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-rw-r--r--gn/packages/bioinformatics.scm51
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+)))