From 194e45f90addf5f9bd3e7e2de1dd50b3071f053b Mon Sep 17 00:00:00 2001
From: Pierre Neidhardt <mail@ambrevar.xyz>
Date: Sat, 18 May 2019 19:26:39 +0200
Subject: gnu: Add vcflib.

* gnu/packages/bioinformatics.scm (vcflib): New variable.
---
 gnu/packages/bioinformatics.scm | 105 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 105 insertions(+)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4dae22082d..7808976a1f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14868,6 +14868,24 @@ (define-public tabixpp
 some of the details of opening and jumping in tabix-indexed files.")
    (license license:expat)))
 
+(define tabixpp-freebayes
+  ;; This version works with FreeBayes while the released
+  ;; version doesn't. The released creates a variable with the name \"vcf\"
+  ;; somewhere, which is also the name of a namespace in vcflib.
+  (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7"))
+    (package
+      (inherit tabixpp)
+      (name "tabixpp-freebayes")
+      (version (git-version "0.0.0" "1" commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/ekg/tabixpp/")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32 "017qsmsc2kyiyzqr9nl8cc6pfldxf16dbn8flx5i59mbqr9ydi7g")))))))
+
 (define-public smithwaterman
   ;; TODO: Upgrading smithwaterman breaks FreeBayes.
   (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1"))
@@ -14995,3 +15013,90 @@ (define-public fastahack
 which would benefit from directly reading subsequences from FASTA files.  The
 library automatically handles index file generation and use.")
       (license (list license:expat license:gpl2)))))
+
+(define-public vcflib
+  (let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92")
+        (revision "1"))
+      (name "vcflib")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/vcflib/vcflib/")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1gijvcz1lcdn5kvgzb671l6iby0379qk00nqmcrszgk67hfwx6kq"))))
+      (build-system gnu-build-system)
+      (inputs
+       `(("zlib" ,zlib)))
+      (native-inputs
+       `(("perl" ,perl)
+         ("python" ,python-2)
+         ;; Submodules.
+         ;; This package builds against the .o files so we need to extract the source.
+         ("tabixpp-src" ,(package-source tabixpp-freebayes))
+         ("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))
+         ("intervaltree-src"
+          ,(origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/ekg/intervaltree/")
+                   (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
+             (file-name "intervaltree-src-checkout")
+             (sha256
+              (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))))
+      (arguments
+       `(#:tests? #f ; no tests
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (delete 'check)
+           (add-after 'unpack 'unpack-submodule-sources
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((unpack (lambda (source target)
+                               (with-directory-excursion target
+                                 (if (file-is-directory? (assoc-ref inputs source))
+                                     (copy-recursively (assoc-ref inputs source) ".")
+                                     (invoke "tar" "xvf"
+                                             (assoc-ref inputs source)
+                                             "--strip-components=1"))))))
+                 (and
+                  (unpack "intervaltree-src" "intervaltree")
+                  (unpack "fastahack-src" "fastahack")
+                  (unpack "filevercmp-src" "filevercmp")
+                  (unpack "fsom-src" "fsom")
+                  (unpack "multichoose-src" "multichoose")
+                  (unpack "smithwaterman-src" "smithwaterman")
+                  (unpack "tabixpp-src" "tabixpp")))))
+           (replace 'build
+             (lambda* (#:key inputs make-flags #:allow-other-keys)
+               (with-directory-excursion "tabixpp"
+                 (invoke "make"))
+               (invoke "make" "CC=gcc"
+                       (string-append "CFLAGS=\"" "-Itabixpp " "\"")
+                       "all")))
+           (replace 'install
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+                     (lib (string-append (assoc-ref outputs "out") "/lib")))
+                 (for-each (lambda (file)
+                             (install-file file bin))
+                           (find-files "bin" ".*"))
+                 ;; The header files in src/ do not interface libvcflib,
+                 ;; therefore they are left out.
+                 (install-file "libvcflib.a" lib))
+               #t)))))
+      (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))))
-- 
cgit v1.2.3