[gentoo-commits] proj/sci:master commit in: sci-biology/stampy/

[gentoo-commits] proj/sci:master commit in: sci-biology/stampy/

[Martin Mokrejs]

commit:     e48ef93babd11710d0e39fdea396cbd12f594968
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 15 13:13:31 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 15 13:13:31 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e48ef93b

sci-biology/stampy: new package; installs into wrong PYTHON library path

Package-Manager: portage-2.2.28

 sci-biology/stampy/metadata.xml         | 12 ++++++++++++
 sci-biology/stampy/stampy-1.0.28.ebuild | 30 ++++++++++++++++++++++++++++++
 2 files changed, 42 insertions(+)

diff --git a/sci-biology/stampy/metadata.xml b/sci-biology/stampy/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/stampy/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>

diff --git a/sci-biology/stampy/stampy-1.0.28.ebuild b/sci-biology/stampy/stampy-1.0.28.ebuild
new file mode 100644
index 0000000..c820e6a
--- /dev/null
+++ b/sci-biology/stampy/stampy-1.0.28.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="Map highly divergent short reads to a reference"
+HOMEPAGE="http://www.well.ox.ac.uk/project-stampy"
+SRC_URI="${P}.tar.gz"
+
+LICENSE="stampy-academic"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+RESTRICT="fetch"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_install(){
+	dobin *.py
+	local dest=/usr/$(get_libdir) # FIXME: still not correct
+	insinto "${dest}"
+	doins maptools.so
+	fperms a+x ${dest}/maptools.so
+	dodoc README.txt
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/stampy/

[Martin Mokrejs]

commit:     576445046f5ea458cdc48be6f22b38b08e3a80d5
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 15 14:23:15 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 15 14:23:15 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=57644504

sci-biology/stampy: does not work with python-3.4 at least, works with 2.7

Package-Manager: portage-2.2.28

 sci-biology/stampy/stampy-1.0.28.ebuild | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/sci-biology/stampy/stampy-1.0.28.ebuild b/sci-biology/stampy/stampy-1.0.28.ebuild
index c820e6a..9dbf6de 100644
--- a/sci-biology/stampy/stampy-1.0.28.ebuild
+++ b/sci-biology/stampy/stampy-1.0.28.ebuild
@@ -2,7 +2,8 @@
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=6
+EAPI=5
+PYTHON_COMPAT=( python{2_7} )
 
 inherit toolchain-funcs
 
@@ -20,6 +21,7 @@ RESTRICT="fetch"
 DEPEND=""
 RDEPEND="${DEPEND}"
 
+# FIXME: the makefile calls python but fails if that is under python-3.4, 2.7 works
 src_install(){
 	dobin *.py
 	local dest=/usr/$(get_libdir) # FIXME: still not correct

[gentoo-commits] proj/sci:master commit in: sci-biology/stampy/

[Martin Mokrejs]

commit:     f09ae7878a4999af31bcbc40eb30c5e4172b5550
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jul 30 22:39:41 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jul 30 22:39:41 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f09ae787

sci-biology/stampy: install shared library into site-packages

Package-Manager: portage-2.3.0

 sci-biology/stampy/stampy-1.0.28.ebuild | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/sci-biology/stampy/stampy-1.0.28.ebuild b/sci-biology/stampy/stampy-1.0.28.ebuild
index 9dbf6de..02fc2cf 100644
--- a/sci-biology/stampy/stampy-1.0.28.ebuild
+++ b/sci-biology/stampy/stampy-1.0.28.ebuild
@@ -3,9 +3,9 @@
 # $Id$
 
 EAPI=5
-PYTHON_COMPAT=( python{2_7} )
+PYTHON_COMPAT=( python2_7 )
 
-inherit toolchain-funcs
+inherit toolchain-funcs python-single-r1
 
 DESCRIPTION="Map highly divergent short reads to a reference"
 HOMEPAGE="http://www.well.ox.ac.uk/project-stampy"
@@ -24,9 +24,10 @@ RDEPEND="${DEPEND}"
 # FIXME: the makefile calls python but fails if that is under python-3.4, 2.7 works
 src_install(){
 	dobin *.py
-	local dest=/usr/$(get_libdir) # FIXME: still not correct
-	insinto "${dest}"
+	insinto $(python_get_sitedir)
 	doins maptools.so
-	fperms a+x ${dest}/maptools.so
+	# doins -r stampy-1.0.28/build/python2.7/Stampy # only *.pyc files available
+	# doins -r python2.7/ext # only *.pyc files available
+	fperms a+x "$(python_get_sitedir)"/maptools.so
 	dodoc README.txt
 }

[gentoo-commits] proj/sci:master commit in: sci-biology/stampy/

[Martin Mokrejs]

commit:     e6d24877d78b288c57387387ba8ee3fcd1ee1c55
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jul 31 17:09:24 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jul 31 17:09:24 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e6d24877

sci-biology/stampy: renamed to stampy-bin

 sci-biology/stampy/metadata.xml         | 12 ------------
 sci-biology/stampy/stampy-1.0.28.ebuild | 33 ---------------------------------
 2 files changed, 45 deletions(-)

diff --git a/sci-biology/stampy/metadata.xml b/sci-biology/stampy/metadata.xml
deleted file mode 100644
index f68a1b6..0000000
--- a/sci-biology/stampy/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="person">
-    <email>mmokrejs@fold.natur.cuni.cz</email>
-    <name>Martin Mokrejs</name>
-  </maintainer>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>

diff --git a/sci-biology/stampy/stampy-1.0.28.ebuild b/sci-biology/stampy/stampy-1.0.28.ebuild
deleted file mode 100644
index 02fc2cf..0000000
--- a/sci-biology/stampy/stampy-1.0.28.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-PYTHON_COMPAT=( python2_7 )
-
-inherit toolchain-funcs python-single-r1
-
-DESCRIPTION="Map highly divergent short reads to a reference"
-HOMEPAGE="http://www.well.ox.ac.uk/project-stampy"
-SRC_URI="${P}.tar.gz"
-
-LICENSE="stampy-academic"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-RESTRICT="fetch"
-
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-# FIXME: the makefile calls python but fails if that is under python-3.4, 2.7 works
-src_install(){
-	dobin *.py
-	insinto $(python_get_sitedir)
-	doins maptools.so
-	# doins -r stampy-1.0.28/build/python2.7/Stampy # only *.pyc files available
-	# doins -r python2.7/ext # only *.pyc files available
-	fperms a+x "$(python_get_sitedir)"/maptools.so
-	dodoc README.txt
-}