02/02: gnu: Add samblaster.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit 8205534569cb2a09d53b7c925a349cd7f4e3599d
Author: Ricardo Wurmus <address@hidden>
Date:   Fri Sep 6 15:00:16 2019 +0200

    gnu: Add samblaster.
    
    * gnu/packages/bioinformatics.scm (samblaster): New variable.
---
 gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f98f10a..cf2dc57 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15232,3 +15232,37 @@ indels (insertions and deletions), MNPs 
(multi-nucleotide polymorphisms), and
 complex events (composite insertion and substitution events) smaller than the
 length of a short-read sequencing alignment.")
       (license license:expat))))
+
+(define-public samblaster
+  (package
+    (name "samblaster")
+    (version "0.1.24")
+    (source (origin
+      (method git-fetch)
+      (uri (git-reference
+            (url "https://github.com/GregoryFaust/samblaster.git";)
+            (commit (string-append "v." version))))
+      (file-name (git-file-name name version))
+      (sha256
+       (base32
+        "0iv2ddfw8363vb2x8gr3p8g88whb6mb9m0pf71i2cqsbv6jghap7"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; there are none
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure) ; There is no configure phase.
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (install-file "samblaster"
+                           (string-append (assoc-ref outputs "out") "/bin"))
+             #t)))))
+    (home-page "https://github.com/GregoryFaust/samblaster";)
+    (synopsis "Mark duplicates in paired-end SAM files")
+    (description "Samblaster is a fast and flexible program for marking
+duplicates in read-id grouped paired-end SAM files.  It can also optionally
+output discordant read pairs and/or split read mappings to separate SAM files,
+and/or unmapped/clipped reads to a separate FASTQ file. When marking
+duplicates, samblaster will require approximately 20MB of memory per 1M read
+pairs.")
+    (license license:expat)))