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01/07: gnu: Add tabixpp.
From: |
guix-commits |
Subject: |
01/07: gnu: Add tabixpp. |
Date: |
Thu, 8 Aug 2019 08:19:11 -0400 (EDT) |
efraim pushed a commit to branch master
in repository guix.
commit 62a031afc438dcf2c2b38259334cb6e3b369a908
Author: Pierre Neidhardt <address@hidden>
Date: Sat May 18 19:26:34 2019 +0200
gnu: Add tabixpp.
* gnu/packages/bioinformatics.scm (tabixpp): New variable.
---
gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++
1 file changed, 40 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 991a3c6..5a63399 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14827,3 +14827,43 @@ trees by inserting random mutations. The tbsp package
implements an
alternative method to detect significant, cell type specific sequence
mutations from scRNA-Seq data.")
(license license:expat))))
+
+(define-public tabixpp
+ (package
+ (name "tabixpp")
+ (version "1.0.0")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/tabixpp")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "08vx6nsipk971cyr8z53rnzwkvlld63kcn1fw0pwddynz91xfny8"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("htslib" ,htslib)
+ ("zlib" ,zlib)))
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ ;; The build phase needs overriding the location of htslib.
+ (replace 'build
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((htslib-ref (assoc-ref inputs "htslib")))
+ (invoke "make"
+ (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
+ "HTS_HEADERS=" ; No need to check for headers here.
+ (string-append "LIBPATH=-L. -L" htslib-ref
"/include")))))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (install-file "tabix++" bin))
+ #t)))))
+ (home-page "https://github.com/ekg/tabixpp")
+ (synopsis "C++ wrapper around tabix project")
+ (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)))
- branch master updated (8378c87 -> 173e046), guix-commits, 2019/08/08
- 06/07: gnu: Add vcflib., guix-commits, 2019/08/08
- 03/07: gnu: Add multichoose., guix-commits, 2019/08/08
- 07/07: gnu: Add freebayes., guix-commits, 2019/08/08
- 05/07: gnu: Add fastahack., guix-commits, 2019/08/08
- 01/07: gnu: Add tabixpp.,
guix-commits <=
- 02/07: gnu: Add smithwaterman., guix-commits, 2019/08/08
- 04/07: gnu: Add fsom., guix-commits, 2019/08/08