Merge branch 'master' of https://github.com/genenetwork/guix-bioinformatics

1 files changed, 1 insertions, 51 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 1f6052e..68095e9 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -78,7 +78,7 @@
     (propagated-inputs
      `(("python" ,python-2)
        ("r" ,r)
-       ("r-dnacopy" ,r-dnacopy)
+       ;; ("r-dnacopy" ,r-dnacopy) <-- missing in Pjotr's tree
        ("bedtools" ,bedtools)
        ("samtools" ,samtools)))
     (arguments
@@ -1049,56 +1049,6 @@ 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 ""))))
-    (build-system gnu-build-system)
-    (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+)))
 
 (define-public vcflib
   (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))