* [gentoo-commits] proj/sci:master commit in: sci-biology/bamql/
@ 2018-03-30 23:13 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2018-03-30 23:13 UTC (permalink / raw
To: gentoo-commits
commit: ee649bc48962c51c37ae92acdd85e65f480e48bf
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 30 23:13:32 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 30 23:13:32 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ee649bc4
sci-biology/bamql: new package
Package-Manager: Portage-2.3.24, Repoman-2.3.6
sci-biology/bamql/bamql-1.5.ebuild | 28 ++++++++++++++++++++++++++++
sci-biology/bamql/metadata.xml | 12 ++++++++++++
2 files changed, 40 insertions(+)
diff --git a/sci-biology/bamql/bamql-1.5.ebuild b/sci-biology/bamql/bamql-1.5.ebuild
new file mode 100644
index 000000000..ef78e3753
--- /dev/null
+++ b/sci-biology/bamql/bamql-1.5.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools
+
+DESCRIPTION="Extract reads from BAM files"
+HOMEPAGE="https://github.com/BoutrosLaboratory/bamql
+ https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1162-y"
+SRC_URI="https://github.com/BoutrosLaboratory/bamql/archive/v1.5.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="
+ sys-devel/llvm:=
+ sys-apps/util-linux
+ sci-libs/htslib
+ dev-libs/libpcre"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+ eautoreconf
+ default
+}
diff --git a/sci-biology/bamql/metadata.xml b/sci-biology/bamql/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/bamql/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>
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bamql/
@ 2018-05-01 5:55 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2018-05-01 5:55 UTC (permalink / raw
To: gentoo-commits
commit: 35f7bda074493d740f250c2b434f66636082272d
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May 1 05:55:21 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May 1 05:55:21 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=35f7bda0
sci-biology/bamql: add live ebuild
Package-Manager: Portage-2.3.31, Repoman-2.3.9
sci-biology/bamql/bamql-9999.ebuild | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
diff --git a/sci-biology/bamql/bamql-9999.ebuild b/sci-biology/bamql/bamql-9999.ebuild
new file mode 100644
index 000000000..44a7d85f5
--- /dev/null
+++ b/sci-biology/bamql/bamql-9999.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools git-r3
+
+DESCRIPTION="Extract reads from BAM files"
+HOMEPAGE="https://github.com/BoutrosLaboratory/bamql
+ https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1162-y"
+EGIT_REPO_URI="https://github.com/BoutrosLaboratory/bamql.git"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+ sys-devel/llvm:=
+ sys-apps/util-linux
+ sci-libs/htslib
+ dev-libs/libpcre"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+ eautoreconf
+ default
+}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bamql/
@ 2019-03-23 15:01 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2019-03-23 15:01 UTC (permalink / raw
To: gentoo-commits
commit: 565f9b0c0ef3c2c6917d27a17495dbc279bc92de
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Mar 23 15:01:39 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Mar 23 15:01:39 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=565f9b0c
sci-biology/bamql: add IUSE="static-libs"
Provided one specifies `--enable-static=no --enable-static-llvm=no` the
patch in
https://github.com/BoutrosLaboratory/bamql/commit/94417720bc7653a90cd9edd932ba6ba52d7bb89b
is really needed (as these two args are enough to compile bamql-1.6 and
llvm with only shared libs).
See https://github.com/BoutrosLaboratory/bamql/issues/14
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/bamql/{bamql-1.5.ebuild => bamql-1.6.ebuild} | 15 +++++++++++----
sci-biology/bamql/bamql-9999.ebuild | 11 +++++++++--
2 files changed, 20 insertions(+), 6 deletions(-)
diff --git a/sci-biology/bamql/bamql-1.5.ebuild b/sci-biology/bamql/bamql-1.6.ebuild
similarity index 53%
rename from sci-biology/bamql/bamql-1.5.ebuild
rename to sci-biology/bamql/bamql-1.6.ebuild
index ef78e3753..535b31f44 100644
--- a/sci-biology/bamql/bamql-1.5.ebuild
+++ b/sci-biology/bamql/bamql-1.6.ebuild
@@ -1,19 +1,19 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
-inherit autotools
+inherit autotools eutils
DESCRIPTION="Extract reads from BAM files"
HOMEPAGE="https://github.com/BoutrosLaboratory/bamql
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1162-y"
-SRC_URI="https://github.com/BoutrosLaboratory/bamql/archive/v1.5.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/BoutrosLaboratory/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
+IUSE="static-libs"
DEPEND="
sys-devel/llvm:=
@@ -26,3 +26,10 @@ src_prepare(){
eautoreconf
default
}
+
+src_configure(){
+ local mycmakeargs=()
+ use static-libs && mycmakeargs+=( "--enable-static=yes" "--enable-static-llvm=yes" ) || \
+ mycmakeargs+=( "--enable-static=no" "--enable-static-llvm=no" )
+ econf ${mycmakeargs[@]}
+}
diff --git a/sci-biology/bamql/bamql-9999.ebuild b/sci-biology/bamql/bamql-9999.ebuild
index 44a7d85f5..409804dc7 100644
--- a/sci-biology/bamql/bamql-9999.ebuild
+++ b/sci-biology/bamql/bamql-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -13,7 +13,7 @@ EGIT_REPO_URI="https://github.com/BoutrosLaboratory/bamql.git"
LICENSE="MIT"
SLOT="0"
KEYWORDS=""
-IUSE=""
+IUSE="static-libs"
DEPEND="
sys-devel/llvm:=
@@ -26,3 +26,10 @@ src_prepare(){
eautoreconf
default
}
+
+src_configure(){
+ local mycmakeargs=()
+ use static-libs && mycmakeargs+=( "--enable-static=yes" "--enable-static-llvm=yes" ) || \
+ mycmakeargs+=( "--enable-static=no" "--enable-static-llvm=no" )
+ econf ${mycmakeargs[@]}
+}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bamql/
@ 2019-03-25 8:25 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2019-03-25 8:25 UTC (permalink / raw
To: gentoo-commits
commit: 87e5a20b2aa7f097ab01530ee9997b611e10808b
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 25 08:25:37 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 25 08:25:37 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=87e5a20b
sci-biology/bamql: bump to version with less greedy LLVM linking
The https://github.com/BoutrosLaboratory/bamql/blob/master/m4/ax_llvm.m4#L31
forces preference for static libs. The code was improved by Andre
Masella. Although the original code is based on ax_llvm.m4 which
is 4 versions behind current version at
http://git.savannah.gnu.org/gitweb/?p=autoconf-archive.git;a=blob_plain;f=m4/ax_llvm.m4
it does better job at the moment.
https://github.com/BoutrosLaboratory/bamql/issues/14#issuecomment-475947032
Many thanks to François Bissey (@kiwifb) and Andre Masella (@apmasell)
for discussion and Andre for the changes in
https://github.com/BoutrosLaboratory/bamql/commit/9441772
which enable use to overcome the requirement for static libs and
proceed with shared versions using:
`--enable-static=no --enable-static-llvm=no`
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/bamql/{bamql-1.6.ebuild => bamql-1.6.1.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/bamql/bamql-1.6.ebuild b/sci-biology/bamql/bamql-1.6.1.ebuild
similarity index 100%
rename from sci-biology/bamql/bamql-1.6.ebuild
rename to sci-biology/bamql/bamql-1.6.1.ebuild
^ permalink raw reply [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bamql/
@ 2019-03-25 8:40 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2019-03-25 8:40 UTC (permalink / raw
To: gentoo-commits
commit: 47b0727a452b00a0552a3094eff49fc44a2ea9fe
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 25 08:40:46 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 25 08:40:46 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=47b0727a
sci-biology/bamql: bump to EAPI7
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/bamql/bamql-1.6.1.ebuild | 2 +-
sci-biology/bamql/bamql-9999.ebuild | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/bamql/bamql-1.6.1.ebuild b/sci-biology/bamql/bamql-1.6.1.ebuild
index 535b31f44..146793318 100644
--- a/sci-biology/bamql/bamql-1.6.1.ebuild
+++ b/sci-biology/bamql/bamql-1.6.1.ebuild
@@ -1,7 +1,7 @@
# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit autotools eutils
diff --git a/sci-biology/bamql/bamql-9999.ebuild b/sci-biology/bamql/bamql-9999.ebuild
index 409804dc7..e9730e73b 100644
--- a/sci-biology/bamql/bamql-9999.ebuild
+++ b/sci-biology/bamql/bamql-9999.ebuild
@@ -1,7 +1,7 @@
# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit autotools git-r3
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bamql/
@ 2019-03-25 23:56 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2019-03-25 23:56 UTC (permalink / raw
To: gentoo-commits
commit: f96c7ec91d0add7dfef7af06a4d81bc97cf0b7d9
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 25 23:56:31 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 25 23:56:31 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f96c7ec9
sci-biology/bamql: switch to `$(use_enable ...)`
https://github.com/gentoo/sci/issues/907#issuecomment-476420962
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/bamql/bamql-1.6.1.ebuild | 6 ++----
sci-biology/bamql/bamql-9999.ebuild | 6 ++----
2 files changed, 4 insertions(+), 8 deletions(-)
diff --git a/sci-biology/bamql/bamql-1.6.1.ebuild b/sci-biology/bamql/bamql-1.6.1.ebuild
index dacad6029..f11a50278 100644
--- a/sci-biology/bamql/bamql-1.6.1.ebuild
+++ b/sci-biology/bamql/bamql-1.6.1.ebuild
@@ -30,8 +30,6 @@ src_prepare(){
}
src_configure(){
- local myeconfargs=()
- use static-libs && myeconfargs+=( "--enable-static=yes" ) || \
- myeconfargs+=( "--enable-static=no" )
- econf ${myeconfargs[@]}
+ econf \
+ $(use_enable static-libs static)
}
diff --git a/sci-biology/bamql/bamql-9999.ebuild b/sci-biology/bamql/bamql-9999.ebuild
index cda5043a7..288aef6bc 100644
--- a/sci-biology/bamql/bamql-9999.ebuild
+++ b/sci-biology/bamql/bamql-9999.ebuild
@@ -30,8 +30,6 @@ src_prepare(){
}
src_configure(){
- local myeconfargs=()
- use static-libs && myeconfargs+=( "--enable-static=yes" ) || \
- myeconfargs+=( "--enable-static=no" )
- econf ${myeconfargs[@]}
+ econf \
+ $(use_enable static-libs static)
}
^ permalink raw reply related [flat|nested] 6+ messages in thread
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