* [gentoo-commits] proj/sci:master commit in: sci-biology/amos/
@ 2016-03-23 19:09 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2016-03-23 19:09 UTC (permalink / raw
To: gentoo-commits
commit: 4a386700427979e83e4338695563aec7a1b1cfe9
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 23 19:09:23 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 23 19:09:23 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4a386700
sci-biology/amos: document 'Could not open file LIBGUESTFS_PATH=/usr/share/guestfs/appliance' error to be solved; add support for a system-wide config file via AMOSCONF env variable
Package-Manager: portage-2.2.26
sci-biology/amos/amos-3.1.0-r2.ebuild | 9 ++++++++-
sci-biology/amos/amos-9999.ebuild | 10 +++++++++-
2 files changed, 17 insertions(+), 2 deletions(-)
diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild
index bbf768f..ff04169 100644
--- a/sci-biology/amos/amos-3.1.0-r2.ebuild
+++ b/sci-biology/amos/amos-3.1.0-r2.ebuild
@@ -10,7 +10,7 @@ inherit eutils python-r1
PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module eutils toolchain-funcs
-DESCRIPTION="A Modular, Open-Source whole genome assembler"
+DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple assemblies"
HOMEPAGE="http://amos.sourceforge.net/"
SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
@@ -38,6 +38,9 @@ src_prepare() {
epatch \
"${FILESDIR}"/${P}-gcc-4.7.patch \
"${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
+ # $ gap-links
+ # ERROR: Could not open file LIBGUESTFS_PATH=/usr/share/guestfs/appliance/
+ # $
}
# --with-jellyfish location of Jellyfish headers
@@ -57,4 +60,8 @@ src_install() {
# zap the mis-placed files ('make install' is at fault)
rm -f "${D}"/usr/lib64/AMOS/*.pm
rm -rf "${D}"/usr/lib64/TIGR
+ echo AMOSCONF="${EPREFIX}"/etc/amos.acf > "${S}"/99amos || die
+ mkdir -p "${ED}"/etc || die
+ touch "${ED}"/etc/amos.acf || die
+ doenvd "${S}/99amos"
}
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index 07a140a..fca8f2e 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -10,7 +10,7 @@ inherit perl-module eutils toolchain-funcs
AUTOTOOLS_AUTORECONF=true
inherit autotools-utils git-r3
-DESCRIPTION="Genome assembly package live cvs sources"
+DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple assemblies"
HOMEPAGE="http://sourceforge.net/projects/amos"
SRC_URI=""
EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos"
@@ -34,6 +34,10 @@ RDEPEND="${DEPEND}
# --with-jellyfish location of Jellyfish headers
+# $ gap-links
+# ERROR: Could not open file LIBGUESTFS_PATH=/usr/share/guestfs/appliance/
+# $
+
src_install() {
default
python_replicate_script "${ED}"/usr/bin/goBambus2
@@ -49,4 +53,8 @@ src_install() {
# zap the mis-placed files ('make install' is at fault)
rm -f "${D}"/usr/lib64/AMOS/*.pm
rm -rf "${D}"/usr/lib64/TIGR
+ echo AMOSCONF="${EPREFIX}"/etc/amos.acf > "${S}"/99amos || die
+ mkdir -p "${ED}"/etc || die
+ touch "${ED}"/etc/amos.acf || die
+ doenvd "${S}/99amos"
}
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/amos/
@ 2018-01-20 21:28 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2018-01-20 21:28 UTC (permalink / raw
To: gentoo-commits
commit: 68140835d8a583ce291fe8ffb4f5fb787eada5d0
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jan 20 21:28:45 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jan 20 21:28:45 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=68140835
sci-biology/amos: no, sourceforge git:// does not run on https://
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/amos/amos-9999.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index 9cd6d64e6..97ae851a3 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -12,7 +12,7 @@ inherit autotools-utils git-r3
DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple assemblies"
HOMEPAGE="http://sourceforge.net/projects/amos"
SRC_URI=""
-EGIT_REPO_URI="https://amos.git.sourceforge.net/gitroot/amos/amos"
+EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos"
LICENSE="Artistic"
SLOT="0"
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/amos/
@ 2018-01-20 21:26 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2018-01-20 21:26 UTC (permalink / raw
To: gentoo-commits
commit: 84ce0e6bab8e2f0f44d94f5777f1fd2b71616967
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jan 20 21:25:02 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jan 20 21:25:02 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=84ce0e6b
sci-biology/amos:
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/amos/amos-9999.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index 9ad4d2d06..9cd6d64e6 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -12,7 +12,7 @@ inherit autotools-utils git-r3
DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple assemblies"
HOMEPAGE="http://sourceforge.net/projects/amos"
SRC_URI=""
-EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos"
+EGIT_REPO_URI="https://amos.git.sourceforge.net/gitroot/amos/amos"
LICENSE="Artistic"
SLOT="0"
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/amos/
@ 2015-05-25 22:48 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-05-25 22:48 UTC (permalink / raw
To: gentoo-commits
commit: 38f08cf23e0e49d8dd0a0b566afb8cb09b2904fe
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 25 22:47:31 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 25 22:47:31 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=38f08cf2
added dev-qt/qt3support:4 to DEPEND because 'scanelf -qn /usr/bin/hawkeye' confirms libQt3Support.so is used (thanks to Davide Pesavento pesa <AT> g.o)
Package-Manager: portage-2.2.18
sci-biology/amos/ChangeLog | 5 +++++
sci-biology/amos/amos-3.1.0-r2.ebuild | 3 ++-
sci-biology/amos/amos-9999.ebuild | 3 ++-
3 files changed, 9 insertions(+), 2 deletions(-)
diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog
index 1a2a11d..74d1a5d 100644
--- a/sci-biology/amos/ChangeLog
+++ b/sci-biology/amos/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ amos-3.1.0-r2.ebuild, amos-9999.ebuild:
+ added dev-qt/qt3support:4 to DEPEND because 'scanelf -qn /usr/bin/hawkeye'
+ confirms libQt3Support.so is used (thanks to Davide Pesavento pesa@g.o)
+
17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
amos-3.1.0-r2.ebuild, amos-9999.ebuild:
sci-biology/amos: fixed installation of perl-related files
diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild
index fd81df6..0b777e2 100644
--- a/sci-biology/amos/amos-3.1.0-r2.ebuild
+++ b/sci-biology/amos/amos-3.1.0-r2.ebuild
@@ -22,7 +22,8 @@ IUSE="mpi qt4"
DEPEND="
mpi? ( virtual/mpi )
dev-libs/boost
- qt4? ( dev-qt/qtcore:4[qt3support] )
+ qt4? ( dev-qt/qtcore:4[qt3support]
+ dev-qt/qt3support:4 )
sci-biology/blat
sci-biology/jellyfish"
RDEPEND="${DEPEND}
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index c47a5b6..9ac9c4c 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -23,7 +23,8 @@ IUSE="mpi qt4"
DEPEND="
mpi? ( virtual/mpi )
dev-libs/boost
- qt4? ( dev-qt/qtcore:4[qt3support] )
+ qt4? ( dev-qt/qtcore:4[qt3support]
+ dev-qt/qt3support:4 )
sci-biology/blat
sci-biology/jellyfish"
RDEPEND="${DEPEND}
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/amos/
@ 2015-05-23 21:25 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-05-23 21:25 UTC (permalink / raw
To: gentoo-commits
commit: 8a1a5bf1ebdff1e93246e54e4d922bd2d5fdd18e
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat May 23 21:25:13 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat May 23 21:25:13 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8a1a5bf1
sci-biology/amos: add qt3support requirement so that we actually compile hawkeye, add mpi to IUSE, drop mis-placed *.pm files, cleanup deps
Package-Manager: portage-2.2.18
sci-biology/amos/amos-3.1.0-r2.ebuild | 24 ++++++++----------------
sci-biology/amos/amos-9999.ebuild | 5 ++++-
2 files changed, 12 insertions(+), 17 deletions(-)
diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild
index eadcc43..fd81df6 100644
--- a/sci-biology/amos/amos-3.1.0-r2.ebuild
+++ b/sci-biology/amos/amos-3.1.0-r2.ebuild
@@ -17,16 +17,18 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE="qt4"
+IUSE="mpi qt4"
DEPEND="
+ mpi? ( virtual/mpi )
dev-libs/boost
- qt4? ( dev-qt/qtcore:4 )"
+ qt4? ( dev-qt/qtcore:4[qt3support] )
+ sci-biology/blat
+ sci-biology/jellyfish"
RDEPEND="${DEPEND}
dev-lang/perl
dev-perl/DBI
dev-perl/Statistics-Descriptive
- sci-biology/blat
sci-biology/mummer"
MAKEOPTS+=" -j1"
@@ -37,19 +39,6 @@ src_prepare() {
"${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
}
-# amos-3.1.0-r2/work/amos-3.1.0/src/Bambus/Untangler/DotLib.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/Bambus/Untangler/AsmLib.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAreader.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/AmosFoundation.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/Foundation.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/AmosLib.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTArecord.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/ParseFasta.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/xfig.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAwriter.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAgrammar.pm
-# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAiterator.pm
-
# --with-jellyfish location of Jellyfish headers
src_install() {
@@ -64,4 +53,7 @@ src_install() {
doins "${D}"/usr/lib64/TIGR/*.pm
# move also /usr/lib64/AMOS/AMOS.py to /usr/bin
mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
+ # zap the mis-placed files ('make install' is at fault)
+ rm -f "${D}"/usr/lib64/AMOS/*.pm
+ rm -rf "${D}"/usr/lib64/TIGR
}
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index 110e7c7..c47a5b6 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -23,7 +23,7 @@ IUSE="mpi qt4"
DEPEND="
mpi? ( virtual/mpi )
dev-libs/boost
- qt4? ( dev-qt/qtcore:4 )
+ qt4? ( dev-qt/qtcore:4[qt3support] )
sci-biology/blat
sci-biology/jellyfish"
RDEPEND="${DEPEND}
@@ -45,4 +45,7 @@ src_install() {
doins "${D}"/usr/lib64/TIGR/*.pm
# move also /usr/lib64/AMOS/AMOS.py to /usr/bin
mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
+ # zap the mis-placed files ('make install' is at fault)
+ rm -f "${D}"/usr/lib64/AMOS/*.pm
+ rm -rf "${D}"/usr/lib64/TIGR
}
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/amos/
@ 2015-04-17 23:56 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-04-17 23:56 UTC (permalink / raw
To: gentoo-commits
commit: 0366b5335160e2632293c0265f720f146e31d8cc
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 23:11:25 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 23:11:25 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0366b533
sci-biology/amos: use doins instead of dobin
Package-Manager: portage-2.2.18
sci-biology/amos/ChangeLog | 4 ++++
sci-biology/amos/amos-3.1.0-r2.ebuild | 4 ++--
sci-biology/amos/amos-9999.ebuild | 4 ++--
3 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog
index 94d1ad5..cc8ed4c 100644
--- a/sci-biology/amos/ChangeLog
+++ b/sci-biology/amos/ChangeLog
@@ -4,6 +4,10 @@
17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
amos-3.1.0-r2.ebuild, amos-9999.ebuild:
+ sci-biology/amos: use doins instead of dobin
+
+ 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ amos-3.1.0-r2.ebuild, amos-9999.ebuild:
sci-biology/amos: fixed installation of perl-related files
*amos-3.1.0-r2 (31 Mar 2015)
diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild
index 2b9473d..2162308 100644
--- a/sci-biology/amos/amos-3.1.0-r2.ebuild
+++ b/sci-biology/amos/amos-3.1.0-r2.ebuild
@@ -59,9 +59,9 @@ src_install() {
# configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
perl_set_version
insinto ${VENDOR_LIB}
- dobin "${D}"/usr/lib64/AMOS/*.pm
+ doins "${D}"/usr/lib64/AMOS/*.pm
insinto ${VENDOR_LIB}/TIGR
- dobin "${D}"/usr/lib64/TIGR/*.pm
+ doins "${D}"/usr/lib64/TIGR/*.pm
# move also /usr/lib64/AMOS/AMOS.py to /usr/bin
mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
}
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index 71b247d..d3f756f 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -40,9 +40,9 @@ src_install() {
# configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
perl_set_version
insinto ${VENDOR_LIB}
- dobin "${D}"/usr/lib64/AMOS/*.pm
+ doins "${D}"/usr/lib64/AMOS/*.pm
insinto ${VENDOR_LIB}/TIGR
- dobin "${D}"/usr/lib64/TIGR/*.pm
+ doins "${D}"/usr/lib64/TIGR/*.pm
# move also /usr/lib64/AMOS/AMOS.py to /usr/bin
mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
}
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/amos/
@ 2015-04-17 23:56 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-04-17 23:56 UTC (permalink / raw
To: gentoo-commits
commit: 3a9a10ae625a0b5a460a6daf1af69a150bbbac70
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 23:30:21 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 23:30:21 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a9a10ae
sci-biology/amos: fixed installation of perl-related files
Package-Manager: portage-2.2.18
sci-biology/amos/ChangeLog | 4 ++++
sci-biology/amos/amos-3.1.0-r2.ebuild | 2 +-
sci-biology/amos/amos-9999.ebuild | 2 +-
3 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog
index cc8ed4c..1a2a11d 100644
--- a/sci-biology/amos/ChangeLog
+++ b/sci-biology/amos/ChangeLog
@@ -4,6 +4,10 @@
17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
amos-3.1.0-r2.ebuild, amos-9999.ebuild:
+ sci-biology/amos: fixed installation of perl-related files
+
+ 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ amos-3.1.0-r2.ebuild, amos-9999.ebuild:
sci-biology/amos: use doins instead of dobin
17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild
index 2162308..eadcc43 100644
--- a/sci-biology/amos/amos-3.1.0-r2.ebuild
+++ b/sci-biology/amos/amos-3.1.0-r2.ebuild
@@ -58,7 +58,7 @@ src_install() {
# bambus needs TIGR::FASTAreader.pm and others
# configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
perl_set_version
- insinto ${VENDOR_LIB}
+ insinto ${VENDOR_LIB}/AMOS
doins "${D}"/usr/lib64/AMOS/*.pm
insinto ${VENDOR_LIB}/TIGR
doins "${D}"/usr/lib64/TIGR/*.pm
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index d3f756f..110e7c7 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -39,7 +39,7 @@ src_install() {
# bambus needs TIGR::FASTAreader.pm and others
# configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
perl_set_version
- insinto ${VENDOR_LIB}
+ insinto ${VENDOR_LIB}/AMOS
doins "${D}"/usr/lib64/AMOS/*.pm
insinto ${VENDOR_LIB}/TIGR
doins "${D}"/usr/lib64/TIGR/*.pm
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/amos/
@ 2015-04-17 22:23 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-04-17 22:23 UTC (permalink / raw
To: gentoo-commits
commit: 812a886bdcc45c891f93fb5caf73e5cee20c9aab
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 22:22:17 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 22:22:17 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=812a886b
sci-biology/amos: fixed installation of perl-related files
Package-Manager: portage-2.2.18
sci-biology/amos/ChangeLog | 4 ++++
sci-biology/amos/amos-3.1.0-r2.ebuild | 15 ++++++++-------
sci-biology/amos/amos-9999.ebuild | 15 ++++++++-------
3 files changed, 20 insertions(+), 14 deletions(-)
diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog
index 9bdce77..94d1ad5 100644
--- a/sci-biology/amos/ChangeLog
+++ b/sci-biology/amos/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ amos-3.1.0-r2.ebuild, amos-9999.ebuild:
+ sci-biology/amos: fixed installation of perl-related files
+
*amos-3.1.0-r2 (31 Mar 2015)
31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild
index ab8a404..2b9473d 100644
--- a/sci-biology/amos/amos-3.1.0-r2.ebuild
+++ b/sci-biology/amos/amos-3.1.0-r2.ebuild
@@ -5,9 +5,11 @@
EAPI=5
PYTHON_COMPAT=( python2_7 )
-
inherit eutils python-r1
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
+
DESCRIPTION="A Modular, Open-Source whole genome assembler"
HOMEPAGE="http://amos.sourceforge.net/"
SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
@@ -55,12 +57,11 @@ src_install() {
python_replicate_script "${ED}"/usr/bin/goBambus2
# bambus needs TIGR::FASTAreader.pm and others
# configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
- mkdir -p "${D}"/usr/share/"${PN}"/perl/AMOS || die
- mv "${D}"/usr/lib64/AMOS/*.pm "${D}"/usr/share/"${PN}"/perl/AMOS || die
- mkdir -p "${D}"/usr/share/"${PN}"/perl/TIGR || die
- mv "${D}"/usr/lib64/TIGR/*.pm "${D}"/usr/share/"${PN}"/perl/TIGR || die
- echo "PERL5LIB=/usr/share/${PN}/perl" > "${S}/99${PN}"
- doenvd "${S}/99${PN}" || die
+ perl_set_version
+ insinto ${VENDOR_LIB}
+ dobin "${D}"/usr/lib64/AMOS/*.pm
+ insinto ${VENDOR_LIB}/TIGR
+ dobin "${D}"/usr/lib64/TIGR/*.pm
# move also /usr/lib64/AMOS/AMOS.py to /usr/bin
mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
}
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index 610c3d6..71b247d 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -4,8 +4,10 @@
EAPI=5
-AUTOTOOLS_AUTORECONF=true
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
+AUTOTOOLS_AUTORECONF=true
inherit autotools-utils git-r3
DESCRIPTION="Genome assembly package live cvs sources"
@@ -36,12 +38,11 @@ src_install() {
python_replicate_script "${ED}"/usr/bin/goBambus2
# bambus needs TIGR::FASTAreader.pm and others
# configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
- mkdir -p "${D}/usr/share/${PN}/perl/AMOS" || die
- mv "${D}"/usr/lib64/AMOS/*.pm "${D}/usr/share/${PN}/perl/AMOS" || die
- mkdir -p "${D}"/usr/share/"${PN}"/perl/TIGR || die
- mv "${D}"/usr/lib64/TIGR/*.pm "${D}"/usr/share/"${PN}"/perl/TIGR || die
- echo "PERL5LIB=/usr/share/${PN}/perl" > "${S}/99${PN}"
- doenvd "${S}/99${PN}" || die
+ perl_set_version
+ insinto ${VENDOR_LIB}
+ dobin "${D}"/usr/lib64/AMOS/*.pm
+ insinto ${VENDOR_LIB}/TIGR
+ dobin "${D}"/usr/lib64/TIGR/*.pm
# move also /usr/lib64/AMOS/AMOS.py to /usr/bin
mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
}
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/amos/
@ 2013-03-21 6:54 Justin Lecher
0 siblings, 0 replies; 10+ messages in thread
From: Justin Lecher @ 2013-03-21 6:54 UTC (permalink / raw
To: gentoo-commits
commit: 78f3677f181e4c375599aa5656e08fc97557bc83
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 19 07:43:55 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 19 07:43:55 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=78f3677f
sci-biology/amos: Bump to latest git HEAD, fixes qt problems, #348031
Package-Manager: portage-2.2.0_alpha166
---
sci-biology/amos/ChangeLog | 3 ++
sci-biology/amos/amos-9999.ebuild | 45 ++++++++----------------------------
2 files changed, 13 insertions(+), 35 deletions(-)
diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog
index 26c68ea..f121b16 100644
--- a/sci-biology/amos/ChangeLog
+++ b/sci-biology/amos/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 19 Mar 2013; Justin Lecher <jlec@gentoo.org> amos-9999.ebuild:
+ Bump to latest git HEAD, fixes qt problems, #348031
+
03 Mar 2013; Justin Lecher <jlec@gentoo.org> amos-9999.ebuild, metadata.xml:
Update to new qt deps names
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index fc0e050..67180f8 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -2,52 +2,27 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=4
+EAPI=5
-[ "$PV" == "9999" ] && CVS=cvs
+[ "$PV" == "9999" ] && VCS=git-2
-inherit eutils ${CVS}
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils ${VCS}
DESCRIPTION="Genome assembly package live cvs sources"
HOMEPAGE="http://sourceforge.net/projects/amos"
-ECVS_SERVER="amos.cvs.sourceforge.net:/cvsroot/amos"
-ECVS_AUTH="pserver"
-ECVS_MODULE="AMOS"
-ECVS_BRANCH="HEAD"
-ECVS_USER="anonymous"
-ECVS_PASS=""
+SRC_URI=""
+EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos"
-LICENSE="GPL-2"
+LICENSE="Artistic"
SLOT="0"
-IUSE=""
KEYWORDS=""
+IUSE=""
DEPEND="
dev-libs/boost
- dev-qt/qt3support"
+ dev-qt/qtcore:4"
RDEPEND="${DEPEND}
dev-perl/DBI
sci-biology/mummer"
-
-S="${DISTDIR}"/cvs-src/AMOS/AMOS/
-
-src_unpack() {
- ECVS_TOP_DIR="${DISTDIR}/cvs-src/${ECVS_MODULE}"
- cvs_src_unpack
-}
-
-src_prepare(){
- epatch "${FILESDIR}"/amos.m4.patch
-}
-
-src_configure() {
- ./bootstrap || die
- #CFLAGS=$CFLAGS' -I/usr/include/qt4/Qt' CXXFLAGS=$CXXFLAGS' -I/usr/include/qt4/Qt' econf --enable-all --with-Qt-include-dir=/usr/include/qt4 --with-Qt-lib-dir=/usr/lib/qt4 --with-Qt-bin-dir=/usr/bin --with-Qt-lib=Qt3Support
- econf --enable-all
- einfo "No hawkeye and other Qt3-based apps installed, sorry, no qt3 anynore on Gentoo"
-}
-
-src_compile() {
- # TODO: force MAKEOPTS=-j1 because it seems -j6 is exploting some dependency issue in Makefiles
- MAKEOPTS=-j1 emake DESTDIR="${D}"
-}
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/amos/
@ 2012-05-22 19:43 Justin Lecher
0 siblings, 0 replies; 10+ messages in thread
From: Justin Lecher @ 2012-05-22 19:43 UTC (permalink / raw
To: gentoo-commits
commit: ed863d2fb6f4e2d0fa67cbec7af540eefb429b5b
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue May 22 18:51:31 2012 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue May 22 18:51:31 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ed863d2f
sci-biology/amos: Bump to EAPI=4, remove unnecessary bits
(Portage version: 2.2.0_alpha107/git/Linux x86_64, unsigned Manifest commit)
---
sci-biology/amos/ChangeLog | 7 +++++++
sci-biology/amos/amos-9999.ebuild | 28 ++++++++++++----------------
2 files changed, 19 insertions(+), 16 deletions(-)
diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog
new file mode 100644
index 0000000..7009cae
--- /dev/null
+++ b/sci-biology/amos/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-biology/amos
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 22 May 2012; Justin Lecher <jlec@gentoo.org> amos-9999.ebuild:
+ Bump to EAPI=4, remove unnecessary bits
+
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index bcbf49d..ed45785 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -1,13 +1,14 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
-[ "$PV" == "9999" ] && inherit cvs
+EAPI=4
-inherit eutils
+[ "$PV" == "9999" ] && CVS=cvs
-DESCRIPTION="AMOS genome assembly package live cvs sources"
+inherit eutils ${CVS}
+
+DESCRIPTION="Genome assembly package live cvs sources"
HOMEPAGE="http://sourceforge.net/projects/amos"
ECVS_SERVER="amos.cvs.sourceforge.net:/cvsroot/amos"
ECVS_AUTH="pserver"
@@ -21,10 +22,9 @@ SLOT="0"
IUSE=""
KEYWORDS=""
-#DEPEND=">=x11-libs/qt-3.3:3"
-DEPEND="dev-vcs/cvs
- dev-libs/boost
- x11-libs/qt-qt3support"
+DEPEND="
+ dev-libs/boost
+ x11-libs/qt-qt3support"
RDEPEND="${DEPEND}
dev-perl/DBI
sci-biology/mummer"
@@ -37,21 +37,17 @@ src_unpack() {
}
src_prepare(){
- epatch "${FILESDIR}"/amos.m4.patch || die
+ epatch "${FILESDIR}"/amos.m4.patch
}
src_configure() {
./bootstrap || die
#CFLAGS=$CFLAGS' -I/usr/include/qt4/Qt' CXXFLAGS=$CXXFLAGS' -I/usr/include/qt4/Qt' econf --enable-all --with-Qt-include-dir=/usr/include/qt4 --with-Qt-lib-dir=/usr/lib/qt4 --with-Qt-bin-dir=/usr/bin --with-Qt-lib=Qt3Support
- econf --enable-all || die
+ econf --enable-all
einfo "No hawkeye and other Qt3-based apps installed, sorry, no qt3 anynore on Gentoo"
}
src_compile() {
# TODO: force MAKEOPTS=-j1 because it seems -j6 is exploting some dependency issue in Makefiles
- MAKEOPTS=-j1 emake DESTDIR="${D}" || die "emake failed"
-}
-
-src_install() {
- emake DESTDIR="${D}" install || die "emake install failed"
+ MAKEOPTS=-j1 emake DESTDIR="${D}"
}
^ permalink raw reply related [flat|nested] 10+ messages in thread
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