* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas/
@ 2015-01-10 14:07 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2015-01-10 14:07 UTC (permalink / raw
To: gentoo-commits
commit: 3fb0e8b842288c6a03c8d9421d0a264c151ec5d4
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 13:48:03 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 13:48:03 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3fb0e8b8
sci-biology/Atlas: Fix license
Package-Manager: portage-2.2.15
---
sci-biology/Atlas/Atlas-2005.ebuild | 2 +-
sci-biology/Atlas/ChangeLog | 3 +++
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/sci-biology/Atlas/Atlas-2005.ebuild b/sci-biology/Atlas/Atlas-2005.ebuild
index 29b546d..b51c535 100644
--- a/sci-biology/Atlas/Atlas-2005.ebuild
+++ b/sci-biology/Atlas/Atlas-2005.ebuild
@@ -9,7 +9,7 @@ HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-whole-genome-assembly-suite"
SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas-src.tgz"
# https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas2005-linux.tgz
-LICENSE=""
+LICENSE="ATLAS"
SLOT="0"
KEYWORDS=""
IUSE=""
diff --git a/sci-biology/Atlas/ChangeLog b/sci-biology/Atlas/ChangeLog
index d8bcd83..3cfb2f0 100644
--- a/sci-biology/Atlas/ChangeLog
+++ b/sci-biology/Atlas/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 10 Jan 2015; Justin Lecher <jlec@gentoo.org> Atlas-2005.ebuild:
+ Fix license
+
*Atlas-2005 (07 Jan 2015)
07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +Atlas-2005.ebuild,
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas/
@ 2020-09-27 22:43 Horea Christian
0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2020-09-27 22:43 UTC (permalink / raw
To: gentoo-commits
commit: ae508e533a7c8d143dbee04f123f5e71b94c6b4a
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 22:34:55 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 22:43:20 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ae508e53
sci-biology/Atlas: removed discontinued package
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/Atlas/Atlas-2005.ebuild | 40 -------------------------------------
sci-biology/Atlas/metadata.xml | 12 -----------
2 files changed, 52 deletions(-)
diff --git a/sci-biology/Atlas/Atlas-2005.ebuild b/sci-biology/Atlas/Atlas-2005.ebuild
deleted file mode 100644
index cfe09e0f7..000000000
--- a/sci-biology/Atlas/Atlas-2005.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION="Atlas Whole Genome Assembly Suite"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-whole-genome-assembly-suite"
-SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas-src.tgz"
-# https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas2005-linux.tgz
-
-LICENSE="ATLAS"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-libs/boost"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/atlas-src/CBT
-
-src_prepare(){
- sed -e "s/^CC = .*/CC = $(tc-getCC)/" -e "s/^GCC = .*/GCC = $(tc-getCXX)/" -i Makefile || die
- sed -e "s/^CC = .*/CC = $(tc-getCC)/" -e "s/^GCC = .*/GCC = $(tc-getCXX)/" -i ../CBTApps/Makefile.in || die
- sed -e "s@^# CBT_DEVEL_USER = .*@CBT_DEVEL_USER = ${EPREFIX}/@" -i Makefile || die
- sed -e "s@^# CBT_DEVEL_USER = .*@CBT_DEVEL_USER = ${EPREFIX}/@" -i Makefile.in || die
- sed -e "s#^CBT_INSTALL_LIB = /home/hgsc/lib/#CBT_INSTALL_LIB = ${EPREFIX}/usr/lib/#" -i Makefile || die
- sed -e "s#^CBT_INSTALL_LIB = /home/hgsc/lib/#CBT_INSTALL_LIB = ${EPREFIX}/usr/lib/#" -i Makefile.in || die
- sed -e "s#^BOOST_DIR = .*#BOOST_DIR = ${EPREFIX}/usr/lib/#" -i Makefile || die
- sed -e "s#^BOOST_DIR = .*#BOOST_DIR = ${EPREFIX}/usr/lib/#" -i Makefile.in || die
- sed -e "s#^CXX = .*#CXX = $(tc-getCXX)#" -i gzstream/Makefile || die
-}
-
-src_compile(){
- # install headers, bins and libs into CBT_DEVEL_USER, then compile apps
- emake CBT_DEVEL_DIR="${WORKDIR}/atlas-src/CBT" CBT_INSTALL_DIR="${D}"/"${EPREFIX}"
- cd ../CBTApps || die
- emake CBT_DEVEL_DIR="${WORKDIR}/atlas-src/CBTApps" CBT_INSTALL_DIR="${D}"/"${EPREFIX}"
-}
diff --git a/sci-biology/Atlas/metadata.xml b/sci-biology/Atlas/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/Atlas/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas/
@ 2016-09-23 17:29 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-09-23 17:29 UTC (permalink / raw
To: gentoo-commits
commit: 91fe67bb6be48a87da506a96a06548cbc06fcaba
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Sep 23 17:29:12 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Sep 23 17:29:12 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=91fe67bb
sci-biology/Atlas: a lot more hackery to fix Makefile
Package-Manager: portage-2.3.0
sci-biology/Atlas/Atlas-2005.ebuild | 17 ++++++++++++-----
1 file changed, 12 insertions(+), 5 deletions(-)
diff --git a/sci-biology/Atlas/Atlas-2005.ebuild b/sci-biology/Atlas/Atlas-2005.ebuild
index 4806d1c..318b493 100644
--- a/sci-biology/Atlas/Atlas-2005.ebuild
+++ b/sci-biology/Atlas/Atlas-2005.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -22,13 +22,20 @@ RDEPEND="${DEPEND}"
S="${WORKDIR}"/atlas-src/CBT
src_prepare(){
- sed -e "s/^CC =/CC = $(tc-getCC)/" -e "s/^GCC =/GCC = $(tc-getCXX)/" -i Makefile || die
- sed -e "s/^GCC =/GCC = $(tc-getCXX)/" -i ../CBTApps/Makefile.in || die
+ sed -e "s/^CC = .*/CC = $(tc-getCC)/" -e "s/^GCC = .*/GCC = $(tc-getCXX)/" -i Makefile || die
+ sed -e "s/^CC = .*/CC = $(tc-getCC)/" -e "s/^GCC = .*/GCC = $(tc-getCXX)/" -i ../CBTApps/Makefile.in || die
+ sed -e "s@^# CBT_DEVEL_USER = .*@CBT_DEVEL_USER = ${EPREFIX}/@" -i Makefile || die
+ sed -e "s@^# CBT_DEVEL_USER = .*@CBT_DEVEL_USER = ${EPREFIX}/@" -i Makefile.in || die
+ sed -e "s#^CBT_INSTALL_LIB = /home/hgsc/lib/#CBT_INSTALL_LIB = ${EPREFIX}/usr/lib/#" -i Makefile || die
+ sed -e "s#^CBT_INSTALL_LIB = /home/hgsc/lib/#CBT_INSTALL_LIB = ${EPREFIX}/usr/lib/#" -i Makefile.in || die
+ sed -e "s#^BOOST_DIR = .*#BOOST_DIR = ${EPREFIX}/usr/lib/#" -i Makefile || die
+ sed -e "s#^BOOST_DIR = .*#BOOST_DIR = ${EPREFIX}/usr/lib/#" -i Makefile.in || die
+ sed -e "s#^CXX = .*#CXX = $(tc-getCXX)#" -i gzstream/Makefile || die
}
src_compile(){
# install headers, bins and libs into CBT_DEVEL_USER, then compile apps
- emake CBT_DEVEL_DIR="${S}" CBT_INSTALL_DIR="${D}"
+ emake CBT_DEVEL_DIR="${WORKDIR}/atlas-src/CBT" CBT_INSTALL_DIR="${D}"/"${EPREFIX}"
cd ../CBTApps || die
- emake CBT_DEVEL_DIR="${S}" CBT_INSTALL_DIR="${D}"
+ emake CBT_DEVEL_DIR="${WORKDIR}/atlas-src/CBTApps" CBT_INSTALL_DIR="${D}"/"${EPREFIX}"
}
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas/
@ 2016-06-30 18:06 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-06-30 18:06 UTC (permalink / raw
To: gentoo-commits
commit: 50c01592d588fb2dadc5e4ca17aefc2943cb9f96
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 30 18:06:03 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 30 18:06:03 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=50c01592
sci-biology/Atlas: fix Makefiles at least, will need to unbundle some gzstream library too
Package-Manager: portage-2.2.28
sci-biology/Atlas/Atlas-2005.ebuild | 14 ++++++++++----
1 file changed, 10 insertions(+), 4 deletions(-)
diff --git a/sci-biology/Atlas/Atlas-2005.ebuild b/sci-biology/Atlas/Atlas-2005.ebuild
index c95df06..4806d1c 100644
--- a/sci-biology/Atlas/Atlas-2005.ebuild
+++ b/sci-biology/Atlas/Atlas-2005.ebuild
@@ -4,6 +4,8 @@
EAPI=5
+inherit toolchain-funcs
+
DESCRIPTION="Atlas Whole Genome Assembly Suite"
HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-whole-genome-assembly-suite"
SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas-src.tgz"
@@ -17,12 +19,16 @@ IUSE=""
DEPEND="dev-libs/boost"
RDEPEND="${DEPEND}"
-S="${WORKDIR}"/atlas-src
+S="${WORKDIR}"/atlas-src/CBT
+
+src_prepare(){
+ sed -e "s/^CC =/CC = $(tc-getCC)/" -e "s/^GCC =/GCC = $(tc-getCXX)/" -i Makefile || die
+ sed -e "s/^GCC =/GCC = $(tc-getCXX)/" -i ../CBTApps/Makefile.in || die
+}
src_compile(){
# install headers, bins and libs into CBT_DEVEL_USER, then compile apps
- cd src || die
- emake CBT_DEVEL_DIR="${S}"/CBT CBT_INSTALL_DIR="${D}"
+ emake CBT_DEVEL_DIR="${S}" CBT_INSTALL_DIR="${D}"
cd ../CBTApps || die
- emake CBT_DEVEL_DIR="${S}"/CBT CBT_INSTALL_DIR="${D}"
+ emake CBT_DEVEL_DIR="${S}" CBT_INSTALL_DIR="${D}"
}
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas/
@ 2016-06-23 16:39 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-06-23 16:39 UTC (permalink / raw
To: gentoo-commits
commit: 4fb5985d99147d5e886518ce226c2143251de123
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 23 16:39:16 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 23 16:39:16 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4fb5985d
sci-biology/Atlas: improve ebuild, still does not work
Package-Manager: portage-2.2.28
sci-biology/Atlas/Atlas-2005.ebuild | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/sci-biology/Atlas/Atlas-2005.ebuild b/sci-biology/Atlas/Atlas-2005.ebuild
index c66660b..c95df06 100644
--- a/sci-biology/Atlas/Atlas-2005.ebuild
+++ b/sci-biology/Atlas/Atlas-2005.ebuild
@@ -14,5 +14,15 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND=""
+DEPEND="dev-libs/boost"
RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/atlas-src
+
+src_compile(){
+ # install headers, bins and libs into CBT_DEVEL_USER, then compile apps
+ cd src || die
+ emake CBT_DEVEL_DIR="${S}"/CBT CBT_INSTALL_DIR="${D}"
+ cd ../CBTApps || die
+ emake CBT_DEVEL_DIR="${S}"/CBT CBT_INSTALL_DIR="${D}"
+}
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas/
@ 2015-01-07 21:55 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-01-07 21:55 UTC (permalink / raw
To: gentoo-commits
commit: 8a4f06abb087cbf0c736ab5e9bb53c252e955d1e
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 7 21:54:27 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 7 21:54:27 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8a4f06ab
initial ebuild for a new package
---
sci-biology/Atlas/Atlas-2005.ebuild | 18 ++++++++++++++++++
sci-biology/Atlas/ChangeLog | 10 ++++++++++
sci-biology/Atlas/metadata.xml | 9 +++++++++
3 files changed, 37 insertions(+)
diff --git a/sci-biology/Atlas/Atlas-2005.ebuild b/sci-biology/Atlas/Atlas-2005.ebuild
new file mode 100644
index 0000000..29b546d
--- /dev/null
+++ b/sci-biology/Atlas/Atlas-2005.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Atlas Whole Genome Assembly Suite"
+HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas-whole-genome-assembly-suite"
+SRC_URI="https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas-src.tgz"
+# https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas2005-linux.tgz
+
+LICENSE=""
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/Atlas/ChangeLog b/sci-biology/Atlas/ChangeLog
new file mode 100644
index 0000000..d8bcd83
--- /dev/null
+++ b/sci-biology/Atlas/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/Atlas
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*Atlas-2005 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +Atlas-2005.ebuild,
+ +metadata.xml:
+ initial ebuild
+
diff --git a/sci-biology/Atlas/metadata.xml b/sci-biology/Atlas/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/Atlas/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>
^ permalink raw reply related [flat|nested] 6+ messages in thread
end of thread, other threads:[~2020-09-27 22:43 UTC | newest]
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