>From 07f041559f7f023c56c23f81ac7e90441c44f91b Mon Sep 17 00:00:00 2001
From: Roel Janssen <address@hidden>
Date: Tue, 22 Mar 2016 16:06:45 +0100
Subject: [PATCH 8/8] gnu: Add vcflib.

* gnu/packages/bioinformatics.scm (tabixpp-vcflib): New variable.
* gnu/packages/bioinformatics.scm (vcflib): New variable.
---
 gnu/packages/bioinformatics.scm | 96 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 96 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5a0eb16..34aadab 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4831,6 +4831,22 @@ group or two ChIP groups run under different conditions.")
 some of the details of opening and jumping in tabix-indexed files.")
    (license license:expat)))
 
+;; This version works with FreeBayes while the released version doesn't. The
+;; release creates a variable with the name "vcf" somewhere, which is also the
+;; name of a namespace in vcflib.
+(define-public tabixpp-vcflib
+  (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7"))
+    (package (inherit tabixpp)
+      (name "tabixpp-vcflib")
+      (version (string-append "0-1." (string-take commit 7)))
+      (source (origin
+        (method url-fetch)
+        (uri (string-append "https://github.com/ekg/tabixpp/archive/"
+                            commit ".tar.gz"))
+        (file-name (string-append name "-" version "-checkout.tar.gz"))
+        (sha256
+         (base32 "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77")))))))
+
 (define-public smithwaterman
   (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1"))
     (package
@@ -5017,4 +5033,82 @@ automatically handles index file generation and use.")
 tree using C++ templates, allowing the insertion of arbitrary types into the
 tree.")
       (license license:expat))))
+
+(define-public vcflib
+  (let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92"))
+    (package
+      (name "vcflib")
+      (version (string-append "0-1." (string-take commit 7)))
+      (source (origin
+         (method url-fetch)
+         (uri (string-append "https://github.com/vcflib/vcflib/archive/"
+                commit ".tar.gz"))
+         (file-name (string-append name "-" version ".tar.gz"))
+         (sha256
+          (base32 "0ywshwpif059z5h0g7zzrdfzzdj2gr8xvwlwcsdxrms3p9iy35h8"))))
+      (build-system gnu-build-system)
+      (inputs
+       `(("intervaltree" ,intervaltree)
+         ("htslib" ,htslib)
+         ("zlib" ,zlib)))
+      (native-inputs
+       `(("python" ,python-2)
+         ("perl" ,perl)
+         ("r" ,r)
+         ("node" ,node)
+         ("tabixpp-src" ,(package-source tabixpp-vcflib))
+         ("smithwaterman-src" ,(package-source smithwaterman))
+         ("multichoose-src" ,(package-source multichoose))
+         ("fsom-src" ,(package-source fsom))
+         ("filevercmp-src" ,(package-source filevercmp))
+         ("fastahack-src" ,(package-source fastahack))))
+      (arguments
+       `(#:tests? #f ; There are no tests to run.
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (add-after 'unpack 'unpack-submodule-sources
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((unpack (lambda (source target)
+                               (with-directory-excursion target
+                                 (zero? (system* "tar" "xvf"
+                                        (assoc-ref inputs source)
+                                        "--strip-components=1"))))))
+                 (and
+                  (unpack "fastahack-src" "fastahack")
+                  (unpack "filevercmp-src" "filevercmp")
+                  (unpack "fsom-src" "fsom")
+                  (unpack "multichoose-src" "multichoose")
+                  (unpack "smithwaterman-src" "smithwaterman")
+                  (unpack "tabixpp-src" "tabixpp")))))
+           (add-after 'unpack-submodule-sources 'fix-makefile
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* '("Makefile")
+                 (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0"))))
+           (replace 'build
+            (lambda* (#:key inputs make-flags #:allow-other-keys)
+              (with-directory-excursion "tabixpp"
+                (zero? (system* "make")))
+              (zero? (system* "make" "CC=gcc"
+                (string-append
+                  "CFLAGS=\"" "-Itabixpp "
+                  "-I" (assoc-ref inputs "htslib") "/include "
+                  "-I" (assoc-ref inputs "intervaltree") "/include "
+                  "\"") "all"))))
+           (replace 'install
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let* ((out (assoc-ref outputs "out"))
+                     (bin (string-append out "/bin"))
+                     (lib (string-append out "/lib")))
+                (for-each (lambda (file)
+                            (install-file file bin))
+                          (find-files "bin" ".*"))
+                (install-file "libvcflib.a" lib)))))))
+      (home-page "https://github.com/vcflib/vcflib/")
+      (synopsis "Library for parsing and manipulating VCF files")
+      (description "Vcflib provides methods to manipulate and interpret
+sequence variation as it can be described by VCF. It is both an API for parsing
+and operating on records of genomic variation as it can be described by the VCF
+format, and a collection of command-line utilities for executing complex
+manipulations on VCF files.")
+      (license license:expat))))
-- 
2.5.5