[bug#35792,1/7] gnu: Add tabixpp.
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Message ID 20190518172640.7165-1-mail@ambrevar.xyz
State New
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  • Package freebayes
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cbaines/applying patch success Successfully applied

Commit Message

Pierre Neidhardt May 18, 2019, 5:26 p.m. UTC
* gnu/packages/bioinformatics.scm (tabixpp): New variable.
---
 gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

Patch
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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)))