diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 40 |
1 files changed, 36 insertions, 4 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9cdc692d07..c3ba9634ba 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -51,7 +51,9 @@ #:use-module (gnu packages gawk) #:use-module (gnu packages gcc) #:use-module (gnu packages gd) + #:use-module (gnu packages gtk) #:use-module (gnu packages image) + #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) #:use-module (gnu packages linux) #:use-module (gnu packages logging) @@ -70,6 +72,7 @@ #:use-module (gnu packages ruby) #:use-module (gnu packages statistics) #:use-module (gnu packages tbb) + #:use-module (gnu packages tex) #:use-module (gnu packages textutils) #:use-module (gnu packages time) #:use-module (gnu packages tls) @@ -1603,6 +1606,33 @@ data and settings.") (license (license:non-copyleft "file://src/COPYING" "See src/COPYING in the distribution.")))) +(define-public discrover + (package + (name "discrover") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/maaskola/discrover/archive/" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k")))) + (build-system cmake-build-system) + (arguments `(#:tests? #f)) ; there are no tests + (inputs + `(("boost" ,boost) + ("cairo" ,cairo))) + (native-inputs + `(("texlive" ,texlive) + ("imagemagick" ,imagemagick))) + (home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/") + (synopsis "Discover discriminative nucleotide sequence motifs") + (description "Discrover is a motif discovery method to find binding sites +of nucleic acid binding proteins.") + (license license:gpl3+))) + (define-public eigensoft (let ((revision "1") (commit "b14d1e202e21e532536ff8004f0419cd5e259dc7")) @@ -2108,6 +2138,8 @@ basic tasks but can change to using POSIX regular expressions, PCRE, hash lookups or multi-pattern searching as required. By default fxtract looks in the sequence of each record but can also be told to look in the header, comment or quality sections.") + ;; 'util' requires SSE instructions. + (supported-systems '("x86_64-linux")) (license license:expat)))) (define-public grit @@ -4645,13 +4677,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.18.1") + (version "1.18.6") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "1jdpdnp7l81xfprba2ykfnj6i64fd84vxaax0wvrz6qahxvnjzyw")))) + "17q2b3wlv3250v6qm114srkarxykpd5rqmg4kzymmqsn1b8hynhv")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -5273,7 +5305,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") (define-public r-genomationdata (package (name "r-genomationdata") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) ;; We cannot use bioconductor-uri here because this tarball is @@ -5283,7 +5315,7 @@ genomic intervals. In addition, it can use BAM or BigWig files as input.") "genomationData_" version ".tar.gz")) (sha256 (base32 - "1xzq2j722d8lcn5bc3aq3yb34xwis2d0bpsf6jsq4xw1bg0bsy79")))) + "1zl7gg144fs7zfycsmq5492sm1bqy7l527xbc2zj04schd9wsan2")))) (build-system r-build-system) ;; As this package provides little more than large data files, it doesn't ;; make sense to build substitutes. |