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* [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
* [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/
@ 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/
@ 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/
@ 2015-05-23 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/
@ 2015-05-25 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/
@ 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 21:26 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/
@ 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
end of thread, other threads:[~2018-01-20 21:28 UTC | newest]

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2015-04-17 23:56 Martin Mokrejs
2015-04-17 23:56 Martin Mokrejs
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