From fc68a4593db1449bb8d55a4d8edee0a0fd05ee64 Mon Sep 17 00:00:00 2001 From: Roel Janssen Date: Mon, 4 Apr 2016 14:06:33 +0200 Subject: [PATCH] gnu: vcftools: Update to 0.1.14. * gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.14. [home-page]: Update to new homepage. --- gnu/packages/bioinformatics.scm | 29 ++++++++++++++++++----------- 1 file changed, 18 insertions(+), 11 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 250deb9..ff8d961 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3692,15 +3692,15 @@ Cuffdiff or Ballgown programs.") (define-public vcftools (package (name "vcftools") - (version "0.1.12b") + (version "0.1.14") (source (origin (method url-fetch) (uri (string-append - "mirror://sourceforge/vcftools/vcftools_" + "https://github.com/vcftools/vcftools/archive/v" version ".tar.gz")) (sha256 (base32 - "148al9h7f8g8my2qdnpax51kdd2yjrivlx6frvakf4lz5r8j88wx")))) + "1pvgv9vzlgny5h3ljcy7fl2iyn98v366kdxnxv0h36aycj20ai5s")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no "check" target @@ -3710,16 +3710,23 @@ Cuffdiff or Ballgown programs.") (string-append "MANDIR=" (assoc-ref %outputs "out") "/share/man/man1")) #:phases - (alist-cons-after - 'unpack 'patch-manpage-install - (lambda _ - (substitute* "Makefile" - (("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1"))) - (alist-delete 'configure %standard-phases)))) + (modify-phases %standard-phases + (add-after 'configure 'patch-manpage-install + (lambda _ + (substitute* "Makefile" + (("cp \\$\\{PREFIX\\}/cpp/vcftools.1") "cp ./cpp/vcftools.1")))) + (add-before 'configure 'run-autogen + (lambda _ + (zero? (system* "sh" "autogen.sh"))))))) + (native-inputs + `(("autoconf" ,(autoconf-wrapper)) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) (inputs `(("perl" ,perl) ("zlib" ,zlib))) - (home-page "http://vcftools.sourceforge.net/") + (home-page "https://vcftools.github.io/") (synopsis "Tools for working with VCF files") (description "VCFtools is a program package designed for working with VCF files, such @@ -3727,7 +3734,7 @@ as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.") ;; The license is declared as LGPLv3 in the README and - ;; at http://vcftools.sourceforge.net/license.html + ;; at https://github.com/vcftools/vcftools/blob/master/README.md (license license:lgpl3))) (define-public vsearch -- 2.5.5