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| author |   Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2011-07-30 12:33:38 +0200 |
|---|---|---|
| committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2011-07-30 12:33:38 +0200 |
| commit | 09c93bc43d5edf8bbbc90ba765d17a027ecf4132 (patch) | |
| tree | d57bb41cf374be5c85783c7b5a4cc63a63860c94 /dev-perl/Bio-BigFile | |
| parent | [sci-physics/fastjet] general QA (diff) | |
| download | sci-09c93bc43d5edf8bbbc90ba765d17a027ecf4132.tar.gz sci-09c93bc43d5edf8bbbc90ba765d17a027ecf4132.tar.bz2 sci-09c93bc43d5edf8bbbc90ba765d17a027ecf4132.zip | |
dev-perl/Bio-DB-Das-Chado: new package required by sci-biology/gbrowse
(Portage version: 2.1.10.7/git/Linux i686, unsigned Manifest commit)
Diffstat (limited to 'dev-perl/Bio-BigFile')
| -rw-r--r-- | dev-perl/Bio-BigFile/Bio-BigFile-1.06.ebuild | 27 | ||||
| -rw-r--r-- | dev-perl/Bio-BigFile/Manifest | 4 | ||||
| -rw-r--r-- | dev-perl/Bio-BigFile/files/Build.PL.patch | 40 | ||||
| -rw-r--r-- | dev-perl/Bio-BigFile/metadata.xml | 9 |
4 files changed, 80 insertions, 0 deletions
diff --git a/dev-perl/Bio-BigFile/Bio-BigFile-1.06.ebuild b/dev-perl/Bio-BigFile/Bio-BigFile-1.06.ebuild new file mode 100644 index 000000000..74d055422 --- /dev/null +++ b/dev-perl/Bio-BigFile/Bio-BigFile-1.06.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=3 + +MODULE_AUTHOR="LDS" +inherit perl-module + +DESCRIPTION="BigWig and BigBed file perl-based interface for Gbrowse-2" + +#LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND="sci-biology/ucsc-genome-browser" +DEPEND="${RDEPEND} + virtual/perl-Module-Build" + +SRC_TEST="do" + +src_prepare(){ + epatch "${FILESDIR}"/Build.PL.patch || die "Failed to patch Build.PL" +} + +CFLAGS="${CFLAGS} -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64" diff --git a/dev-perl/Bio-BigFile/Manifest b/dev-perl/Bio-BigFile/Manifest new file mode 100644 index 000000000..2f1063527 --- /dev/null +++ b/dev-perl/Bio-BigFile/Manifest @@ -0,0 +1,4 @@ +AUX Build.PL.patch 1350 RMD160 74a62e75c72cce3b11eac3df94cba4347383a884 SHA1 3eb47d1d7aeaf31efdf3d7fba1356f7e2d0b7ec2 SHA256 2f9fc8d8eb469e7b5758e306f9933a69fa4347eba6d31e43d5469cba19369429 +DIST Bio-BigFile-1.06.tar.gz 603786 RMD160 4a8e0bf325ccb93c3d4e7a1e577815f6b908ed6f SHA1 5a9fd3149847fe30703f36658693bc6cd4e30004 SHA256 15f1ece2563096a301cff533a9ac91b8fc31af7643b4c4d7fd5d4fa75d4cb5ef +EBUILD Bio-BigFile-1.06.ebuild 639 RMD160 f134d8ec7052b996749a58161d639e8c99f8611e SHA1 da1ff4de41e53e8961800c5d432aad32cc90396d SHA256 dc0ada94ec2397a2ac26a30aae09016b278ddfe9c38791372a46f12f5d5b02c1 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 diff --git a/dev-perl/Bio-BigFile/files/Build.PL.patch b/dev-perl/Bio-BigFile/files/Build.PL.patch new file mode 100644 index 000000000..b6dc709d7 --- /dev/null +++ b/dev-perl/Bio-BigFile/files/Build.PL.patch @@ -0,0 +1,40 @@ +--- Bio-BigFile-1.06/Build.PL.ori 2011-07-14 01:36:32.000000000 +0200 ++++ Bio-BigFile-1.06/Build.PL 2011-07-14 02:01:27.000000000 +0200 +@@ -47,12 +47,10 @@ + sub find_jk { + my ($jk_include,$jk_lib); + +- if (my $jksrc = $ENV{KENT_SRC}) { +- $jk_include = "$jksrc/inc" +- if -e "$jksrc/inc/$HeaderFile"; +- $jk_lib = "$jksrc/lib/$ENV{MACHTYPE}" +- if -e "$jksrc/lib/$ENV{MACHTYPE}/$LibFile"; +- } ++ $jk_include = "/usr/include/ucsc-genome-browser" ++ if -e "/usr/include/ucsc-genome-browser/$HeaderFile"; ++ $jk_lib = "/usr/lib" ++ if -e "/usr/lib/$LibFile"; + + unless ($jk_include && $jk_lib) { + print STDERR <<END; +@@ -67,15 +65,15 @@ + + END + my $prompt = "Please enter the location of Kent source tree: "; +- my $found; ++ my $found = 1; + while (!$found) { + my $path = prompt($prompt); + print STDERR "\n"; + last unless $path; +- $jk_include = "$path/inc" +- if -e "$path/inc/$HeaderFile"; +- $jk_lib = "$path/lib/$ENV{MACHTYPE}" +- if -e "$path/lib/$ENV{MACHTYPE}/$LibFile"; ++ $jk_include = "/usr/include/ucsc-genome-browser" ++ if -e "/usr/include/ucsc-genome-browser/$HeaderFile"; ++ $jk_lib = "/usr/lib" ++ if -e "/usr/lib/$LibFile"; + $found = $jk_include && $jk_lib; + unless ($found) { + print STDERR "Can't find the $HeaderFile and $LibFile files at this location.\n"; diff --git a/dev-perl/Bio-BigFile/metadata.xml b/dev-perl/Bio-BigFile/metadata.xml new file mode 100644 index 000000000..07b525505 --- /dev/null +++ b/dev-perl/Bio-BigFile/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> |