* [gentoo-commits] proj/sci:master commit in: sci-biology/manatee-igs/
@ 2012-01-08 12:14 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2012-01-08 12:14 UTC (permalink / raw
To: gentoo-commits
commit: e7df2fee99694eb290f7646148bf8aef3e9f4ac5
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jan 8 12:06:34 2012 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jan 8 12:06:34 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e7df2fee
sci-biology/manatee-igs: new package for prokaryotic genome annotation and editing using chado
---
sci-biology/manatee-igs/ChangeLog | 10 +++
sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild | 77 +++++++++++++++++++++
sci-biology/manatee-igs/metadata.xml | 9 +++
3 files changed, 96 insertions(+), 0 deletions(-)
diff --git a/sci-biology/manatee-igs/ChangeLog b/sci-biology/manatee-igs/ChangeLog
new file mode 100644
index 0000000..163f6a4
--- /dev/null
+++ b/sci-biology/manatee-igs/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/manatee-igs
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*manatee-igs-2.23.1 (08 Jan 2012)
+
+ 08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +manatee-igs-2.23.1.ebuild, +metadata.xml:
+ new package for prokaryotic genome annotation and editing
+
diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
new file mode 100644
index 0000000..b2f4e39
--- /dev/null
+++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION="IGS-modified version of the genome annotation tool that can view, modify and store annotation for prokaryotic and eukaryotic genomes."
+HOMEPAGE="http://manatee.sourceforge.net/igs"
+SRC_URI="http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz
+ http://manatee.sourceforge.net/igs/docs/README_Linux.txt"
+
+LICENSE="Artistic-IGS"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="
+ >=dev-libs/expat-1.95.8
+ >=media-libs/gd-2.0.34
+ virtual/perl-CGI
+ dev-perl/DBI
+ dev-perl/DBD-mysql
+ dev-perl/XML-Parser
+ dev-perl/XML-Twig
+ dev-perl/XML-Simple
+ dev-perl/XML-Writer
+ dev-perl/HTML-Template
+ dev-perl/Tree-DAG_Node
+ virtual/perl-File-Spec
+ virtual/perl-Data-Dumper
+ dev-perl/GD
+ dev-perl/GDTextUtil
+ dev-perl/GDGraph
+ virtual/perl-Storable
+ dev-perl/Log-Log4perl
+ dev-perl/Log-Cabin
+ dev-perl/DateManip
+ dev-perl/IO-Tee
+ dev-perl/MLDBM
+ dev-perl/JSON
+ dev-perl/JSON-Any
+ sci-biology/bioperl"
+RDEPEND="${DEPEND}
+ >=dev-db/mysql-5.0
+ >=www-servers/apache-2.2"
+
+S="${WORKDIR}"/manatee-"${PV}"_linux
+
+src_prepare(){
+ find "${S}" -name \*.cgi | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
+ find "${S}" -name \*.pl | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
+ find "${S}" -name \*.pm | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
+}
+
+#src_configure(){
+# there used to be manateee-="${PV}".tgz file which contained configure script in the past
+# now the layout is different, temporarily commenting out untill we find the current full sources back again
+# econf HTTPD=/usr/sbin/httpd HTTPD_SCRIPT_HOME=/var/www/cgi-bin HTTPD_DOC_HOME=/var/www/htdocs MYSQLD=/usr/sbin/mysqld || die
+#}
+#
+#src_compile(){
+# emake || die
+#}
+
+src_install(){
+ dodoc ${DISTDIR}"/README_Linux.txt"
+ dodir /var/www/localhost/cgi-bin
+ cp -r src/cgi-bin/chado_prok_manatee "${D}"/var/www/localhost/cgi-bin
+ dodir /var/www/localhost/htdocs/manatee
+ cp -r src/htdocs/tdb "${D}"/var/www/localhost/htdocs/manatee
+
+ einfo "Please read the "${S}"/databases/Makefile.PL and import the databases into your MySQL database"
+
+ einfo "You have to fetch the 1.1 GB large file from http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/lookups-"${PV}"_linux.tgz"
+ einfo "You need to update it regularly."
+ einfo "Also fetch http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/blastdb-"${PV}".tgz (about 2MB in size)"
+}
diff --git a/sci-biology/manatee-igs/metadata.xml b/sci-biology/manatee-igs/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/manatee-igs/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] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/manatee-igs/
@ 2013-08-29 14:17 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2013-08-29 14:17 UTC (permalink / raw
To: gentoo-commits
commit: cfecfd293133b3bd4028c3ff87345d7dac6f1a3f
Author: Martin Mokrejš <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Thu Aug 29 14:17:02 2013 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Aug 29 14:17:02 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cfecfd29
Added dev-perl/Bio-DB-Das-Chado and improved description line. Renamed the License file.
Package-Manager: portage-2.1.12.5
---
sci-biology/manatee-igs/ChangeLog | 8 ++++++++
sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild | 5 +++--
2 files changed, 11 insertions(+), 2 deletions(-)
diff --git a/sci-biology/manatee-igs/ChangeLog b/sci-biology/manatee-igs/ChangeLog
index 66c444c..6bc3a81 100644
--- a/sci-biology/manatee-igs/ChangeLog
+++ b/sci-biology/manatee-igs/ChangeLog
@@ -2,6 +2,14 @@
# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ manatee-igs-2.23.1.ebuild:
+ Renamed the License file.
+
+ 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ manatee-igs-2.23.1.ebuild:
+ Added dev-perl/Bio-DB-Das-Chado and improved description line.
+
03 Mar 2013; Justin Lecher <jlec@gentoo.org> manatee-igs-2.23.1.ebuild,
metadata.xml:
Shorten DESCRIPTION
diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
index d97e8de..fc9d410 100644
--- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
+++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
@@ -4,12 +4,12 @@
EAPI=3
-DESCRIPTION="IGS-modified version of the genome annotation tool"
+DESCRIPTION="IGS-modified version of the genome annotation tool using Chado database schema"
HOMEPAGE="http://manatee.sourceforge.net/igs"
SRC_URI="http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz
http://manatee.sourceforge.net/igs/docs/README_Linux.txt"
-LICENSE="Artistic-IGS"
+LICENSE="Artistic-Manatee-IGS"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
@@ -18,6 +18,7 @@ DEPEND="
>=dev-libs/expat-1.95.8
>=media-libs/gd-2.0.34
virtual/perl-CGI
+ dev-perl/Bio-DB-Das-Chado
dev-perl/DBI
dev-perl/DBD-mysql
dev-perl/XML-Parser
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/manatee-igs/
@ 2013-08-29 14:23 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2013-08-29 14:23 UTC (permalink / raw
To: gentoo-commits
commit: 0ceb33a6bb4dc45e3a998a73d1b84193c912f898
Author: Martin Mokrejš <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Thu Aug 29 14:22:57 2013 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Aug 29 14:22:57 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0ceb33a6
Both versions of manatee have same license, so rename unify the license filename.
Package-Manager: portage-2.1.12.5
---
sci-biology/manatee-igs/ChangeLog | 5 +++++
sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild | 2 +-
2 files changed, 6 insertions(+), 1 deletion(-)
diff --git a/sci-biology/manatee-igs/ChangeLog b/sci-biology/manatee-igs/ChangeLog
index 6bc3a81..2c85c80 100644
--- a/sci-biology/manatee-igs/ChangeLog
+++ b/sci-biology/manatee-igs/ChangeLog
@@ -4,6 +4,11 @@
29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
manatee-igs-2.23.1.ebuild:
+ Both versions of manatee have same license, so rename unify the license
+ filename.
+
+ 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ manatee-igs-2.23.1.ebuild:
Renamed the License file.
29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
index fc9d410..c5b1c00 100644
--- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
+++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
@@ -9,7 +9,7 @@ HOMEPAGE="http://manatee.sourceforge.net/igs"
SRC_URI="http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz
http://manatee.sourceforge.net/igs/docs/README_Linux.txt"
-LICENSE="Artistic-Manatee-IGS"
+LICENSE="Artistic-Manatee"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/manatee-igs/
@ 2015-06-15 7:24 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2015-06-15 7:24 UTC (permalink / raw
To: gentoo-commits
commit: 6f9bc02910243a77c9c67f768877a511868b8706
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jun 15 07:21:37 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jun 15 07:21:37 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6f9bc029
sci-biology/manatee-igs: Fix dependency problems due to recent mask of perl-core packages
Package-Manager: portage-2.2.20
sci-biology/manatee-igs/ChangeLog | 7 ++-
sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild | 65 ++++++++++++-----------
2 files changed, 38 insertions(+), 34 deletions(-)
diff --git a/sci-biology/manatee-igs/ChangeLog b/sci-biology/manatee-igs/ChangeLog
index 2c85c80..8a60b08 100644
--- a/sci-biology/manatee-igs/ChangeLog
+++ b/sci-biology/manatee-igs/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/manatee-igs
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 15 Jun 2015; Justin Lecher <jlec@gentoo.org> manatee-igs-2.23.1.ebuild:
+ sci-biology/manatee-igs: Fix dependency problems due to recent mask of perl-
+ core packages
+
29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
manatee-igs-2.23.1.ebuild:
Both versions of manatee have same license, so rename unify the license
@@ -24,4 +28,3 @@
08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+manatee-igs-2.23.1.ebuild, +metadata.xml:
new package for prokaryotic genome annotation and editing
-
diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
index b858a9d..fb0fa9f 100644
--- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
+++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
@@ -1,13 +1,14 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI=5
DESCRIPTION="IGS-modified version of the genome annotation tool using Chado database schema"
HOMEPAGE="http://manatee.sourceforge.net/igs"
-SRC_URI="http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz
- http://manatee.sourceforge.net/igs/docs/README_Linux.txt"
+SRC_URI="
+ http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz
+ http://manatee.sourceforge.net/igs/docs/README_Linux.txt"
LICENSE="Artistic-Manatee"
SLOT="0"
@@ -15,35 +16,35 @@ KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND="
- >=dev-libs/expat-1.95.8
- >=media-libs/gd-2.0.34
- virtual/perl-CGI
- dev-perl/Bio-DB-Das-Chado
- dev-perl/DBI
- dev-perl/DBD-mysql
- dev-perl/XML-Parser
- dev-perl/XML-Twig
- dev-perl/XML-Simple
- dev-perl/XML-Writer
- dev-perl/HTML-Template
- dev-perl/Tree-DAG_Node
- virtual/perl-File-Spec
- virtual/perl-Data-Dumper
- dev-perl/GD
- dev-perl/GDTextUtil
- dev-perl/GDGraph
- virtual/perl-Storable
- dev-perl/Log-Log4perl
- dev-perl/Log-Cabin
- dev-perl/DateManip
- dev-perl/IO-Tee
- dev-perl/MLDBM
- dev-perl/JSON
- dev-perl/JSON-Any
- sci-biology/bioperl"
+ >=dev-libs/expat-1.95.8
+ >=media-libs/gd-2.0.34
+ dev-perl/CGI
+ dev-perl/Bio-DB-Das-Chado
+ dev-perl/DBI
+ dev-perl/DBD-mysql
+ dev-perl/XML-Parser
+ dev-perl/XML-Twig
+ dev-perl/XML-Simple
+ dev-perl/XML-Writer
+ dev-perl/HTML-Template
+ dev-perl/Tree-DAG_Node
+ virtual/perl-File-Spec
+ virtual/perl-Data-Dumper
+ dev-perl/GD
+ dev-perl/GDTextUtil
+ dev-perl/GDGraph
+ virtual/perl-Storable
+ dev-perl/Log-Log4perl
+ dev-perl/Log-Cabin
+ dev-perl/DateManip
+ dev-perl/IO-Tee
+ dev-perl/MLDBM
+ dev-perl/JSON
+ dev-perl/JSON-Any
+ sci-biology/bioperl"
RDEPEND="${DEPEND}
- >=dev-db/mysql-5.0
- >=www-servers/apache-2.2"
+ >=dev-db/mysql-5.0
+ >=www-servers/apache-2.2"
S="${WORKDIR}"/manatee-"${PV}"_linux
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/manatee-igs/
@ 2015-10-27 9:55 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2015-10-27 9:55 UTC (permalink / raw
To: gentoo-commits
commit: edde16d884c59dc11f1248d956fceb7107b09796
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Oct 27 09:54:50 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Oct 27 09:54:50 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=edde16d8
sci-biology/manatee-igs: depend on virtual/mysql
Package-Manager: portage-2.2.18
sci-biology/manatee-igs/ChangeLog | 4 ++++
sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/manatee-igs/ChangeLog b/sci-biology/manatee-igs/ChangeLog
index 01247af..e998238 100644
--- a/sci-biology/manatee-igs/ChangeLog
+++ b/sci-biology/manatee-igs/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 27 Oct 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ manatee-igs-2.23.1.ebuild:
+ sci-biology/manatee-igs: depend on virtual/mysql
+
15 Jun 2015; Justin Lecher <jlec@gentoo.org> manatee-igs-2.23.1.ebuild:
sci-biology/manatee-igs: Fix dependency problems due to recent mask of perl-
core packages
diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
index b30b966..a78d5a5 100644
--- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
+++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
@@ -43,7 +43,7 @@ DEPEND="
dev-perl/JSON-Any
sci-biology/bioperl"
RDEPEND="${DEPEND}
- >=dev-db/mysql-5.0
+ >=virtual/mysql-5:*
>=www-servers/apache-2.2"
S="${WORKDIR}"/manatee-"${PV}"_linux
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/manatee-igs/
@ 2016-03-29 17:21 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2016-03-29 17:21 UTC (permalink / raw
To: gentoo-commits
commit: 58963a4ba9708879315ff21e69ad1fa0675a7223
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Mar 29 17:19:16 2016 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Mar 29 17:19:16 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=58963a4b
sci-biology/manatee-igs: Fix typo in deps
* Bump to EAPI=6
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
index a78d5a5..aa8f6ca 100644
--- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
+++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
DESCRIPTION="IGS-modified version of the genome annotation tool using Chado database schema"
HOMEPAGE="http://manatee.sourceforge.net/igs"
@@ -36,7 +36,7 @@ DEPEND="
virtual/perl-Storable
dev-perl/Log-Log4perl
dev-perl/Log-Cabin
- dev-perl/DateManip
+ dev-perl/Date-Manip
dev-perl/IO-Tee
dev-perl/MLDBM
dev-perl/JSON
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/manatee-igs/
@ 2021-01-19 12:18 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 12:18 UTC (permalink / raw
To: gentoo-commits
commit: ceed30c6026675c078281eb668ef28bedbbd0999
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 12:17:16 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 12:17:16 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ceed30c6
sci-biology/manatee-igs: EAPI bump, fix fetch, use https
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild | 27 ++++++-----------------
1 file changed, 7 insertions(+), 20 deletions(-)
diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
index 65dda0367..8a21f8f36 100644
--- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
+++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild
@@ -1,18 +1,15 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
DESCRIPTION="IGS-modified version of the genome annotation tool using Chado database schema"
HOMEPAGE="http://manatee.sourceforge.net/igs" # no https
-SRC_URI="
- https://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz
- http://manatee.sourceforge.net/igs/docs/README_Linux.txt"
+SRC_URI="https://downloads.sourceforge.net/project/manatee/igs_manatee/${PV}/manatee-${PV}_linux.tgz"
LICENSE="Artistic-Manatee"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
DEPEND="
>=dev-libs/expat-1.95.8
@@ -45,26 +42,16 @@ RDEPEND="${DEPEND}
>=virtual/mysql-5:*
>=www-servers/apache-2.2"
-S="${WORKDIR}"/manatee-"${PV}"_linux
+S="${WORKDIR}/manatee-${PV}_linux"
src_prepare(){
+ default
find "${S}" -name \*.cgi | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
find "${S}" -name \*.pl | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
find "${S}" -name \*.pm | while read f; do sed -e 's|#!/usr/local/bin/perl|#!/usr/bin/perl|' -i $f; done
}
-#src_configure(){
-# there used to be manateee-="${PV}".tgz file which contained configure script in the past
-# now the layout is different, temporarily commenting out untill we find the current full sources back again
-# econf HTTPD=/usr/sbin/httpd HTTPD_SCRIPT_HOME=/var/www/cgi-bin HTTPD_DOC_HOME=/var/www/htdocs MYSQLD=/usr/sbin/mysqld || die
-#}
-#
-#src_compile(){
-# default
-#}
-
src_install(){
- dodoc ${DISTDIR}"/README_Linux.txt"
dodir /var/www/localhost/cgi-bin
cp -r src/cgi-bin/chado_prok_manatee "${D}"/var/www/localhost/cgi-bin
dodir /var/www/localhost/htdocs/manatee
@@ -72,7 +59,7 @@ src_install(){
einfo "Please read the "${S}"/databases/Makefile.PL and import the databases into your MySQL database"
- einfo "You have to fetch the 1.1 GB large file from http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/lookups-"${PV}"_linux.tgz"
+ einfo "You have to fetch the 1.1 GB large file from https://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/lookups-"${PV}"_linux.tgz"
einfo "You need to update it regularly."
- einfo "Also fetch http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/blastdb-"${PV}".tgz (about 2MB in size)"
+ einfo "Also fetch https://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/blastdb-"${PV}".tgz (about 2MB in size)"
}
^ permalink raw reply related [flat|nested] 7+ messages in thread
end of thread, other threads:[~2021-01-19 12:18 UTC | newest]
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2016-03-29 17:21 [gentoo-commits] proj/sci:master commit in: sci-biology/manatee-igs/ Justin Lecher
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2021-01-19 12:18 Andrew Ammerlaan
2015-10-27 9:55 Martin Mokrejs
2015-06-15 7:24 Justin Lecher
2013-08-29 14:23 Martin Mokrejs
2013-08-29 14:17 Martin Mokrejs
2012-01-08 12:14 Martin Mokrejs
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