summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorRobin H. Johnson <robbat2@gentoo.org>2015-08-08 13:49:04 -0700
committerRobin H. Johnson <robbat2@gentoo.org>2015-08-08 17:38:18 -0700
commit56bd759df1d0c750a065b8c845e93d5dfa6b549d (patch)
tree3f91093cdb475e565ae857f1c5a7fd339e2d781e /sci-biology/emboss/emboss-6.6.0.ebuild
downloadgentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.gz
gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.tar.bz2
gentoo-56bd759df1d0c750a065b8c845e93d5dfa6b549d.zip
proj/gentoo: Initial commit
This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson <robbat2@gentoo.org> X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed
Diffstat (limited to 'sci-biology/emboss/emboss-6.6.0.ebuild')
-rw-r--r--sci-biology/emboss/emboss-6.6.0.ebuild61
1 files changed, 61 insertions, 0 deletions
diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild
new file mode 100644
index 00000000000..22d650f1107
--- /dev/null
+++ b/sci-biology/emboss/emboss-6.6.0.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=1
+inherit autotools-utils emboss-r1 eutils readme.gentoo
+
+DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz"
+
+KEYWORDS="~amd64 ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE+=" minimal"
+LICENSE+=" Apache-2.0 GPL-3+ CC-BY-3.0"
+
+RDEPEND+=" !sys-devel/cons"
+PDEPEND+="
+ !minimal? (
+ sci-biology/aaindex
+ sci-biology/cutg
+ sci-biology/primer3
+ sci-biology/prints
+ sci-biology/prosite
+ sci-biology/rebase
+ )"
+
+S="${WORKDIR}"/EMBOSS-${PV}
+
+DOCS=( ChangeLog AUTHORS NEWS THANKS FAQ )
+
+PATCHES=(
+ "${FILESDIR}"/${P}_fix-build-system.patch
+ "${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch
+ "${FILESDIR}"/${P}_plplot-declarations.patch
+ "${FILESDIR}"/${P}_qa-implicit-declarations.patch
+)
+
+src_install() {
+ # Use autotools-utils_* to remove useless *.la files
+ autotools-utils_src_install
+
+ readme.gentoo_create_doc
+
+ # Install env file for setting libplplot and acd files path.
+ cat > 22emboss <<- EOF
+ # ACD files location
+ EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd"
+ EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data"
+ EOF
+ doenvd 22emboss
+
+ # Remove useless dummy files
+ find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files."
+
+ # Move the provided codon files to a different directory. This will avoid
+ # user confusion and file collisions on case-insensitive file systems (see
+ # bug #115446). This change is documented in "README.gentoo".
+ mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
+ die "Failed to move CODON directory."
+}