diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 66 |
1 files changed, 49 insertions, 17 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b3d882761b..4dd2ee6f92 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -26,6 +26,7 @@ #:use-module (guix utils) #:use-module (guix download) #:use-module (guix git-download) + #:use-module (guix build-system ant) #:use-module (guix build-system gnu) #:use-module (guix build-system cmake) #:use-module (guix build-system perl) @@ -2002,24 +2003,17 @@ from high-throughput sequencing assays.") (snippet '(substitute* "build.xml" (("failifexecutionfails=\"true\"") "failifexecutionfails=\"false\""))))) - (build-system gnu-build-system) + (build-system ant-build-system) (arguments - `(#:modules ((srfi srfi-1) - (guix build gnu-build-system) - (guix build utils)) - #:phases (alist-replace - 'build - (lambda _ - (setenv "JAVA_HOME" (assoc-ref %build-inputs "jdk")) - (zero? (system* "ant" "all" - (string-append "-Ddist=" - (assoc-ref %outputs "out") - "/share/java/htsjdk/")))) - (fold alist-delete %standard-phases - '(configure install check))))) - (native-inputs - `(("ant" ,ant) - ("jdk" ,icedtea "jdk"))) + `(#:tests? #f ; test require Internet access + #:make-flags + (list (string-append "-Ddist=" (assoc-ref %outputs "out") + "/share/java/htsjdk/")) + #:build-target "all" + #:phases + (modify-phases %standard-phases + ;; The build phase also installs the jars + (delete 'install)))) (home-page "http://samtools.github.io/htsjdk/") (synopsis "Java API for high-throughput sequencing data (HTS) formats") (description @@ -2556,6 +2550,44 @@ the phenotype as it models the data.") generated using the PacBio Iso-Seq protocol.") (license license:bsd-3)))) +(define-public pyicoteo + (package + (name "pyicoteo") + (version "2.0.7") + (source + (origin + (method url-fetch) + (uri (string-append "https://bitbucket.org/regulatorygenomicsupf/" + "pyicoteo/get/v" version ".tar.bz2")) + (file-name (string-append name "-" version ".tar.bz2")) + (sha256 + (base32 + "0d6087f29xp8wxwlj111c3sylli98n0l8ry58c51ixzq0zfm50wa")))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 ; does not work with Python 3 + #:tests? #f)) ; there are no tests + (inputs + `(("python2-matplotlib" ,python2-matplotlib))) + (home-page "https://bitbucket.org/regulatorygenomicsupf/pyicoteo") + (synopsis "Analyze high-throughput genetic sequencing data") + (description + "Pyicoteo is a suite of tools for the analysis of high-throughput genetic +sequencing data. It works with genomic coordinates. There are currently six +different command-line tools: + +@enumerate +@item pyicoregion: for generating exploratory regions automatically; +@item pyicoenrich: for differential enrichment between two conditions; +@item pyicoclip: for calling CLIP-Seq peaks without a control; +@item pyicos: for genomic coordinates manipulation; +@item pyicoller: for peak calling on punctuated ChIP-Seq; +@item pyicount: to count how many reads from N experiment files overlap in a + region file; +@item pyicotrocol: to combine operations from pyicoteo. +@end enumerate\n") + (license license:gpl3+))) + (define-public prodigal (package (name "prodigal") |