diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 51 |
1 files changed, 1 insertions, 50 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 75b9de7..af5cfba 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -26,6 +26,7 @@ #:use-module (gnu packages graphviz) #:use-module (gnu packages java) #:use-module (gnu packages linux) + #:use-module (gnu packages ldc) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages ncurses) @@ -34,7 +35,6 @@ #:use-module (gnu packages popt) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) - #:use-module (gnu packages ruby) #:use-module (gnu packages statistics) #:use-module (gnu packages tbb) #:use-module (gnu packages textutils) @@ -492,52 +492,3 @@ subset of samtools functionality, including view, index, sort, markdup, and depth.") (license license:gpl2+))) -(define-public picard - (package - (name "picard") - (version "2.1.0") - (source - (origin - (method url-fetch) - (uri (string-append - "https://github.com/broadinstitute/picard/archive/" - version ".tar.gz")) - (sha256 - (base32 "")))) - (home-page "http://broadinstitute.github.io/picard/") - (synopsis "A set of Java command line tools for manipulating high-throughput -sequencing data (HTS) data and formats") - (description "Picard comprises Java-based command-line utilities that -manipulate SAM files, and a Java API (HTSJDK) for creating new programs that -read and write SAM files. Both SAM text format and SAM binary (BAM) format are -supported.") - ;; The license is MIT. - (license license:expat) -)) - -(define-public fastqc - (package - (name "fastqc") - (version "0.11.4") - (source - (origin - (method url-fetch) - (uri (string-append - "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v" - version "_source.zip")) - (sha256 - (base32 "")))) - (build-system gnu-build-system) - (arguments - `(("perl" ,perl) ; Needed to run the java command. - ("jdk" ,icedtea "jdk"))) - (native-inputs - `(("ant" ,ant) ; TODO: Most Java packages need Ant, but in this case, IDK.. - ("jdk" ,icedtea "jdk") - ;;("htsjdk" ,htsjdk) ; It is based on htsjdk, but it ships its own copy. - ("unzip" ,unzip))) - (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/") - (synopsis "A quality control tool for high throughput sequence data") - (description - "FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.") - (license license:gpl3+))) |