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: 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))))
--
cgit v1.2.3