diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 85 |
1 files changed, 77 insertions, 8 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d404ff839c..6a90aa9456 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1482,7 +1482,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.8.1") + (version "0.8.5") (source (origin (method url-fetch) (uri (string-append @@ -1491,7 +1491,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1dqancz32c2l7w1b2vkvh5zqa2jnf99j1c41djnx1l8pxn044zdc")))) + "18zx8k3axnsrg016kikl8xs1ifnjmj36dk1sv3fq1jgpg9j9584b")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -2670,10 +2670,10 @@ the phenotype as it models the data.") (license license:asl2.0))) (define-public pbtranscript-tofu - (let ((commit "8f5467fe6")) + (let ((commit "8f5467fe6a4472bcfb4226c8720993c8507adfe4")) (package (name "pbtranscript-tofu") - (version (string-append "2.2.3." commit)) + (version (string-append "2.2.3." (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference @@ -3009,7 +3009,7 @@ viewer.") (delete 'configure)))))))) (define-public mosaik - (let ((commit "5c25216d")) + (let ((commit "5c25216d3522d6a33e53875cd76a6d65001e4e67")) (package (name "mosaik") (version "2.2.30") @@ -3259,10 +3259,10 @@ subsequent visualization, annotation and storage of results.") (define-public smithlab-cpp (let ((revision "1") - (commit "728a097")) + (commit "728a097bec88c6f4b8528b685932049e660eff2e")) (package (name "smithlab-cpp") - (version (string-append "0." revision "." commit)) + (version (string-append "0." revision "." (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference @@ -3885,6 +3885,47 @@ Needleman-Wunsch).") ;; Dual licensed; also includes public domain source. (license (list license:gpl3 license:bsd-2)))) +(define-public pardre + (package + (name "pardre") + (version "1.1.5") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel" + version ".tar.gz")) + (sha256 + (base32 + "0zkyjzv4s8q2h5npalhirbk17r5b1h0n2a42mh7njzlf047h9bhy")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no tests included + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (mkdir-p bin) + (install-file "ParDRe" bin) + #t)))))) + (inputs + `(("openmpi" ,openmpi) + ("zlib" ,zlib))) + (synopsis "Parallel tool to remove duplicate DNA reads") + (description + "ParDRe is a parallel tool to remove duplicate genetic sequence reads. +Duplicate reads can be seen as identical or nearly identical sequences with +some mismatches. This tool lets users avoid the analysis of unnecessary +reads, reducing the time of subsequent procedures with the +dataset (e.g. assemblies, mappings, etc.). The tool is implemented with MPI +in order to exploit the parallel capabilities of multicore clusters. It is +faster than multithreaded counterparts (end of 2015) for the same number of +cores and, thanks to the message-passing technology, it can be executed on +clusters.") + (home-page "https://sourceforge.net/projects/pardre/") + (license license:gpl3+))) + (define-public bio-locus (package (name "bio-locus") @@ -4735,6 +4776,34 @@ genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, it can use BAM or BigWig files as input.") (license license:artistic2.0))) +(define-public r-genomationdata + (package + (name "r-genomationdata") + (version "1.4.0") + (source (origin + (method url-fetch) + ;; We cannot use bioconductor-uri here because this tarball is + ;; located under "data/annotation/" instead of "bioc/". + (uri (string-append "https://bioconductor.org/packages/" + "release/data/experiment/src/contrib/" + "genomationData_" version ".tar.gz")) + (sha256 + (base32 + "1xzq2j722d8lcn5bc3aq3yb34xwis2d0bpsf6jsq4xw1bg0bsy79")))) + (build-system r-build-system) + ;; As this package provides little more than large data files, it doesn't + ;; make sense to build substitutes. + (arguments `(#:substitutable? #f)) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "http://bioinformatics.mdc-berlin.de/genomation/") + (synopsis "Experimental data for use with the genomation package") + (description + "This package contains experimental genetic data for use with the +genomation package. Included are Chip Seq, Methylation and Cage data, +downloaded from Encode.") + (license license:gpl3+))) + (define-public r-org-hs-eg-db (package (name "r-org-hs-eg-db") @@ -5100,7 +5169,7 @@ libraries for systems that do not have these available via other means.") ("samtools" ,samtools-0.1) ("gsl" ,gsl) ("smithlab-cpp" - ,(let ((commit "3723e2d")) + ,(let ((commit "3723e2db438c51501d0423429ff396c3035ba46a")) (origin (method git-fetch) (uri (git-reference |