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

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

[Martin Mokrejs]

commit:     12acccc65945ccccb9e06f6788ad8ab9dc63463f
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Feb 10 16:28:35 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 10 16:28:35 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=12acccc6

sci-biology/smalt: finally a package to build from sources

Package-Manager: portage-2.2.26

 sci-biology/smalt/metadata.xml       | 12 ++++++++++++
 sci-biology/smalt/smalt-0.7.6.ebuild | 29 +++++++++++++++++++++++++++++
 2 files changed, 41 insertions(+)

diff --git a/sci-biology/smalt/metadata.xml b/sci-biology/smalt/metadata.xml
new file mode 100644
index 0000000..1699e58
--- /dev/null
+++ b/sci-biology/smalt/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/smalt/smalt-0.7.6.ebuild b/sci-biology/smalt/smalt-0.7.6.ebuild
new file mode 100644
index 0000000..25d0104
--- /dev/null
+++ b/sci-biology/smalt/smalt-0.7.6.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+MY_PN="${PN%-bin}"
+MY_P="${MY_PN}-${PV}"
+
+DESCRIPTION="Successor of ssaha2: pairwise sequence alignment mapping DNA reads"
+HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/"
+SRC_URI="http://sourceforge.net/projects/${PN}/files/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+S="${WORKDIR}"/${MY_P}
+
+src_install(){
+	dobin src/smalt
+	insinto /usr/share/"${PN}"
+	doins misc/*.py
+	dodoc README NEWS
+}
+# is the tarball with source code lacking the manual?
+#	dodoc NEWS ${MY_PN}_manual.pdf
+#	doman ${MY_PN}.1

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

[Martin Mokrejs]

commit:     63e8ba87eeb8b788f5003ef5d36d2a298cacd22d
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 10 18:09:26 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 10 18:09:26 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=63e8ba87

sci-biology/smalt: new package

Package-Manager: portage-2.2.28

 sci-biology/smalt/smalt-0.7.6.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/smalt/smalt-0.7.6.ebuild b/sci-biology/smalt/smalt-0.7.6.ebuild
index 25d0104..9fd8f0e 100644
--- a/sci-biology/smalt/smalt-0.7.6.ebuild
+++ b/sci-biology/smalt/smalt-0.7.6.ebuild
@@ -13,7 +13,7 @@ SRC_URI="http://sourceforge.net/projects/${PN}/files/${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
 IUSE=""
 
 S="${WORKDIR}"/${MY_P}
@@ -24,6 +24,6 @@ src_install(){
 	doins misc/*.py
 	dodoc README NEWS
 }
-# is the tarball with source code lacking the manual?
+# is the tarball with source code lacking the manual? Upstream contacted.
 #	dodoc NEWS ${MY_PN}_manual.pdf
 #	doman ${MY_PN}.1

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

[Martin Mokrejs]

commit:     801ae3ef893596610f23cd6860a4fdff4684e583
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 24 09:30:49 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 24 09:30:49 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=801ae3ef

sci-biology/smalt: document unclear instakll steps, fix DESCRIPTION

Package-Manager: portage-2.2.28

 sci-biology/smalt/smalt-0.7.6.ebuild | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/sci-biology/smalt/smalt-0.7.6.ebuild b/sci-biology/smalt/smalt-0.7.6.ebuild
index 9fd8f0e..19d8588 100644
--- a/sci-biology/smalt/smalt-0.7.6.ebuild
+++ b/sci-biology/smalt/smalt-0.7.6.ebuild
@@ -7,7 +7,7 @@ EAPI=5
 MY_PN="${PN%-bin}"
 MY_P="${MY_PN}-${PV}"
 
-DESCRIPTION="Successor of ssaha2: pairwise sequence alignment mapping DNA reads"
+DESCRIPTION="DNA read mapper using k=20 (successor of ssaha2)"
 HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/"
 SRC_URI="http://sourceforge.net/projects/${PN}/files/${P}.tar.gz"
 
@@ -16,6 +16,14 @@ SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""
 
+DEPEND=""
+RDEPEND="${DEPEND}"
+# TODO: add https://github.com/gt1/bambamc dependency
+# ./configure --with-bambamc=yes BAMBAMC_CFLAGS="-I$BAMBAMC_INSTALL_DIR/include" BAMBAMC_LIBS="-L$BAMBAMC_INSTALL_DIR/lib -lbambamc"
+#
+# but NEWS states
+# - Ammended installation instructions with the bambamc library.
+
 S="${WORKDIR}"/${MY_P}
 
 src_install(){