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authorStephen Diener <sediener@gentoo.org>2003-12-16 00:35:22 +0000
committerStephen Diener <sediener@gentoo.org>2003-12-16 00:35:22 +0000
commit0d24f3ac2039ff1f912ce7384a97ab255133877a (patch)
treee424664e36e55945e2bbce01a2b2641296dc0752 /app-sci
parentstable on amd64 (diff)
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New Package-
Diffstat (limited to 'app-sci')
-rw-r--r--app-sci/bioperl-pipeline/ChangeLog10
-rw-r--r--app-sci/bioperl-pipeline/Manifest4
-rw-r--r--app-sci/bioperl-pipeline/bioperl-pipeline-0.1.ebuild60
-rw-r--r--app-sci/bioperl-pipeline/files/digest-bioperl-pipeline-0.11
-rw-r--r--app-sci/bioperl-pipeline/metadata.xml6
5 files changed, 81 insertions, 0 deletions
diff --git a/app-sci/bioperl-pipeline/ChangeLog b/app-sci/bioperl-pipeline/ChangeLog
new file mode 100644
index 000000000000..ecfea3e5b956
--- /dev/null
+++ b/app-sci/bioperl-pipeline/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for app-sci/bioperl-pipeline
+# Copyright 2000-2003 Gentoo Technologies, Inc.; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/app-sci/bioperl-pipeline/ChangeLog,v 1.1 2003/12/16 00:35:07 sediener Exp $
+
+*bioperl-pipeline-0.1 (15 Dec 2003)
+
+ 15 Dec 2003; Stephen Diener <sediener@gentoo.org>
+ bioperl-pipeline-0.1.ebuild:
+ New ebuild -- initial release
+
diff --git a/app-sci/bioperl-pipeline/Manifest b/app-sci/bioperl-pipeline/Manifest
new file mode 100644
index 000000000000..639146b0a9ea
--- /dev/null
+++ b/app-sci/bioperl-pipeline/Manifest
@@ -0,0 +1,4 @@
+MD5 5bd5f9a6fe13ddfede72c3b2f3bf4cf4 bioperl-pipeline-0.1.ebuild 1636
+MD5 d91ccb7494c6cf5f6f440e733da2c241 ChangeLog 385
+MD5 e8b4df3df76800c376905734d8043cfa metadata.xml 216
+MD5 cea8881ae00a651493915c7732732233 files/digest-bioperl-pipeline-0.1 72
diff --git a/app-sci/bioperl-pipeline/bioperl-pipeline-0.1.ebuild b/app-sci/bioperl-pipeline/bioperl-pipeline-0.1.ebuild
new file mode 100644
index 000000000000..a267c7ebacbf
--- /dev/null
+++ b/app-sci/bioperl-pipeline/bioperl-pipeline-0.1.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2003 Gentoo Technologies, Inc.
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/app-sci/bioperl-pipeline/bioperl-pipeline-0.1.ebuild,v 1.1 2003/12/16 00:35:07 sediener Exp $
+
+inherit perl-module
+CATEGORY="app-sci"
+
+DESCRIPTION="Collection of tools for bioinformatics, genomics and life science research : Biopipe "
+HOMEPAGE="http://www.biopipe.org/"
+SRC_URI="mirror://gentoo/$P.tar.gz"
+
+LICENSE="Artistic GPL-2"
+SLOT="0"
+KEYWORDS="~x86"
+IUSE=""
+
+RDEPEND="
+ dev-db/mysql
+ >=app-sci/bioperl-1.2.3
+ >=app-sci/bioperl-run-1.2.2
+ dev-perl/XML-SimpleObject
+ dev-perl/XML-Parser
+ dev-perl/Data-ShowTable"
+
+DEPEND="${RDEPEND}"
+
+src_unpack() {
+ unpack ${A}
+ cd ${S}
+}
+
+src_compile() {
+ # there's a test to run for BioGFFDB if using mysql
+ perl-module_src_compile || die "compile failed"
+ # make test
+ ## perl-module_src_test || die "src test failed"
+ # tests will fail unless mysq root user has no password
+}
+
+src_install() {
+ mydoc="AUTHORS README LICENSE INSTALL FAQ database_schema.doc database_tables.txt"
+ perl-module_src_install
+
+ # bioperl scripts and examples
+ einfo "Adding bioperl-pipeline scripts, sql and xml directories to /usr/share/${PF}..."
+ dodir /usr/share/${PF}/scripts
+ cd ${S}/scripts/
+ tar cf - ./ | ( cd ${D}/usr/share/${PF}/scripts; tar xf -)
+ dodir /usr/share/${PF}/sql
+ cd ${S}/sql/
+ tar cf - ./ | ( cd ${D}/usr/share/${PF}/sql; tar xf -)
+ dodir /usr/share/${PF}/xml
+ cd ${S}/xml/
+ tar cf - ./ | ( cd ${D}/usr/share/${PF}/xml; tar xf -)
+ dodir /usr/share/doc/${PF}/
+ cd ${S}/doc/
+ tar cf - ./ | ( cd ${D}/usr/share/doc/${PF}; tar xf -)
+ cd ${S}
+
+}
diff --git a/app-sci/bioperl-pipeline/files/digest-bioperl-pipeline-0.1 b/app-sci/bioperl-pipeline/files/digest-bioperl-pipeline-0.1
new file mode 100644
index 000000000000..a489d75fab99
--- /dev/null
+++ b/app-sci/bioperl-pipeline/files/digest-bioperl-pipeline-0.1
@@ -0,0 +1 @@
+MD5 91cd12769a4e22889a2c508c290a8965 bioperl-pipeline-0.1.tar.gz 633893
diff --git a/app-sci/bioperl-pipeline/metadata.xml b/app-sci/bioperl-pipeline/metadata.xml
new file mode 100644
index 000000000000..8a4bcd47220d
--- /dev/null
+++ b/app-sci/bioperl-pipeline/metadata.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci</herd>
+<maintainer><email>sediener@gentoo.org</email></maintainer>
+</pkgmetadata>