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

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

[Martin Mokrejs]

commit:     a7cb73596d30fba276ce0826af521d22907c9eaf
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 28 14:03:36 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 28 14:03:36 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a7cb7359

sci-biology/stacks: skeleton for a new package; needs webapp team help, *some* Makefile's need proper DESTDIR support

Package-Manager: portage-2.2.7

---
 sci-biology/stacks/ChangeLog          | 10 +++++++
 sci-biology/stacks/metadata.xml       |  9 +++++++
 sci-biology/stacks/stacks-1.16.ebuild | 49 +++++++++++++++++++++++++++++++++++
 3 files changed, 68 insertions(+)

diff --git a/sci-biology/stacks/ChangeLog b/sci-biology/stacks/ChangeLog
new file mode 100644
index 0000000..ea6c94c
--- /dev/null
+++ b/sci-biology/stacks/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/stacks
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*stacks-1.16 (28 Mar 2014)
+
+  28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+  +stacks-1.16.ebuild:
+  sci-biology/stacks: skeleton for a new package; needs webapp team help, *some*
+  Makefile's need proper DESTDIR support

diff --git a/sci-biology/stacks/metadata.xml b/sci-biology/stacks/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/stacks/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>

diff --git a/sci-biology/stacks/stacks-1.16.ebuild b/sci-biology/stacks/stacks-1.16.ebuild
new file mode 100644
index 0000000..f55dd68
--- /dev/null
+++ b/sci-biology/stacks/stacks-1.16.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit flag-o-matic eutils perl-module webapp
+
+DESCRIPTION="Analyze Restriction enzyme-based data, draw genetic maps, population genomics (RAD-seq Illumina sequencing)"
+HOMEPAGE="http://creskolab.uoregon.edu/stacks"
+SRC_URI="http://creskolab.uoregon.edu/stacks/source/stacks-1.16.tar.gz"
+
+LICENSE="GPL-3"
+# SLOT="0" # webapp ebuilds do not set SLOT
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sys-cluster/openmpi
+	dev-cpp/sparsehash
+	sci-biology/samtools
+	sci-biology/bamtools"
+RDEPEND="${DEPEND}
+	dev-lang/perl
+	>=dev-lang/php-5
+	dev-perl/DBD-mysql"
+
+src_configure() {
+	econf --enable-bam --enable-sparsehash
+	webapp_src_preinst
+	sed -i 's#/usr/lib/libbam.a#-lbam#' Makefile || die
+}
+
+src_compile(){
+	emake DESTDIR="${D}"
+}
+
+src_install() {
+	emake install DESTDIR="${D}"
+	mydoc="Changes README TODO INSTALL"
+	perl-module_src_install DESTDIR="${D}"
+	webapp_src_install || die "Failed running webapp_src_install"
+}
+
+
+pkg_postinst() {
+	webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+}

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

[Nicolas Bock]

commit:     1f2d059a9dabfde3feba094757e22afdb4ee2567
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 28 14:03:36 2014 +0000
Commit:     Nicolas Bock <nicolasbock <AT> gmail <DOT> com>
CommitDate: Mon Mar 31 15:27:34 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1f2d059a

sci-biology/stacks: skeleton for a new package; needs webapp team help, *some* Makefile's need proper DESTDIR support

Package-Manager: portage-2.2.7

---
 sci-biology/stacks/ChangeLog          | 10 +++++++
 sci-biology/stacks/metadata.xml       |  9 +++++++
 sci-biology/stacks/stacks-1.16.ebuild | 49 +++++++++++++++++++++++++++++++++++
 3 files changed, 68 insertions(+)

diff --git a/sci-biology/stacks/ChangeLog b/sci-biology/stacks/ChangeLog
new file mode 100644
index 0000000..ea6c94c
--- /dev/null
+++ b/sci-biology/stacks/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/stacks
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*stacks-1.16 (28 Mar 2014)
+
+  28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+  +stacks-1.16.ebuild:
+  sci-biology/stacks: skeleton for a new package; needs webapp team help, *some*
+  Makefile's need proper DESTDIR support

diff --git a/sci-biology/stacks/metadata.xml b/sci-biology/stacks/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/stacks/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>

diff --git a/sci-biology/stacks/stacks-1.16.ebuild b/sci-biology/stacks/stacks-1.16.ebuild
new file mode 100644
index 0000000..f55dd68
--- /dev/null
+++ b/sci-biology/stacks/stacks-1.16.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=yes
+
+inherit flag-o-matic eutils perl-module webapp
+
+DESCRIPTION="Analyze Restriction enzyme-based data, draw genetic maps, population genomics (RAD-seq Illumina sequencing)"
+HOMEPAGE="http://creskolab.uoregon.edu/stacks"
+SRC_URI="http://creskolab.uoregon.edu/stacks/source/stacks-1.16.tar.gz"
+
+LICENSE="GPL-3"
+# SLOT="0" # webapp ebuilds do not set SLOT
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sys-cluster/openmpi
+	dev-cpp/sparsehash
+	sci-biology/samtools
+	sci-biology/bamtools"
+RDEPEND="${DEPEND}
+	dev-lang/perl
+	>=dev-lang/php-5
+	dev-perl/DBD-mysql"
+
+src_configure() {
+	econf --enable-bam --enable-sparsehash
+	webapp_src_preinst
+	sed -i 's#/usr/lib/libbam.a#-lbam#' Makefile || die
+}
+
+src_compile(){
+	emake DESTDIR="${D}"
+}
+
+src_install() {
+	emake install DESTDIR="${D}"
+	mydoc="Changes README TODO INSTALL"
+	perl-module_src_install DESTDIR="${D}"
+	webapp_src_install || die "Failed running webapp_src_install"
+}
+
+
+pkg_postinst() {
+	webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+}

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

[Christoph Junghans]

commit:     516e1786c44625083bf64955835be31d5b7f9331
Author:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 16 16:26:19 2014 +0000
Commit:     Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Tue Sep 16 16:26:19 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=516e1786

clean up

Package-Manager: portage-2.2.8-r1

---
 sci-biology/stacks/ChangeLog          | 3 +++
 sci-biology/stacks/stacks-1.16.ebuild | 3 +--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/sci-biology/stacks/ChangeLog b/sci-biology/stacks/ChangeLog
index ea6c94c..c842760 100644
--- a/sci-biology/stacks/ChangeLog
+++ b/sci-biology/stacks/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> stacks-1.16.ebuild:
+  clean up
+
 *stacks-1.16 (28 Mar 2014)
 
   28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,

diff --git a/sci-biology/stacks/stacks-1.16.ebuild b/sci-biology/stacks/stacks-1.16.ebuild
index f55dd68..d8a9410 100644
--- a/sci-biology/stacks/stacks-1.16.ebuild
+++ b/sci-biology/stacks/stacks-1.16.ebuild
@@ -8,7 +8,7 @@ AUTOTOOLS_AUTORECONF=yes
 
 inherit flag-o-matic eutils perl-module webapp
 
-DESCRIPTION="Analyze Restriction enzyme-based data, draw genetic maps, population genomics (RAD-seq Illumina sequencing)"
+DESCRIPTION="Analyze Restriction enzyme data, draw gen. maps, population genomics (RAD-seq Illumina sequencing)"
 HOMEPAGE="http://creskolab.uoregon.edu/stacks"
 SRC_URI="http://creskolab.uoregon.edu/stacks/source/stacks-1.16.tar.gz"
 
@@ -43,7 +43,6 @@ src_install() {
 	webapp_src_install || die "Failed running webapp_src_install"
 }
 
-
 pkg_postinst() {
 	webapp_pkg_postinst || die "webapp_pkg_postinst failed"
 }

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

[Martin Mokrejs]

commit:     54a60219b2133d354c713da37c7fbc85d42242c9
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 27 10:59:22 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 27 10:59:22 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=54a60219

sci-biology/stacks: SRC_URI cleanup

Package-Manager: portage-2.2.18

 sci-biology/stacks/ChangeLog          | 5 ++++-
 sci-biology/stacks/stacks-1.16.ebuild | 4 ++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/sci-biology/stacks/ChangeLog b/sci-biology/stacks/ChangeLog
index c842760..d0465fc 100644
--- a/sci-biology/stacks/ChangeLog
+++ b/sci-biology/stacks/ChangeLog
@@ -1,7 +1,10 @@
 # ChangeLog for sci-biology/stacks
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> stacks-1.16.ebuild:
+  sci-biology/stacks: SRC_URI cleanup
+
   16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> stacks-1.16.ebuild:
   clean up
 

diff --git a/sci-biology/stacks/stacks-1.16.ebuild b/sci-biology/stacks/stacks-1.16.ebuild
index d8a9410..bf75b12 100644
--- a/sci-biology/stacks/stacks-1.16.ebuild
+++ b/sci-biology/stacks/stacks-1.16.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -10,7 +10,7 @@ inherit flag-o-matic eutils perl-module webapp
 
 DESCRIPTION="Analyze Restriction enzyme data, draw gen. maps, population genomics (RAD-seq Illumina sequencing)"
 HOMEPAGE="http://creskolab.uoregon.edu/stacks"
-SRC_URI="http://creskolab.uoregon.edu/stacks/source/stacks-1.16.tar.gz"
+SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz"
 
 LICENSE="GPL-3"
 # SLOT="0" # webapp ebuilds do not set SLOT

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

[Martin Mokrejs]

commit:     5ad65da4ea4fab1b11538dad050e8f7c17313206
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 27 18:35:58 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 27 18:35:58 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5ad65da4

sci-biology/stacks: commented out sys-cluster/openmpi DEPENDency

Package-Manager: portage-2.2.18

 sci-biology/stacks/ChangeLog          | 3 +++
 sci-biology/stacks/stacks-1.16.ebuild | 3 ++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/sci-biology/stacks/ChangeLog b/sci-biology/stacks/ChangeLog
index d0465fc..5730b3d 100644
--- a/sci-biology/stacks/ChangeLog
+++ b/sci-biology/stacks/ChangeLog
@@ -3,6 +3,9 @@
 # $Header: $
 
   27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> stacks-1.16.ebuild:
+  sci-biology/stacks: commented out sys-cluster/openmpi DEPENDency
+
+  27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> stacks-1.16.ebuild:
   sci-biology/stacks: SRC_URI cleanup
 
   16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> stacks-1.16.ebuild:

diff --git a/sci-biology/stacks/stacks-1.16.ebuild b/sci-biology/stacks/stacks-1.16.ebuild
index bf75b12..36b1573 100644
--- a/sci-biology/stacks/stacks-1.16.ebuild
+++ b/sci-biology/stacks/stacks-1.16.ebuild
@@ -17,7 +17,8 @@ LICENSE="GPL-3"
 KEYWORDS=""
 IUSE=""
 
-DEPEND="sys-cluster/openmpi
+# sys-cluster/openmpi
+DEPEND="
 	dev-cpp/sparsehash
 	sci-biology/samtools
 	sci-biology/bamtools"

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

[Martin Mokrejs]

commit:     7ce5ca59fd2297afcb385fc468de7f45b44d4210
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Dec  1 16:36:41 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Dec  1 16:36:41 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7ce5ca59

sci-biology/stacks: version bump; drop bundled htslib sources, bug #601366

Package-Manager: portage-2.3.2

 .../stacks/{stacks-1.16.ebuild => stacks-1.44.ebuild}  | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/sci-biology/stacks/stacks-1.16.ebuild b/sci-biology/stacks/stacks-1.44.ebuild
similarity index 62%
rename from sci-biology/stacks/stacks-1.16.ebuild
rename to sci-biology/stacks/stacks-1.44.ebuild
index d5efc0c..131f562 100644
--- a/sci-biology/stacks/stacks-1.16.ebuild
+++ b/sci-biology/stacks/stacks-1.44.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
 # $Id$
 
@@ -6,9 +6,9 @@ EAPI=5
 
 AUTOTOOLS_AUTORECONF=yes
 
-inherit flag-o-matic eutils perl-module webapp
+inherit flag-o-matic eutils perl-module webapp autotools
 
-DESCRIPTION="Analyze Restriction enzyme data, draw gen. maps, population genomics (RAD-seq Illumina sequencing)"
+DESCRIPTION="Analyze restriction enzyme data, draw gen. maps, population genomics (RAD-seq sequencing)"
 HOMEPAGE="http://creskolab.uoregon.edu/stacks"
 SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz"
 
@@ -17,16 +17,23 @@ LICENSE="GPL-3"
 KEYWORDS=""
 IUSE=""
 
-# sys-cluster/openmpi
 DEPEND="
+	>=sci-libs/htslib-1.3.1
 	dev-cpp/sparsehash
-	sci-biology/samtools
+	sci-biology/samtools:*
 	sci-biology/bamtools"
 RDEPEND="${DEPEND}
 	dev-lang/perl
 	>=dev-lang/php-5
 	dev-perl/DBD-mysql"
 
+src_prepare(){
+	sed -e 's/SUBDIRS = htslib/SUBDIRS = /' -i Makefile.am || die
+	mycppflags=`pkg-config --cflags htslib` # is blocked by bug #601366
+	sed -e "s#-I./htslib/htslib#-I${mycppflags}#" -i configure.ac || die
+	eautoreconf
+}
+
 src_configure() {
 	econf --enable-bam --enable-sparsehash
 	webapp_src_preinst
@@ -34,6 +41,7 @@ src_configure() {
 }
 
 src_compile(){
+	rm -rf htslib # zap bundled htslib-1.3.1
 	emake DESTDIR="${D}"
 }
 

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

[Martin Mokrejs]

commit:     8aec8372c9bdfd17983c8d1de3ddad33b7c6945e
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Dec  2 21:31:16 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Dec  2 21:31:16 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8aec8372

sci-biology/stacks: add missing dependency

Package-Manager: portage-2.3.2

 sci-biology/stacks/stacks-1.44.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/stacks/stacks-1.44.ebuild b/sci-biology/stacks/stacks-1.44.ebuild
index 131f562..0b4ca80 100644
--- a/sci-biology/stacks/stacks-1.44.ebuild
+++ b/sci-biology/stacks/stacks-1.44.ebuild
@@ -21,7 +21,8 @@ DEPEND="
 	>=sci-libs/htslib-1.3.1
 	dev-cpp/sparsehash
 	sci-biology/samtools:*
-	sci-biology/bamtools"
+	sci-biology/bamtools
+	sci-biology/gmap" # Source code for both GMAP and GSNAP
 RDEPEND="${DEPEND}
 	dev-lang/perl
 	>=dev-lang/php-5

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

[Martin Mokrejs]

commit:     2272938e78efe357468c8e1b4c3420f6bfe73284
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 30 13:34:47 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 30 13:34:47 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2272938e

sci-biology/stacks:

Package-Manager: Portage-2.3.5, Repoman-2.3.2

 sci-biology/stacks/stacks-1.44.ebuild | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/sci-biology/stacks/stacks-1.44.ebuild b/sci-biology/stacks/stacks-1.44.ebuild
index a7ac01a1f..a4d473e91 100644
--- a/sci-biology/stacks/stacks-1.44.ebuild
+++ b/sci-biology/stacks/stacks-1.44.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -29,15 +29,16 @@ RDEPEND="${DEPEND}
 
 src_prepare(){
 	sed -e 's/SUBDIRS = htslib/SUBDIRS = /' -i Makefile.am || die
-	mycppflags=`pkg-config --cflags htslib` # is blocked by bug #601366
-	sed -e "s#-I./htslib/htslib#-I${mycppflags}#" -i configure.ac || die
+	#mycppflags=`pkg-config --cflags htslib` # is blocked by bug #601366
+	if [ -z "$mycppflags" ]; then mycppflags="."; fi
+	sed -e "s#-I./htslib/htslib#-I/usr/include/bam -I${mycppflags}#" -i configure.ac || die
 	eautoreconf
 }
 
 src_configure() {
 	econf --enable-bam --enable-sparsehash
 	webapp_src_preinst
-	sed -i 's#/usr/lib/libbam.a#-lbam#' Makefile || die
+	sed -i 's#/usr/lib/libbam.a#-lbam#;#./htslib/libhts.a#-lhts#' Makefile || die
 }
 
 src_compile(){

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

[Martin Mokrejs]

commit:     e775d986b79d735a837a50360915536b2b28a080
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 30 13:36:58 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 30 13:36:58 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e775d986

sci-biology/stacks: rely on SLOT 0 of htslib < 1.4

Supposedly stacks would not work with htslib-1.4 which provides libhtslib.so.2

Package-Manager: Portage-2.3.5, Repoman-2.3.2

 sci-biology/stacks/stacks-1.44.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/stacks/stacks-1.44.ebuild b/sci-biology/stacks/stacks-1.44.ebuild
index a4d473e91..3106657e9 100644
--- a/sci-biology/stacks/stacks-1.44.ebuild
+++ b/sci-biology/stacks/stacks-1.44.ebuild
@@ -17,7 +17,7 @@ KEYWORDS=""
 IUSE=""
 
 DEPEND="
-	>=sci-libs/htslib-1.3.1
+	>=sci-libs/htslib-1.3.1:0
 	dev-cpp/sparsehash
 	sci-biology/samtools:*
 	sci-biology/bamtools

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

[Andrew Ammerlaan]

commit:     d93f43a0459c27bc0268cc5cec3ad2f780b0e905
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 11:07:16 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 11:07:16 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=d93f43a0

sci-biology/stacks: bump to version 2.60

Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 .../{stacks-2.55.ebuild => stacks-2.60.ebuild}     | 31 ++++++++++------------
 1 file changed, 14 insertions(+), 17 deletions(-)

diff --git a/sci-biology/stacks/stacks-2.55.ebuild b/sci-biology/stacks/stacks-2.60.ebuild
similarity index 66%
rename from sci-biology/stacks/stacks-2.55.ebuild
rename to sci-biology/stacks/stacks-2.60.ebuild
index becd91a5d..4de3f8da8 100644
--- a/sci-biology/stacks/stacks-2.55.ebuild
+++ b/sci-biology/stacks/stacks-2.60.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
 inherit perl-module webapp autotools
 
@@ -10,10 +10,8 @@ HOMEPAGE="http://creskolab.uoregon.edu/stacks"
 SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz"
 
 LICENSE="GPL-3"
-# SLOT="0" # webapp ebuilds do not set SLOT
-KEYWORDS=""
+KEYWORDS="~amd64"
 
-# No rule to make target test
 RESTRICT="test"
 
 DEPEND="
@@ -21,11 +19,14 @@ DEPEND="
 	dev-cpp/sparsehash
 	sci-biology/samtools:*
 	sci-biology/bamtools
-	sci-biology/gmap" # Source code for both GMAP and GSNAP
+	sci-biology/gmap
+"
+
 RDEPEND="${DEPEND}
 	dev-lang/perl
-	>=dev-lang/php-5
-	dev-perl/DBD-mysql"
+	>=dev-lang/php-5:*
+	dev-perl/DBD-mysql
+"
 
 PATCHES=(
 	"${FILESDIR}/${PN}-make-install.patch"
@@ -41,17 +42,13 @@ src_prepare(){
 
 src_configure() {
 	econf
-	webapp_src_preinst
 	sed -e 's#/usr/lib/libbam.a#-lbam#;#./htslib/libhts.a#-lhts#' -i Makefile || die
 }
 
 src_install() {
-	emake install DESTDIR="${ED}"
-	mydoc="Changes README TODO INSTALL"
-	perl-module_src_install DESTDIR="${ED}"
-	webapp_src_install || die "Failed running webapp_src_install"
-}
-
-pkg_postinst() {
-	webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+	webapp_src_preinst
+	DESTDIR="${ED}" default
+	DESTDIR="${ED}" perl-module_src_install
+	dodir /usr/share/webapps/${PN}/${PV}
+	webapp_src_install
 }