conflict resolved

1 files changed, 90 insertions, 0 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index af5cfba..1d65b4c 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -419,6 +419,45 @@ association studies (GWAS).")
     (description "Genenetwork installation sumo.")
     (license license:agpl3+))))
 
+(define-public rdmd
+  (package
+    (name "rdmd")
+    (version "20160217")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/D-Programming-Language/tools.git")
+                    (commit "4dba6877c481c1a911a7d50714da8fbd80022f0e")))
+              (file-name (string-append name "-" version "-checkout"))
+              (sha256
+               (base32
+                "1pcx5lyqzrip86f4vv60x292rpvnwsq2hvl1znm9x9rn68f34m45"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'check)
+         (replace
+          'build
+          (lambda* _
+            (zero? (system* "ldc2" "rdmd.d"))))
+         (replace
+          'install
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+              (mkdir-p bin)
+              (copy-file "rdmd" (string-append bin "/rdmd"))))))))
+    (native-inputs
+     `(("gcc" ,gcc)
+       ("ldc" ,ldc)))
+    (home-page "https://github.com/D-Programming-Language/tools/")
+    (synopsis "Extra tools for building D programs")
+    (description
+     "This repository hosts various tools redistributed with DMD or used
+internally during various build tasks.")
+    (license license:boost1.0)))
+
 (define-public sambamba
   (package
     (name "sambamba")
@@ -444,6 +483,7 @@ association studies (GWAS).")
        ;;("phobos2-ldc" ,phobos2-ldc)
        ("lz4" ,lz4)
        ("gcc" ,gcc)
+       ("rdmd" ,rdmd)
        ("htslib-src"
         ,(origin
            (method url-fetch)
@@ -492,3 +532,53 @@ 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+)))