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Thu, 19 Dec 2019 19:54:15 +0100 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Thu, 19 Dec 2019 19:53:31 +0100 Message-ID: <20191219185331.19702-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.24.1 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1684-8.5.1010-25114.002 X-TM-AS-Result: No-1.112600-8.000000-10 X-TMASE-MatchedRID: 6CoZXopK1tC1HHtIgGMIGNqQ6Du6Gk+zNV9S7O+u3KZy220XpoU/hHZM elkn7fiXrdoLblq9S5rt679iIQuulb4br6qTk1yGhKZybi8qfJ8OHw/yNOkRgST7BShWYMvz2gO r1UdaUdYKaIhVI7dKsI1tYtwPvjHZEfIWTKnSZvmdVNZaI2n6/+JNcHLvRNpE1l38M6aWfEgWkH qHAqxWxNQ5SJ8sqjUcmyiLZetSf8my5/tFZu9S3N9pjzubZ2rHwrbXMGDYqV99R4Ss0oUmJ1ew0 xxk05nOAOfqYdKbo4lTFFK3lDO8NwP8pLOcGT+YcuUXh08eDGBMMJnmTJZD8r5+3oOvZ31k9dtg /C2qGRlU7VSLp9mv6nMlKjd7kJW0P2nrhpzTnX4SFeEaqul3aIOFrOPMaJ4V X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.112600-8.000000 X-TMASE-Version: SMEX-12.5.0.1684-8.5.1010-25114.002 X-TM-SNTS-SMTP: A4A0794137C929B258E5BCD6CA3F2D346D56923E56CC80668816AC3A9B37C9BC2000:9 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-xyz.scm (tophat)[native-inputs]: Add gcc-5. (tophat)[inputs]: Reorder alphabetically the dependencies. (tophat)[home-page]: Swapp to https. --- gnu/packages/bioinformatics.scm | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 528b603476..0f6c120687 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2017 Arun Isaac ;;; Copyright © 2018 Joshua Sierles, Nextjournal ;;; Copyright © 2018 Gábor Boskovits -;;; Copyright © 2018 Mădălin Ionel Patrașcu +;;; Copyright © 2018, 2019 Mădălin Ionel Patrașcu ;;; Copyright © 2019 Maxim Cournoyer ;;; Copyright © 2019 Brian Leung ;;; @@ -1615,7 +1615,7 @@ genome (2.9 GB for paired-end).") #t)))) (build-system gnu-build-system) (arguments - '(#:parallel-build? #f ; not supported + '(#:parallel-build? #f ; not supported #:phases (modify-phases %standard-phases (add-after 'unpack 'use-system-samtools @@ -1639,16 +1639,18 @@ genome (2.9 GB for paired-end).") (("#include ") "#include ") (("#include ") "#include ")) #t))))) + (native-inputs + `(("gcc" ,gcc-5))) ;; doesn't build with later versions (inputs `(("boost" ,boost) ("bowtie" ,bowtie) - ("samtools" ,samtools-0.1) ("ncurses" ,ncurses) - ("python" ,python-2) ("perl" ,perl) - ("zlib" ,zlib) - ("seqan" ,seqan-1))) - (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") + ("python" ,python-2) + ("samtools" ,samtools-0.1) + ("seqan" ,seqan-1) + ("zlib" ,zlib))) + (home-page "https://ccb.jhu.edu/software/tophat/index.shtml") (synopsis "Spliced read mapper for RNA-Seq data") (description "TopHat is a fast splice junction mapper for nucleotide sequence