[gentoo-commits] proj/sci:master commit in: sci-biology/smalt-bin/
commit: 1337d9fce7f3de3d236ae22cc3a0a22422fac06a
Author: Andrew Ammerlaan riseup net>
AuthorDate: Tue Jan 19 09:35:01 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Tue Jan 19 09:35:01 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1337d9fc
sci-biology/smalt-bin: version bump, EAPI bump
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
.../{smalt-bin-0.7.4.ebuild => smalt-bin-0.7.6.ebuild}| 11 +--
1 file changed, 5 insertions(+), 6 deletions(-)
diff --git a/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild
b/sci-biology/smalt-bin/smalt-bin-0.7.6.ebuild
similarity index 69%
rename from sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild
rename to sci-biology/smalt-bin/smalt-bin-0.7.6.ebuild
index 2059abad6..780bf4210 100644
--- a/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild
+++ b/sci-biology/smalt-bin/smalt-bin-0.7.6.ebuild
@@ -1,21 +1,20 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
MY_PN="${PN%-bin}"
MY_P="${MY_PN}-${PV}"
DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic
reference"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/;
-SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}.tgz;
+HOMEPAGE="https://sourceforge.net/projects/smalt/;
+SRC_URI="https://sourceforge.net/projects/${MY_PN}/files/${MY_P}-bin.tar.gz;
LICENSE="all-rights-reserved"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
-S="${WORKDIR}"/${MY_P}
+S="${WORKDIR}/${MY_P}-bin"
QA_PREBUILT="/opt/.*"
[gentoo-commits] proj/sci:master commit in: sci-biology/smalt/
commit: 801ae3ef893596610f23cd6860a4fdff4684e583
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sun Apr 24 09:30:49 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Apr 24 09:30:49 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=801ae3ef
sci-biology/smalt: document unclear instakll steps, fix DESCRIPTION
Package-Manager: portage-2.2.28
sci-biology/smalt/smalt-0.7.6.ebuild | 10 +-
1 file changed, 9 insertions(+), 1 deletion(-)
diff --git a/sci-biology/smalt/smalt-0.7.6.ebuild
b/sci-biology/smalt/smalt-0.7.6.ebuild
index 9fd8f0e..19d8588 100644
--- a/sci-biology/smalt/smalt-0.7.6.ebuild
+++ b/sci-biology/smalt/smalt-0.7.6.ebuild
@@ -7,7 +7,7 @@ EAPI=5
MY_PN="${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}"/${MY_P}
src_install(){
[gentoo-commits] proj/sci:master commit in: sci-biology/smalt/
commit: 63e8ba87eeb8b788f5003ef5d36d2a298cacd22d
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sun Apr 10 18:09:26 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Apr 10 18:09:26 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=63e8ba87
sci-biology/smalt: new package
Package-Manager: portage-2.2.28
sci-biology/smalt/smalt-0.7.6.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/smalt/smalt-0.7.6.ebuild
b/sci-biology/smalt/smalt-0.7.6.ebuild
index 25d0104..9fd8f0e 100644
--- a/sci-biology/smalt/smalt-0.7.6.ebuild
+++ b/sci-biology/smalt/smalt-0.7.6.ebuild
@@ -13,7 +13,7 @@
SRC_URI="http://sourceforge.net/projects/${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/
commit: 12a65945b9e06f6788ad8ab9dc63463f
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Wed Feb 10 16:28:35 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Feb 10 16:28:35 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=12a6
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 000..1699e58
--- /dev/null
+++ b/sci-biology/smalt/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+
+
+sci-biol...@gentoo.org
+Gentoo Biology Project
+
+
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 000..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
