From 1a069a170c636751695d54c2b282a196eda773c6 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Thu, 8 Aug 2019 15:33:37 +0300
Subject: [PATCH] Revert "gnu: Add vcflib."

This reverts commit 194e45f90addf5f9bd3e7e2de1dd50b3071f053b.

This commit does not have a good commit message, and it breaks master
---
 gnu/packages/bioinformatics.scm | 105 --------------------------------
 1 file changed, 105 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7808976a1f..4dae22082d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14868,24 +14868,6 @@ (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"))
@@ -15013,90 +14995,3 @@ (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))))