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[bug#35792] [PATCH 1/7] gnu: Add tabixpp.
From: |
Pierre Neidhardt |
Subject: |
[bug#35792] [PATCH 1/7] gnu: Add tabixpp. |
Date: |
Sat, 18 May 2019 19:26:34 +0200 |
* gnu/packages/bioinformatics.scm (tabixpp): New variable.
---
gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 37f2001ea3..244741854d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14830,3 +14830,42 @@ ATAC-seq results. It was written to make it easier to
spot differences that
might be caused by ATAC-seq library prep or sequencing. The main program,
@code{ataqv}, examines aligned reads and reports some basic metrics.")
(license license:gpl3+)))
+
+(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)))))))
+ (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)))
--
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 <=
- [bug#35792] [PATCH 2/7] gnu: Add smithwaterman., Pierre Neidhardt, 2019/05/18
- [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