneScan.pl"))) + (and (zero? (system* frag ; Test complete genome. "-genome=./example/NC_000913.fna" "-out=./test2" "-complete=1" @@ -2616,7 +2613,13 @@ Illumina, Roche 454, and the SOLiD platform.") (file-exists? "test2.faa") (file-exists? "test2.ffn") (file-exists? "test2.gff") - (file-exists? "test2.out")))))))) + (file-exists? "test2.out") + (zero? (system* ; Test incomplete sequences. + frag + "-genome=./example/NC_000913-fgs.ffn" + "-out=out" + "-complete=0" + "-train=454_30"))))))))) (inputs `(("perl" ,perl) ("python" ,python-2))) ;not compatible with python 3. @@ -2696,6 +2699,46 @@ comment or quality sections.") (supported-systems '("x86_64-linux")) (license license:expat)))) +(define-public gemma + (package + (name "gemma") + (version "0.96") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222")))) + (inputs + `(("gsl" ,gsl) + ("lapack" ,lapack) + ("zlib" ,zlib))) + (build-system gnu-build-system) + (arguments + `(#:make-flags '("FORCE_DYNAMIC=1") ; use shared libs + #:phases + (modify-phases %standard-phases + (delete 'configure) + (add-before 'build 'bin-mkdir + (lambda _ + (mkdir-p "bin"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file "bin/gemma" + (string-append + out "/bin")))))) + #:tests? #f)) ; no tests included yet + (home-page "https://github.com/xiangzhou/GEMMA") + (synopsis "Tool for genome-wide efficient mixed model association") + (description + "Genome-wide Efficient Mixed Model Association (GEMMA) provides a +standard linear mixed model resolver with application in genome-wide +association studies (GWAS).") + (license license:gpl3))) + (define-public grit (package (name "grit") @@ -4054,7 +4097,7 @@ partial genes, and identifies translation initiation sites.") (define-public roary (package (name "roary") - (version "3.7.0") + (version "3.8.2") (source (origin (method url-fetch) @@ -4063,7 +4106,7 @@ partial genes, and identifies translation initiation sites.") version ".tar.gz")) (sha256 (base32 - "0x2hpb3nfsc6x2nq1788w0fhqfzc7cn2dp4xwyva9m3k6xlz0m43")))) + "03dfr2cd5fp80bcr65923zpdzrasvcxl7c2vgh8373v25a1yfap7")))) (build-system perl-build-system) (arguments `(#:phases @@ -5396,18 +5439,13 @@ Cuffdiff or Ballgown programs.") (define-public taxtastic (package (name "taxtastic") - (version "0.5.7") - ;; Versions after 0.5.4 do not appear to be distributed on PyPI so we - ;; download the package from GitHub. + (version "0.6.4") (source (origin (method url-fetch) - (uri (string-append - "https://github.com/fhcrc/taxtastic/archive/v" - version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (uri (pypi-uri "taxtastic" version)) (sha256 (base32 - "1s0h5y1lds1c40jhir5585ffm6yjyn8h5aqimpgv64rhqhfv56xx")))) + "0s79z8kfl853x7l4h8ms05k31q87aw62nrchlk20w9n227j35929")))) (build-system python-build-system) (arguments `(#:python ,python-2 @@ -7904,14 +7942,14 @@ library implementing most of the pipeline's features.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "1.2.0") + (version "1.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "00jh1qklj8jb9j7mwvkfybq368h2wg9yc2cwkgb7yb9vsw72r61d")))) + "1s50diwh1j6vg3mgahh6bczvq74mfdbmwjrad4d5lh723gnc5pjg")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) |