* [gentoo-commits] proj/sci:master commit in: sci-biology/tigr-closure/
@ 2015-01-07 22:14 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2015-01-07 22:14 UTC (permalink / raw
To: gentoo-commits
commit: f7194dde6bb1e013487400d22fa0a663ca909338
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 7 22:13:13 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 7 22:13:13 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f7194dde
Initial ebuild
---
sci-biology/tigr-closure/ChangeLog | 10 ++++
sci-biology/tigr-closure/metadata.xml | 9 +++
.../tigr-closure/tigr-closure-20080106.ebuild | 68 ++++++++++++++++++++++
3 files changed, 87 insertions(+)
diff --git a/sci-biology/tigr-closure/ChangeLog b/sci-biology/tigr-closure/ChangeLog
new file mode 100644
index 0000000..eba3b60
--- /dev/null
+++ b/sci-biology/tigr-closure/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/tigr-closure
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*tigr-closure-20080106 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +tigr-closure-20080106.ebuild, +metadata.xml:
+ initial ebuild
+
diff --git a/sci-biology/tigr-closure/metadata.xml b/sci-biology/tigr-closure/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/tigr-closure/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>
diff --git a/sci-biology/tigr-closure/tigr-closure-20080106.ebuild b/sci-biology/tigr-closure/tigr-closure-20080106.ebuild
new file mode 100644
index 0000000..068dde9
--- /dev/null
+++ b/sci-biology/tigr-closure/tigr-closure-20080106.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+DESCRIPTION="TIGR closure tools for the assembly/finishing stage of DNA sequencing projects"
+HOMEPAGE="http://tigr-closure.sourceforge.net/"
+# http://tigr-closure.svn.sourceforge.net/tigr-closure/
+SRC_URI="tigr-closure-svn-20080106.tar.gz"
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-lang/perl"
+RDEPEND=""
+
+src_compile() {
+ cd TIGR
+ # install the two *.pm files into our perl path?
+ cd ..
+
+ # Closure Work Order Processing (CWP - CLOVER)
+ # clover and oats
+ cd ${WORKDIR}/CWPSystem/trunk/
+ # needs TIGR/EUIDService.pm in PERL paths
+ make dist
+ # how to install the files from install/ ?
+ cd ../..
+
+ #
+ cd ScaffoldMgmt/trunk
+ make dist
+ # FIXME: unpack the .tar file into image during src_install()
+ cd ../..
+
+ # awfull
+ cd ClosureQC/trunk/
+ mkdir sandbox
+ ${SANDBOX}=${WORKDIR}/sandbox
+ # have ./src/, ./doc, ./install, ./test/work/drivers, ./test/work/getqc, ./test/tmp
+ cd test
+ # ...
+ cd ../../..
+
+ #
+ cd ClosureReactionSystem/trunk
+ make BUILD=true
+ cd ../..
+
+ # some Java servlet?
+ cd AserverConsoleEJB3Hibernate
+ # huh?
+ cd ../..
+}
+
+src_install() {
+ cd ${WORKDIR}/SequenceTiling
+ dobin trunk/src/*.pl
+ cd trunk/src/TIGR/SequenceTiling/
+ myinst="DESTDIR=${D}"
+ perl-module_src_install
+ #
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/tigr-closure/
@ 2015-01-10 13:35 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2015-01-10 13:35 UTC (permalink / raw
To: gentoo-commits
commit: cd6e016859ba3b052f662bfc482ebdac830c38a9
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 12:41:42 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 12:41:42 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cd6e0168
sci-biology/tigr-closure: Some QA, add license
Package-Manager: portage-2.2.15
---
sci-biology/tigr-closure/ChangeLog | 3 ++
.../tigr-closure/tigr-closure-20080106.ebuild | 47 ++++++++++------------
2 files changed, 25 insertions(+), 25 deletions(-)
diff --git a/sci-biology/tigr-closure/ChangeLog b/sci-biology/tigr-closure/ChangeLog
index eba3b60..a4bebc8 100644
--- a/sci-biology/tigr-closure/ChangeLog
+++ b/sci-biology/tigr-closure/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 10 Jan 2015; Justin Lecher <jlec@gentoo.org> tigr-closure-20080106.ebuild:
+ Some QA, add license
+
*tigr-closure-20080106 (07 Jan 2015)
07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/tigr-closure/tigr-closure-20080106.ebuild b/sci-biology/tigr-closure/tigr-closure-20080106.ebuild
index 068dde9..f06be63 100644
--- a/sci-biology/tigr-closure/tigr-closure-20080106.ebuild
+++ b/sci-biology/tigr-closure/tigr-closure-20080106.ebuild
@@ -11,7 +11,7 @@ HOMEPAGE="http://tigr-closure.sourceforge.net/"
# http://tigr-closure.svn.sourceforge.net/tigr-closure/
SRC_URI="tigr-closure-svn-20080106.tar.gz"
-LICENSE=""
+LICENSE="all-rights-reserved"
SLOT="0"
KEYWORDS=""
IUSE=""
@@ -20,48 +20,45 @@ DEPEND="dev-lang/perl"
RDEPEND=""
src_compile() {
- cd TIGR
- # install the two *.pm files into our perl path?
- cd ..
# Closure Work Order Processing (CWP - CLOVER)
# clover and oats
- cd ${WORKDIR}/CWPSystem/trunk/
+ cd "${WORKDIR}"/CWPSystem/trunk/ || die
# needs TIGR/EUIDService.pm in PERL paths
- make dist
+ emake dist
# how to install the files from install/ ?
- cd ../..
-
- #
- cd ScaffoldMgmt/trunk
- make dist
+ cd ../.. || die
+
+ #
+ cd ScaffoldMgmt/trunk || die
+ emake dist
# FIXME: unpack the .tar file into image during src_install()
- cd ../..
+ cd ../.. || die
# awfull
- cd ClosureQC/trunk/
- mkdir sandbox
- ${SANDBOX}=${WORKDIR}/sandbox
+ cd ClosureQC/trunk/ || die
+ mkdir sandbox || die
+ ${SANDBOX}="${WORKDIR}"/sandbox
# have ./src/, ./doc, ./install, ./test/work/drivers, ./test/work/getqc, ./test/tmp
- cd test
+ cd test || die
# ...
- cd ../../..
+ cd ../../.. || die
- #
- cd ClosureReactionSystem/trunk
- make BUILD=true
- cd ../..
+ #
+ cd ClosureReactionSystem/trunk || die
+ emake BUILD=true
+ cd ../.. || die
# some Java servlet?
- cd AserverConsoleEJB3Hibernate
+ cd AserverConsoleEJB3Hibernate || die
# huh?
- cd ../..
+ cd ../.. || die
}
src_install() {
- cd ${WORKDIR}/SequenceTiling
+ cd "${WORKDIR}"/SequenceTiling || die
dobin trunk/src/*.pl
- cd trunk/src/TIGR/SequenceTiling/
+ cd trunk/src/TIGR/SequenceTiling/ || die
myinst="DESTDIR=${D}"
perl-module_src_install
#
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/tigr-closure/
@ 2015-09-21 14:04 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2015-09-21 14:04 UTC (permalink / raw
To: gentoo-commits
commit: 6d8df48b8581b1c92254ef9e80fa94f6445a1932
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 13:52:53 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 13:52:53 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6d8df48b
Drop obsolete package Sources unavailable
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/tigr-closure/ChangeLog | 13 -----
sci-biology/tigr-closure/metadata.xml | 9 ---
.../tigr-closure/tigr-closure-20080106.ebuild | 65 ----------------------
3 files changed, 87 deletions(-)
diff --git a/sci-biology/tigr-closure/ChangeLog b/sci-biology/tigr-closure/ChangeLog
deleted file mode 100644
index 4f76625..0000000
--- a/sci-biology/tigr-closure/ChangeLog
+++ /dev/null
@@ -1,13 +0,0 @@
-# ChangeLog for sci-biology/tigr-closure
-# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Id$
-
- 10 Jan 2015; Justin Lecher <jlec@gentoo.org> tigr-closure-20080106.ebuild:
- Some QA, add license
-
-*tigr-closure-20080106 (07 Jan 2015)
-
- 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- +tigr-closure-20080106.ebuild, +metadata.xml:
- initial ebuild
-
diff --git a/sci-biology/tigr-closure/metadata.xml b/sci-biology/tigr-closure/metadata.xml
deleted file mode 100644
index 2bc8930..0000000
--- a/sci-biology/tigr-closure/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?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>
diff --git a/sci-biology/tigr-closure/tigr-closure-20080106.ebuild b/sci-biology/tigr-closure/tigr-closure-20080106.ebuild
deleted file mode 100644
index 3a6f422..0000000
--- a/sci-biology/tigr-closure/tigr-closure-20080106.ebuild
+++ /dev/null
@@ -1,65 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit perl-module
-
-DESCRIPTION="TIGR closure tools for the assembly/finishing stage of DNA sequencing projects"
-HOMEPAGE="http://tigr-closure.sourceforge.net/"
-# http://tigr-closure.svn.sourceforge.net/tigr-closure/
-SRC_URI="tigr-closure-svn-20080106.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-lang/perl"
-RDEPEND=""
-
-src_compile() {
-
- # Closure Work Order Processing (CWP - CLOVER)
- # clover and oats
- cd "${WORKDIR}"/CWPSystem/trunk/ || die
- # needs TIGR/EUIDService.pm in PERL paths
- emake dist
- # how to install the files from install/ ?
- cd ../.. || die
-
- #
- cd ScaffoldMgmt/trunk || die
- emake dist
- # FIXME: unpack the .tar file into image during src_install()
- cd ../.. || die
-
- # awfull
- cd ClosureQC/trunk/ || die
- mkdir sandbox || die
- ${SANDBOX}="${WORKDIR}"/sandbox
- # have ./src/, ./doc, ./install, ./test/work/drivers, ./test/work/getqc, ./test/tmp
- cd test || die
- # ...
- cd ../../.. || die
-
- #
- cd ClosureReactionSystem/trunk || die
- emake BUILD=true
- cd ../.. || die
-
- # some Java servlet?
- cd AserverConsoleEJB3Hibernate || die
- # huh?
- cd ../.. || die
-}
-
-src_install() {
- cd "${WORKDIR}"/SequenceTiling || die
- dobin trunk/src/*.pl
- cd trunk/src/TIGR/SequenceTiling/ || die
- myinst="DESTDIR=${D}"
- perl-module_src_install
- #
-}
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