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| author | Pierre Neidhardt <mail@ambrevar.xyz> | 2019-05-18 19:26:34 +0200 |
|---|---|---|
| committer | Efraim Flashner <efraim@flashner.co.il> | 2019-08-08 15:18:14 +0300 |
| commit | 62a031afc438dcf2c2b38259334cb6e3b369a908 (patch) | |
| tree | 8754c832742fa52d966dd4307c11c416ccaed82b /gnu/packages | |
| parent | 8378c87a590788921b5cb78eae4b4a53280a4d96 (diff) | |
| download | patches-62a031afc438dcf2c2b38259334cb6e3b369a908.tar patches-62a031afc438dcf2c2b38259334cb6e3b369a908.tar.gz | |
gnu: Add tabixpp.
* gnu/packages/bioinformatics.scm (tabixpp): New variable.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 40 |
1 files changed, 40 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 991a3c6487..5a63399967 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))) |