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[bug#35792] [PATCH 2/7] gnu: Add smithwaterman.
From: |
Pierre Neidhardt |
Subject: |
[bug#35792] [PATCH 2/7] gnu: Add smithwaterman. |
Date: |
Sat, 18 May 2019 19:26:35 +0200 |
* gnu/packages/bioinformatics.scm (smithwaterman): New variable.
---
gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 244741854d..1bf33853b0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14869,3 +14869,33 @@ might be caused by ATAC-seq library prep or
sequencing. The main program,
(description "This is a C++ wrapper around the Tabix project which abstracts
some of the details of opening and jumping in tabix-indexed files.")
(license license:expat)))
+
+(define-public smithwaterman
+ ;; TODO: Upgrading smithwaterman breaks FreeBayes.
+ (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1"))
+ (package
+ (name "smithwaterman")
+ (version (string-append "0-1." (string-take commit 7)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/smithwaterman/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "smithwaterman" bin)))))))
+ (home-page "https://github.com/ekg/smithwaterman")
+ (synopsis "Implementation of the Smith-Waterman algorithm")
+ (description "Implementation of the Smith-Waterman algorithm.")
+ ;; The licensing terms are unclear:
https://github.com/ekg/smithwaterman/issues/9.
+ (license (list license:gpl2 license:expat)))))
--
2.21.0
- [bug#35792] [PATCH 0/7] Package freebayes, Pierre Neidhardt, 2019/05/18
- [bug#35792] [PATCH 1/7] gnu: Add tabixpp., Pierre Neidhardt, 2019/05/18
- [bug#35792] [PATCH 2/7] gnu: Add smithwaterman.,
Pierre Neidhardt <=
- [bug#35792] [PATCH 3/7] gnu: Add multichoose., Pierre Neidhardt, 2019/05/18
- [bug#35792] [PATCH 4/7] gnu: Add fsom., Pierre Neidhardt, 2019/05/18
- [bug#35792] [PATCH 5/7] gnu: Add fastahack., Pierre Neidhardt, 2019/05/18
- [bug#35792] [PATCH 7/7] gnu: Add freebayes., Pierre Neidhardt, 2019/05/18
- [bug#35792] [PATCH 6/7] gnu: Add vcflib., Pierre Neidhardt, 2019/05/18