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authorRicardo Wurmus <rekado@elephly.net>2024-01-23 23:47:31 +0100
committerRicardo Wurmus <rekado@elephly.net>2024-01-23 23:47:31 +0100
commitc376298c7c4d4cfcd44f4b0da71260e819959cbc (patch)
tree8828b1ca2ce45b87409ffb21494d95103259b00f
parent825b3ca76367dc9b084eaf535fd7aafc95b3c8fa (diff)
gnu: Add flash.
* gnu/packages/bioinformatics.scm (flash): New variable. Change-Id: Id657ba7850031ad24b4333b6bc79401511e00a85
-rw-r--r--gnu/packages/bioinformatics.scm37
1 files changed, 37 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a1cc041caa..2c2a69052d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6343,6 +6343,43 @@ sequences to the genome---manipulating the sequences to produce better mapping
results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
(license license:agpl3+)))
+(define-public flash
+ (package
+ (name "flash")
+ (version "1.2.11")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/flashpage/FLASH-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1b1ns9ghbcxy92xwa2a53ikqacvnyhvca0zfv0s7986xzvvscp38"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:make-flags #~(list (string-append "CC=" #$(cc-for-target)))
+ #:tests? #f ;no tests
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; No configure script
+ (delete 'configure)
+ ;; No install target
+ (replace 'install
+ (lambda _
+ (install-file "flash"
+ (string-append #$output "/bin")))))))
+ (inputs (list zlib))
+ (home-page "http://ccb.jhu.edu/software/FLASH/")
+ (synopsis "Merge paired-end nucleotide reads from NGS experiments")
+ (description "FLASH (Fast Length Adjustment of SHort reads) is a tool to
+merge paired-end reads from next-generation sequencing experiments. FLASH is
+designed to merge pairs of reads when the original DNA fragments are shorter
+than twice the length of reads. The resulting longer reads can significantly
+improve genome assemblies. They can also improve transcriptome assembly when
+FLASH is used to merge RNA-seq data.")
+ (license license:gpl3+)))
+
(define-public flexbar
(package
(name "flexbar")