[gentoo-commits] proj/sci:master commit in: sci-biology/twinscan/
commit: 21f906c5f5098f455f1a0033fb9a8533f827e84b
Author: Andrew Ammerlaan riseup net>
AuthorDate: Thu Mar 18 18:48:56 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Thu Mar 18 18:48:56 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=21f906c5
sci-biology/twinscan: use perl_domodule
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/twinscan/twinscan-4.1.2-r1.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
index 2568359bd..ce3651f3d 100644
--- a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
+++ b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
@@ -52,8 +52,7 @@ src_install() {
insinto /usr/share/${PN}/src
doins src/*.zhmm
perl_set_version
- insinto ${VENDOR_LIB}/${PN}
- doins lib/perl5/*.pm
+ perl_domodule lib/perl5/*.pm
echo "TWINSCAN=/usr" > "${S}"/99${PN}
doenvd "${S}"/99${PN}
rm -rf examples/tmp
[gentoo-commits] proj/sci:master commit in: sci-biology/twinscan/
commit: 63bc36e1604a2e8ecd79a085b1633b0fca4e5e9b
Author: Andrew Ammerlaan riseup net>
AuthorDate: Sat Mar 6 16:45:03 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Sat Mar 6 16:45:03 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=63bc36e1
sci-biology/twinscan: do not overwrite RESTRICT
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/twinscan/twinscan-4.1.2-r1.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
index b30b58557..2568359bd 100644
--- a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
+++ b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
@@ -12,7 +12,6 @@ HOMEPAGE="https://mblab.wustl.edu/software.html";
# Unable to locally verify the issuer's authority.
# To connect to mblab.wustl.edu insecurely, use `--no-check-certificate'.
SRC_URI="iscan-${PV}.tar.gz"
-RESTRICT="fetch"
LICENSE="all-rights-reserved"
SLOT="0"
@@ -22,7 +21,7 @@ DEPEND="dev-libs/glib:2"
RDEPEND="${DEPEND}"
S="${WORKDIR}/N-SCAN"
-RESTRICT="test"
+RESTRICT="test fetch"
src_prepare() {
default
[gentoo-commits] proj/sci:master commit in: sci-biology/twinscan/
commit: 658ebd5c37578453fb4d563f2b48104bdafaae98
Author: Andrew Ammerlaan riseup net>
AuthorDate: Sat Mar 6 16:44:22 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Sat Mar 6 16:44:22 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=658ebd5c
sci-biology/twinscan: PV instead of P
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/twinscan/twinscan-4.1.2-r1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
index 8b4fdbacf..b30b58557 100644
--- a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
+++ b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
@@ -11,7 +11,7 @@ HOMEPAGE="https://mblab.wustl.edu/software.html";
# ERROR: cannot verify mblab.wustl.edu's certificate, issued by ‘CN=InCommon
RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’:
# Unable to locally verify the issuer's authority.
# To connect to mblab.wustl.edu insecurely, use `--no-check-certificate'.
-SRC_URI="${P}.tar.gz"
+SRC_URI="iscan-${PV}.tar.gz"
RESTRICT="fetch"
LICENSE="all-rights-reserved"
[gentoo-commits] proj/sci:master commit in: sci-biology/twinscan/
commit: cd5d48d30d504aca455e94e58d1a5e0e67076314
Author: Andrew Ammerlaan riseup net>
AuthorDate: Sat Mar 6 16:43:05 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Sat Mar 6 16:43:05 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=cd5d48d3
sci-biology/twinscan: use ${P} in uri
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/twinscan/twinscan-4.1.2-r1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
index 6b9a5f57c..8b4fdbacf 100644
--- a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
+++ b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
@@ -11,8 +11,8 @@ HOMEPAGE="https://mblab.wustl.edu/software.html";
# ERROR: cannot verify mblab.wustl.edu's certificate, issued by ‘CN=InCommon
RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’:
# Unable to locally verify the issuer's authority.
# To connect to mblab.wustl.edu insecurely, use `--no-check-certificate'.
+SRC_URI="${P}.tar.gz"
RESTRICT="fetch"
-SRC_URI="iscan-4.1.2.tar.gz"
LICENSE="all-rights-reserved"
SLOT="0"
[gentoo-commits] proj/sci:master commit in: sci-biology/twinscan/
commit: f1b216aeb5fa865b66a19255465ec4ab5afe908a Author: Andrew Ammerlaan riseup net> AuthorDate: Mon Jan 18 13:33:17 2021 + Commit: Andrew Ammerlaan riseup net> CommitDate: Mon Jan 18 13:33:17 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f1b216ae sci-biology/twinscan: add missing metadata file Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> sci-biology/twinscan/metadata.xml | 8 1 file changed, 8 insertions(+) diff --git a/sci-biology/twinscan/metadata.xml b/sci-biology/twinscan/metadata.xml new file mode 100644 index 0..8417d1580 --- /dev/null +++ b/sci-biology/twinscan/metadata.xml @@ -0,0 +1,8 @@ + +http://www.gentoo.org/dtd/metadata.dtd";> + + + sci-biol...@gentoo.org + Gentoo Biology Project + +
[gentoo-commits] proj/sci:master commit in: sci-biology/twinscan/
commit: fdcbbfa6d96ef8d4eb5a39bc6366bba3a9a743f1
Author: Andrew Ammerlaan riseup net>
AuthorDate: Mon Jan 18 13:10:38 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Mon Jan 18 13:12:58 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=fdcbbfa6
sci-biology/twinscan: re-add, found the download link
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/twinscan/twinscan-4.1.2-r1.ebuild | 69 +++
1 file changed, 69 insertions(+)
diff --git a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
new file mode 100644
index 0..6b9a5f57c
--- /dev/null
+++ b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit perl-module toolchain-funcs
+
+DESCRIPTION="iscan (aka twinscan and N-SCAN), Pairagon wrapper: Gene structure
pred. pipeline"
+HOMEPAGE="https://mblab.wustl.edu/software.html";
+#SRC_URI="https://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz ->
${P}.tar.gz"
+# ERROR: cannot verify mblab.wustl.edu's certificate, issued by ‘CN=InCommon
RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’:
+# Unable to locally verify the issuer's authority.
+# To connect to mblab.wustl.edu insecurely, use `--no-check-certificate'.
+RESTRICT="fetch"
+SRC_URI="iscan-4.1.2.tar.gz"
+
+LICENSE="all-rights-reserved"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="dev-libs/glib:2"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/N-SCAN"
+RESTRICT="test"
+
+src_prepare() {
+ default
+ sed "1 a use lib '/usr/share/${PN}/lib/perl5';" -i "${S}"/bin/*.pl ||
die
+ sed '/my $blast_param/ s/#//' -i "${S}/bin/runTwinscan2.pl" || die
+ tc-export CC AR RANLIB
+
+ sed \
+ -e 's:ar :$(AR) :g' \
+ -e 's:ranlib :$(RANLIB) :g' \
+ -e 's: -o : $(LDFLAGS) -o :g' \
+ -i Makefile || die
+
+ sed \
+ -e "/^GLIB_CFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --cflags
glib-2.0) -DHAS_GLIB:g" \
+ -e "/^GLIB_LFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --libs glib-2.0)
-DHAS_GLIB:g" \
+ -i Makefile.include || die
+}
+
+src_install() {
+ # TODO: prevent file collision with media-gfx/iscan by renaming iscan
to iscan_twinscan
+ # also fix a Genscan++ToZoe.pl Nscan_driver.pl runTwinscan2.pl
run_iscan.pl run_iscan_cons.pl run_iscan_cons_list.pl test.pl
+ rm src/test.pl || die
+ dobin bin/iscan bin/zoe2gtf bin/*.pl src/*.pl
+ dolib.so lib/libzoe.a
+ insinto /usr/share/${PN}
+ doins -r parameters
+ insinto /usr/share/${PN}/src
+ doins src/*.zhmm
+ perl_set_version
+ insinto ${VENDOR_LIB}/${PN}
+ doins lib/perl5/*.pm
+ echo "TWINSCAN=/usr" > "${S}"/99${PN}
+ doenvd "${S}"/99${PN}
+ rm -rf examples/tmp
+ dodoc examples/* README* src/doc/*.txt
+}
+
+pkg_postinst(){
+ einfo "Pairagon acts on output from either: sci-biology/gmap
sci-biology/blat."
+ einfo "It also works on blastn output from WU-BLAST (not provided in
Gentoo)."
+ einfo "It also calls blastz (seems superseded by LASTZ) and genscan++
(not provided in Gentoo)."
+ einfo "For some reason we have pslCDnaFilter provided only by
sci-biology/ucsc-genome-browser"
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/twinscan/, profiles/
commit: 11549cfb4998ee1344504f07e933eb2e224de5f8
Author: Andrew Ammerlaan riseup net>
AuthorDate: Mon Jan 18 12:59:57 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Mon Jan 18 12:59:57 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=11549cfb
sci-biology/twinscan: remove pack, obsolete and replaced upstream
Signed-off-by: Andrew Ammerlaan riseup.net>
profiles/package.mask | 1 -
sci-biology/twinscan/metadata.xml | 8
sci-biology/twinscan/twinscan-4.1.2-r1.ebuild | 64 ---
3 files changed, 73 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 4addb8cbf..04a82cd44 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -113,4 +113,3 @@ sci-biology/swissknife
sci-biology/tablet-bin
sci-biology/TransDecoder
sci-biology/trim_galore
-sci-biology/twinscan
diff --git a/sci-biology/twinscan/metadata.xml
b/sci-biology/twinscan/metadata.xml
deleted file mode 100644
index 8417d1580..0
--- a/sci-biology/twinscan/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd";>
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
diff --git a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
deleted file mode 100644
index 7c8993f9f..0
--- a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-DESCRIPTION="iscan (aka twinscan and N-SCAN), Pairagon wrapper: Gene structure
pred. pipeline"
-HOMEPAGE="http://mblab.wustl.edu/software/twinscan";
-SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz ->
${P}.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="dev-libs/glib:2"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/N-SCAN"
-
-src_prepare() {
- sed "1 a use lib '/usr/share/${PN}/lib/perl5';" -i "${S}"/bin/*.pl ||
die
- sed '/my $blast_param/ s/#//' -i "${S}/bin/runTwinscan2.pl" || die
- tc-export CC AR RANLIB
-
- sed \
- -e 's:ar :$(AR) :g' \
- -e 's:ranlib :$(RANLIB) :g' \
- -e 's: -o : $(LDFLAGS) -o :g' \
- -i Makefile || die
-
- sed \
- -e "/^GLIB_CFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --cflags
glib-2.0) -DHAS_GLIB:g" \
- -e "/^GLIB_LFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --libs glib-2.0)
-DHAS_GLIB:g" \
- -i Makefile.include || die
-}
-
-src_install() {
- # TODO: prevent file collision with media-gfx/iscan by renaming iscan
to iscan_twinscan
- # also fix a Genscan++ToZoe.pl Nscan_driver.pl runTwinscan2.pl
run_iscan.pl run_iscan_cons.pl run_iscan_cons_list.pl test.pl
- rm src/test.pl || die
- dobin bin/iscan bin/zoe2gtf bin/*.pl src/*.pl
- dolib lib/libzoe.a
- insinto /usr/share/${PN}
- doins -r parameters
- insinto /usr/share/${PN}/src
- doins src/*.zhmm
- perl_set_version
- insinto ${VENDOR_LIB}/${PN}
- doins lib/perl5/*.pm
- echo "TWINSCAN=/usr" > "${S}"/99${PN}
- doenvd "${S}"/99${PN}
- rm -rf examples/tmp
- dodoc examples/* README* src/doc/*.txt
-}
-
-pkg_postinst(){
- einfo "Pairagon acts on output from either: sci-biology/gmap
sci-biology/blat."
- einfo "It also works on blastn output from WU-BLAST (not provided in
Gentoo)."
- einfo "It also calls blastz (seems superseded by LASTZ) and genscan++
(not provided in Gentoo)."
- einfo "For some reason we have pslCDnaFilter provided only by
sci-biology/ucsc-genome-browser"
-}
[gentoo-commits] proj/sci:master commit in: sci-biology/twinscan/
commit: 43d7274cf780c83aab2550e0908ed21e38d204af
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Dec 1 14:43:48 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Dec 1 14:43:48 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=43d7274c
sci-biology/twinscan: add missing space breaking GLIB_CFLAGS
Package-Manager: portage-2.3.2
sci-biology/twinscan/twinscan-4.1.2-r1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
index 06c7b8a..5b8c02b 100644
--- a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
+++ b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
@@ -34,7 +34,7 @@ src_prepare() {
sed \
-e "/^GLIB_CFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --cflags
glib-2.0) -DHAS_GLIB:g" \
- -e "/^GLIB_LFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --libs
glib-2.0)-DHAS_GLIB:g" \
+ -e "/^GLIB_LFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --libs glib-2.0)
-DHAS_GLIB:g" \
-i Makefile.include || die
}
[gentoo-commits] proj/sci:master commit in: sci-biology/twinscan/
commit: 385f8ff0d627dc2307515cd6929c276fbae06271
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Mon Aug 1 11:18:19 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Aug 1 11:18:19 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=385f8ff0
sci-biology/twinscan: remove test.pl from the right place
Package-Manager: portage-2.3.0
sci-biology/twinscan/twinscan-4.1.2-r1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
index a4c3258..06c7b8a 100644
--- a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
+++ b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
@@ -41,7 +41,7 @@ src_prepare() {
src_install() {
# TODO: prevent file collision with media-gfx/iscan by renaming iscan
to iscan_twinscan
# also fix a Genscan++ToZoe.pl Nscan_driver.pl runTwinscan2.pl
run_iscan.pl run_iscan_cons.pl run_iscan_cons_list.pl test.pl
- rm bin/test.pl || die
+ rm src/test.pl || die
dobin bin/iscan bin/zoe2gtf bin/*.pl src/*.pl
dolib lib/libzoe.a
insinto /usr/share/${PN}
[gentoo-commits] proj/sci:master commit in: sci-biology/twinscan/
commit: 72d56ebd894309c383e7a1f54b0c13dce2be6d7d
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jul 29 09:20:54 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jul 29 09:20:54 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=72d56ebd
sci-biology/twinscan: do not install test.pl, keep track of file collision
Package-Manager: portage-2.3.0
sci-biology/twinscan/twinscan-4.1.2-r1.ebuild | 7 +--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
index 469ac63..a4c3258 100644
--- a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
+++ b/sci-biology/twinscan/twinscan-4.1.2-r1.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
# $Id$
@@ -7,7 +7,7 @@ EAPI=5
PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module eutils toolchain-funcs
-DESCRIPTION="iscan (aka twinscan and N-SCAN) and wrapper around Pairagon: A
gene structure prediction pipeline"
+DESCRIPTION="iscan (aka twinscan and N-SCAN), Pairagon wrapper: Gene structure
pred. pipeline"
HOMEPAGE="http://mblab.wustl.edu/software/twinscan";
SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz ->
${P}.tar.gz"
@@ -39,6 +39,9 @@ src_prepare() {
}
src_install() {
+ # TODO: prevent file collision with media-gfx/iscan by renaming iscan
to iscan_twinscan
+ # also fix a Genscan++ToZoe.pl Nscan_driver.pl runTwinscan2.pl
run_iscan.pl run_iscan_cons.pl run_iscan_cons_list.pl test.pl
+ rm bin/test.pl || die
dobin bin/iscan bin/zoe2gtf bin/*.pl src/*.pl
dolib lib/libzoe.a
insinto /usr/share/${PN}
[gentoo-commits] proj/sci:master commit in: sci-biology/twinscan/
commit: 6af4aac14e752bcd1bb065b0e09ded7c58ad088a
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sat May 2 13:02:50 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat May 2 13:02:50 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6af4aac1
sci-biology/twinscan: lots of tweaks to install process, install perl modules,
more perl scripts, noted optional external dependencies
Package-Manager: portage-2.2.18
sci-biology/twinscan/ChangeLog| 10 -
sci-biology/twinscan/twinscan-4.1.2-r1.ebuild | 62 +++
sci-biology/twinscan/twinscan-4.1.2.ebuild| 49 -
3 files changed, 70 insertions(+), 51 deletions(-)
diff --git a/sci-biology/twinscan/ChangeLog b/sci-biology/twinscan/ChangeLog
index fedf86e..a377384 100644
--- a/sci-biology/twinscan/ChangeLog
+++ b/sci-biology/twinscan/ChangeLog
@@ -1,7 +1,14 @@
# ChangeLog for sci-biology/twinscan
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*twinscan-4.1.2-r1 (02 May 2015)
+
+ 02 May 2015; Martin Mokrejs
+ +twinscan-4.1.2-r1.ebuild, -twinscan-4.1.2.ebuild:
+ sci-biology/twinscan: lots of tweaks to install process, install perl
modules,
+ more perl scripts, noted optional external dependencies
+
16 Jun 2013; Justin Lecher twinscan-4.1.2.ebuild,
metadata.xml:
Bump to EAPI=5 and fix license
@@ -15,4 +22,3 @@
17 Apr 2009; Andrey Kislyuk ChangeLog:
New package, bug 154939, ebuild written by me
-
diff --git a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
new file mode 100644
index 000..11500ca
--- /dev/null
+++ b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
+
+DESCRIPTION="iscan (aka twinscan and N-SCAN) and wrapper around Pairagon: A
gene structure prediction pipeline"
+HOMEPAGE="http://mblab.wustl.edu/software/twinscan";
+SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz ->
${P}.tar.gz"
+
+LICENSE="all-rights-reserved"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="dev-libs/glib:2"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/N-SCAN"
+
+src_prepare() {
+ sed "1 a use lib '/usr/share/${PN}/lib/perl5';" -i "${S}"/bin/*.pl ||
die
+ sed '/my $blast_param/ s/#//' -i "${S}/bin/runTwinscan2.pl" || die
+ tc-export CC AR RANLIB
+
+ sed \
+ -e 's:ar :$(AR) :g' \
+ -e 's:ranlib :$(RANLIB) :g' \
+ -e 's: -o : $(LDFLAGS) -o :g' \
+ -i Makefile || die
+
+ sed \
+ -e "/^GLIB_CFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --cflags
glib-2.0) -DHAS_GLIB:g" \
+ -e "/^GLIB_LFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --libs
glib-2.0)-DHAS_GLIB:g" \
+ -i Makefile.include || die
+}
+
+src_install() {
+ dobin bin/iscan bin/zoe2gtf bin/*.pl src/*.pl
+ dolib lib/libzoe.a
+ insinto /usr/share/${PN}
+ doins -r parameters
+ insinto /usr/share/${PN}/src
+ doins src/*.zhmm
+ perl_set_version
+ insinto ${VENDOR_LIB}/${PN}
+ doins lib/perl5/*.pm
+ echo "TWINSCAN=/usr" > "${S}"/99${PN}
+ doenvd "${S}"/99${PN}
+ rm -rf examples/tmp
+ dodoc examples/* README* src/doc/*.txt
+}
+
+pkg_postinst(){
+ einfo "Pairagon acts on output from either: sci-biology/gmap
sci-biology/blat."
+ einfo "It also works on blastn output from WU-BLAST (not provided in
Gentoo)."
+ einfo "It also calls blastz (seems superseded by LASTZ) and genscan++
(not provided in Gentoo)."
+ einfo "For some reason we have pslCDnaFilter provided only by
sci-biology/ucsc-genome-browser"
+}
diff --git a/sci-biology/twinscan/twinscan-4.1.2.ebuild
b/sci-biology/twinscan/twinscan-4.1.2.ebuild
deleted file mode 100644
index 4667c0e..000
--- a/sci-biology/twinscan/twinscan-4.1.2.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-inherit toolchain-funcs
-
-DESCRIPTION="TwinScan, N-SCAN, and Pairagon: A gene structure prediction
pipeline"
-HOMEPAGE="http://mblab.wustl.edu/software/twinscan";
-SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz ->
${P}.tar.gz"
-
-LICENSE="all-rights-reserved"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="dev-libs/glib:2"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/N-SCAN"
-
-src_prepare() {
- sed -i "1 a use lib '/usr/share/${PN}/lib/perl5';" "${S}"/bin/*.pl ||
die
- sed -i '/my $blast_param/ s/#//' "${S}/bin/runTwinscan2.pl" || die
- tc-export CC AR RANLIB
-
- sed \
