From 1574a0e0478e921905a2fad4ff3ff0f2c196b6f1 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sun, 21 Feb 2016 08:01:25 +0000
Subject: Removed non-compiling packages

---
 gn/packages/bioinformatics.scm | 51 +-----------------------------------------
 1 file changed, 1 insertion(+), 50 deletions(-)

(limited to 'gn')

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+)))
-- 
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