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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/cutg
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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/cutg')
-rw-r--r--sci-biology/cutg/Manifest1
-rw-r--r--sci-biology/cutg/cutg-160-r1.ebuild50
-rw-r--r--sci-biology/cutg/metadata.xml12
3 files changed, 63 insertions, 0 deletions
diff --git a/sci-biology/cutg/Manifest b/sci-biology/cutg/Manifest
new file mode 100644
index 000000000000..5c0e901d9aba
--- /dev/null
+++ b/sci-biology/cutg/Manifest
@@ -0,0 +1 @@
+DIST cutg-160.tar.xz 178015420 SHA256 faa2e5e4417e5cadd67bfff0c011f2f3e2e0c5d8b324fc441f9346808f6ed1fa SHA512 9b72283f311fb805b7b22f59f3ca8fed2ab0af72b82247900922999792c1b112dcaca9b29b265a1e0e7b9eaf9ff846a1dc4c196fb95ddbfb3ee5175755ffb8e7 WHIRLPOOL 540f9ba9f2f69718688531c85729c567cd6ba260f12d23b5f3c00d9689da93aefab588fe3dd926defacf4a21982406055ebee413e39ce53a2916e5e571037e93
diff --git a/sci-biology/cutg/cutg-160-r1.ebuild b/sci-biology/cutg/cutg-160-r1.ebuild
new file mode 100644
index 000000000000..46163bc2a80f
--- /dev/null
+++ b/sci-biology/cutg/cutg-160-r1.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Codon usage tables calculated from GenBank"
+HOMEPAGE="http://www.kazusa.or.jp/codon/"
+SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+
+SLOT="0"
+LICENSE="public-domain"
+# Minimal build keeps only the indexed files (if applicable) and the
+# documentation. The non-indexed database is not installed.
+IUSE="emboss minimal"
+KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="emboss? ( sci-biology/emboss )"
+RDEPEND="${DEPEND}"
+
+RESTRICT="binchecks strip"
+
+src_compile() {
+ if use emboss; then
+ mkdir CODONS || die
+ ebegin "Indexing CUTG for usage with EMBOSS."
+ EMBOSS_DATA="." cutgextract -auto -directory "${S}" || die \
+ "Indexing CUTG failed."
+ eend
+ fi
+}
+
+src_install() {
+ local file
+ dodoc README CODON_LABEL SPSUM_LABEL
+ if ! use minimal; then
+ dodir /usr/share/${PN}
+ mv *.codon *.spsum "${ED}"/usr/share/${PN} || die \
+ "Installing raw CUTG database failed."
+ fi
+
+ if use emboss; then
+ dodir /usr/share/EMBOSS/data/CODONS
+ cd CODONS || die
+ for file in *; do
+ mv ${file} "${ED}"/usr/share/EMBOSS/data/CODONS/ || die \
+ "Installing the EMBOSS-indexed database failed."
+ done
+ fi
+}
diff --git a/sci-biology/cutg/metadata.xml b/sci-biology/cutg/metadata.xml
new file mode 100644
index 000000000000..59b110912ca6
--- /dev/null
+++ b/sci-biology/cutg/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <longdescription>
+ Codon usage tables maintained at the Kazusa DNA Research Institute.
+ Codon usage in individual genes has been calculated using the
+ nucleotide sequence data obtained from the GenBank Genetic Sequence
+ Database. The compilation of codon usage is synchronized with each
+ major release of GenBank.
+ </longdescription>
+</pkgmetadata>