[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/files/, sci-biology/abyss/
commit: 55988add1d9840ba07f1eea2067a77b6eba3a9e5
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Thu Jan 13 11:17:24 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Thu Jan 13 11:18:40 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=55988add
sci-biology/abyss: move the new versions to ::gentoo
Signed-off-by: Andrew Ammerlaan gentoo.org>
sci-biology/abyss/abyss-2.2.5-r1.ebuild| 58 --
sci-biology/abyss/abyss-2.3.0-r1.ebuild| 58 --
sci-biology/abyss/abyss-2.3.1.ebuild | 58 --
.../files/abyss-2.2.5-ContigProperties.h.patch | 11
.../files/abyss-2.2.5-PathConsensus-assert.patch | 11
sci-biology/abyss/metadata.xml | 18 ---
6 files changed, 214 deletions(-)
diff --git a/sci-biology/abyss/abyss-2.2.5-r1.ebuild
b/sci-biology/abyss/abyss-2.2.5-r1.ebuild
deleted file mode 100644
index d9134813b..0
--- a/sci-biology/abyss/abyss-2.2.5-r1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools toolchain-funcs
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end
sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/";
-SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-cpp/sparsehash
- dev-libs/boost:=
- misc-haskell? (
- dev-libs/gmp:0=
- dev-libs/libffi:0=
- )
- mpi? ( sys-cluster/openmpi )"
-DEPEND="${RDEPEND}
- misc-haskell? (
- dev-lang/ghc
- )"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
- "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
- )
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-pkg_pretend() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-src_prepare() {
- default
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- eautoreconf
-}
-
-src_configure() {
- # disable building haskell tool Misc/samtobreak
- # unless request by user: bug #534412
- use misc-haskell || export ac_cv_prog_ac_ct_GHC=
-
- econf $(use_enable openmp) --enable-maxk=256
-}
diff --git a/sci-biology/abyss/abyss-2.3.0-r1.ebuild
b/sci-biology/abyss/abyss-2.3.0-r1.ebuild
deleted file mode 100644
index d9134813b..0
--- a/sci-biology/abyss/abyss-2.3.0-r1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools toolchain-funcs
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end
sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/";
-SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-cpp/sparsehash
- dev-libs/boost:=
- misc-haskell? (
- dev-libs/gmp:0=
- dev-libs/libffi:0=
- )
- mpi? ( sys-cluster/openmpi )"
-DEPEND="${RDEPEND}
- misc-haskell? (
- dev-lang/ghc
- )"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
- "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
- )
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-pkg_pretend() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-src_prepare() {
- default
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- eautoreconf
-}
-
-src_configure() {
- # disable building haskell tool Misc/samtobreak
- # unless request by user: bug #534412
- use misc-haskell || export ac_cv_prog_ac_ct_GHC=
-
- econf $(use_enable openmp) --enable-maxk=256
-}
diff --git a/sci-biology/abyss/abyss-2.3.1.ebuild
b/sci-biology/abyss/abyss-2.3.1.ebuild
deleted file mode 100644
index d9134813b..0
--- a/sci-biology/abyss/abyss-2.3.1.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools toolchain-funcs
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end
sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/pl
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: 6c252245a4ab18f5d211723f9078682dfa06bd00
Author: Martin Mokrejs gmail com>
AuthorDate: Thu Apr 22 07:23:16 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Apr 22 07:23:16 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6c252245
sci-biology/abyss: add 2.3.1 release but keep patches
The PathConsensus crash fixes were not included by upstream,
keep them.
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/abyss/abyss-2.3.1.ebuild | 58
1 file changed, 58 insertions(+)
diff --git a/sci-biology/abyss/abyss-2.3.1.ebuild
b/sci-biology/abyss/abyss-2.3.1.ebuild
new file mode 100644
index 0..d9134813b
--- /dev/null
+++ b/sci-biology/abyss/abyss-2.3.1.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end
sequence assembler"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/";
+SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="+mpi openmp misc-haskell"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-cpp/sparsehash
+ dev-libs/boost:=
+ misc-haskell? (
+ dev-libs/gmp:0=
+ dev-libs/libffi:0=
+ )
+ mpi? ( sys-cluster/openmpi )"
+DEPEND="${RDEPEND}
+ misc-haskell? (
+ dev-lang/ghc
+ )"
+
+PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
+ "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
+ )
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+pkg_pretend() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+src_prepare() {
+ default
+ sed -i -e "s/-Werror//" configure.ac || die #365195
+ sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
+ eautoreconf
+}
+
+src_configure() {
+ # disable building haskell tool Misc/samtobreak
+ # unless request by user: bug #534412
+ use misc-haskell || export ac_cv_prog_ac_ct_GHC=
+
+ econf $(use_enable openmp) --enable-maxk=256
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/, sci-biology/abyss/files/
commit: f22bb3be4e8f283831edc5f4c38a839442355644
Author: Martin Mokrejs gmail com>
AuthorDate: Wed Apr 14 13:07:12 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Apr 14 13:07:12 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f22bb3be
sci-biology/abyss: fix PathConsensus crashes
Fixes: https://github.com/bcgsc/abyss/issues/267
Fix crashes of PathConsensus during long-scaffolding
step per @sjackman suggestions.
Add back 2.2.5 version which does not have yet the
RResolver which addition broke the paired de Bruijn
graph assembly approach and since that only the
Bloom filter-based approach works in 2.3.0.
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
.../abyss/{abyss-2.3.0.ebuild => abyss-2.2.5-r1.ebuild} | 4
.../abyss/{abyss-2.3.0.ebuild => abyss-2.3.0-r1.ebuild} | 4
sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch | 11 +++
.../abyss/files/abyss-2.2.5-PathConsensus-assert.patch| 11 +++
4 files changed, 30 insertions(+)
diff --git a/sci-biology/abyss/abyss-2.3.0.ebuild
b/sci-biology/abyss/abyss-2.2.5-r1.ebuild
similarity index 91%
copy from sci-biology/abyss/abyss-2.3.0.ebuild
copy to sci-biology/abyss/abyss-2.2.5-r1.ebuild
index 95438d3b4..d9134813b 100644
--- a/sci-biology/abyss/abyss-2.3.0.ebuild
+++ b/sci-biology/abyss/abyss-2.2.5-r1.ebuild
@@ -27,6 +27,10 @@ DEPEND="${RDEPEND}
dev-lang/ghc
)"
+PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
+ "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
+ )
+
# todo: --enable-maxk=N configure option
# todo: fix automagic mpi toggling
diff --git a/sci-biology/abyss/abyss-2.3.0.ebuild
b/sci-biology/abyss/abyss-2.3.0-r1.ebuild
similarity index 91%
rename from sci-biology/abyss/abyss-2.3.0.ebuild
rename to sci-biology/abyss/abyss-2.3.0-r1.ebuild
index 95438d3b4..d9134813b 100644
--- a/sci-biology/abyss/abyss-2.3.0.ebuild
+++ b/sci-biology/abyss/abyss-2.3.0-r1.ebuild
@@ -27,6 +27,10 @@ DEPEND="${RDEPEND}
dev-lang/ghc
)"
+PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
+ "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
+ )
+
# todo: --enable-maxk=N configure option
# todo: fix automagic mpi toggling
diff --git a/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch
b/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch
new file mode 100644
index 0..95181f082
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch
@@ -0,0 +1,11 @@
+--- abyss-2.2.5/Common/ContigProperties.h.ori 2020-09-18 20:42:12.0
+0200
abyss-2.2.5/Common/ContigProperties.h 2021-04-14 12:31:23.682158000
+0200
+@@ -171,7 +171,7 @@
+ template
+ ContigProperties& operator+=(ContigProperties& a, const T& b)
+ {
+- assert((int)a.length + (int)b.distance > 0);
++ assert((int)a.length + (int)b.distance >= 0);
+ a.length += b.distance;
+ return a;
+ }
diff --git a/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch
b/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch
new file mode 100644
index 0..754e25acc
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch
@@ -0,0 +1,11 @@
+--- abyss-2.2.5/MergePaths/PathConsensus.cpp 2020-09-18 20:42:12.0
+0200
abyss-2.2.5/MergePaths/PathConsensus.cpp 2021-04-12 22:26:28.780547000
+0200
+@@ -379,7 +379,7 @@
+ unsigned overlap, Sequence& seq,
+ const Sequence& s, const ContigNode& node, const Path& path)
+ {
+- assert(s.length() > overlap);
++ assert(s.length() >= overlap);
+ Sequence ao;
+ Sequence bo(s, 0, overlap);
+ Sequence o;
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: 85d646372a278f85c05c5c7c717b9e94fa967ddc
Author: Martin Mokrejs gmail com>
AuthorDate: Thu Apr 1 20:11:06 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Apr 1 20:11:06 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=85d64637
sci-biology/abyss: version bump
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/abyss/{abyss-2.2.5.ebuild => abyss-2.3.0.ebuild} | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/abyss/abyss-2.2.5.ebuild
b/sci-biology/abyss/abyss-2.3.0.ebuild
similarity index 97%
rename from sci-biology/abyss/abyss-2.2.5.ebuild
rename to sci-biology/abyss/abyss-2.3.0.ebuild
index 10c2fbff6..95438d3b4 100644
--- a/sci-biology/abyss/abyss-2.2.5.ebuild
+++ b/sci-biology/abyss/abyss-2.3.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: 45d35292cee5f5b1f1f9c17d8fc343bdd99e7088
Author: Andrew Ammerlaan riseup net>
AuthorDate: Thu Dec 31 16:22:46 2020 +
Commit: Aisha Tammy aisha cc>
CommitDate: Thu Dec 31 16:50:12 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=45d35292
sci-biology/abyss: version bump, fix dep
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
Closes: https://github.com/gentoo/sci/pull/1022
Signed-off-by: Aisha Tammy aisha.cc>
sci-biology/abyss/{abyss-2.2.4.ebuild => abyss-2.2.5.ebuild} | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/abyss/abyss-2.2.4.ebuild
b/sci-biology/abyss/abyss-2.2.5.ebuild
similarity index 98%
rename from sci-biology/abyss/abyss-2.2.4.ebuild
rename to sci-biology/abyss/abyss-2.2.5.ebuild
index 307ff68c8..10c2fbff6 100644
--- a/sci-biology/abyss/abyss-2.2.4.ebuild
+++ b/sci-biology/abyss/abyss-2.2.5.ebuild
@@ -19,7 +19,7 @@ RDEPEND="
dev-libs/boost:=
misc-haskell? (
dev-libs/gmp:0=
- virtual/libffi:0=
+ dev-libs/libffi:0=
)
mpi? ( sys-cluster/openmpi )"
DEPEND="${RDEPEND}
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: c7e35e6a3ba60f35a787c02b1472c867ed3e1e3f Author: Horea Christian chymera eu> AuthorDate: Fri Dec 25 10:21:55 2020 + Commit: Horea Christian gmail com> CommitDate: Fri Dec 25 10:21:55 2020 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c7e35e6a sci-biology/abyss: EAPI 7 bump Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Horea Christian chymera.eu> sci-biology/abyss/abyss-2.2.4.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/abyss/abyss-2.2.4.ebuild b/sci-biology/abyss/abyss-2.2.4.ebuild index c81bf292e..307ff68c8 100644 --- a/sci-biology/abyss/abyss-2.2.4.ebuild +++ b/sci-biology/abyss/abyss-2.2.4.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 inherit autotools toolchain-funcs
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: 05629a9dc997950a1bf3dfa002307decc492e4b7
Author: Martin Mokrejs gmail com>
AuthorDate: Thu Feb 20 15:15:16 2020 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Feb 20 15:16:22 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=05629a9d
sci-biology/abyss: version bump
Package-Manager: Portage-2.3.87, Repoman-2.3.20
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/abyss/{abyss-2.2.3.ebuild => abyss-2.2.4.ebuild} | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/abyss/abyss-2.2.3.ebuild
b/sci-biology/abyss/abyss-2.2.4.ebuild
similarity index 97%
rename from sci-biology/abyss/abyss-2.2.3.ebuild
rename to sci-biology/abyss/abyss-2.2.4.ebuild
index 5e80a0a3c..c81bf292e 100644
--- a/sci-biology/abyss/abyss-2.2.3.ebuild
+++ b/sci-biology/abyss/abyss-2.2.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: 08f6cb388ea7db562f4f6a32e9cef76dfd62caff
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Sat Sep 28 13:05:52 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat Sep 28 13:05:52 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=08f6cb38
sci-biology/abyss: version bump to 2.2.3
Release version 2.2.3
Revert memory consumption of Bloom filters to pre 2.2.0 behaviour.
ABySS will now share the specified memory among all Bloom filters
instead of just the counting Bloom filter.
Fix gcc-9 compilation warnings
Release version 2.2.2
Fix abyss-overlap for 32-bit systems
Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/abyss/{abyss-2.2.2.ebuild => abyss-2.2.3.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/abyss/abyss-2.2.2.ebuild
b/sci-biology/abyss/abyss-2.2.3.ebuild
similarity index 100%
rename from sci-biology/abyss/abyss-2.2.2.ebuild
rename to sci-biology/abyss/abyss-2.2.3.ebuild
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: 982e84f44b14e71d4bae96aab4d246a3f0ec0f6f
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Tue Aug 20 13:22:28 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Aug 20 13:22:28 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=982e84f4
sci-biology/abyss: version bump
Package-Manager: Portage-2.3.71, Repoman-2.3.17
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/abyss/{abyss-2.2.1.ebuild => abyss-2.2.2.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/abyss/abyss-2.2.1.ebuild
b/sci-biology/abyss/abyss-2.2.2.ebuild
similarity index 100%
rename from sci-biology/abyss/abyss-2.2.1.ebuild
rename to sci-biology/abyss/abyss-2.2.2.ebuild
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: 581b836c34e32d3e201b8cfc7a4377514d16e2e3
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Thu Aug 15 07:51:31 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Aug 15 07:51:31 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=581b836c
sci-biology/abyss: update LICENSE, version bump
Upstream released abyss 3 years ago under GPL-3, now also another
part of the code is under GPL-3.
https://github.com/bcgsc/abyss/issues/295
Package-Manager: Portage-2.3.69, Repoman-2.3.16
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/abyss/{abyss-2.1.5.ebuild => abyss-2.2.1.ebuild} | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/abyss/abyss-2.1.5.ebuild
b/sci-biology/abyss/abyss-2.2.1.ebuild
similarity index 95%
rename from sci-biology/abyss/abyss-2.1.5.ebuild
rename to sci-biology/abyss/abyss-2.2.1.ebuild
index 66c216fab..5e80a0a3c 100644
--- a/sci-biology/abyss/abyss-2.1.5.ebuild
+++ b/sci-biology/abyss/abyss-2.2.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -9,7 +9,7 @@ DESCRIPTION="Assembly By Short Sequences - a de novo, parallel,
paired-end seque
HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/";
SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
-LICENSE="abyss"
+LICENSE="GPL-3"
SLOT="0"
IUSE="+mpi openmp misc-haskell"
KEYWORDS="~amd64 ~x86"
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: 9eeb095bd6468b0ab9ac265d730eaf458afae83a
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Dec 10 13:28:09 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Dec 10 13:28:09 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9eeb095b
sci-biology/abyss: Force --enable-maxk=256
Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/abyss/abyss-2.1.5.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/abyss/abyss-2.1.5.ebuild
b/sci-biology/abyss/abyss-2.1.5.ebuild
index 007cc7384..66c216fab 100644
--- a/sci-biology/abyss/abyss-2.1.5.ebuild
+++ b/sci-biology/abyss/abyss-2.1.5.ebuild
@@ -50,5 +50,5 @@ src_configure() {
# unless request by user: bug #534412
use misc-haskell || export ac_cv_prog_ac_ct_GHC=
- econf $(use_enable openmp)
+ econf $(use_enable openmp) --enable-maxk=256
}
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: f0b1356038ad8ed9fcfd12298dd5e92749bc6a87
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Thu Dec 6 10:59:50 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Dec 6 10:59:50 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f0b13560
sci-biology/abyss: version bump
Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/abyss/{abyss-2.1.2.ebuild => abyss-2.1.5.ebuild} | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/abyss/abyss-2.1.2.ebuild
b/sci-biology/abyss/abyss-2.1.5.ebuild
similarity index 96%
rename from sci-biology/abyss/abyss-2.1.2.ebuild
rename to sci-biology/abyss/abyss-2.1.5.ebuild
index ccce937c7..007cc7384 100644
--- a/sci-biology/abyss/abyss-2.1.2.ebuild
+++ b/sci-biology/abyss/abyss-2.1.5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: 0e4eaa3b33984588d0d57ca68b0ea877c461c6ab
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Oct 29 13:56:23 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Oct 29 13:56:23 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0e4eaa3b
sci-biology/abyss: version bump
Package-Manager: Portage-2.3.51, Repoman-2.3.10
sci-biology/abyss/{abyss-2.1.1.ebuild => abyss-2.1.2.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/abyss/abyss-2.1.1.ebuild
b/sci-biology/abyss/abyss-2.1.2.ebuild
similarity index 100%
rename from sci-biology/abyss/abyss-2.1.1.ebuild
rename to sci-biology/abyss/abyss-2.1.2.ebuild
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: e09e5ec884dd0210694529c19b81fab9c48a76bc
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Tue Sep 11 21:54:18 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Sep 11 21:54:18 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e09e5ec8
sci-biology/abyss: version bump
An improved version with sealer using OpenMP+OpenMPI now.
https://github.com/bcgsc/abyss/releases/tag/2.1.1
Package-Manager: Portage-2.3.48, Repoman-2.3.10
sci-biology/abyss/abyss-2.1.1.ebuild | 54
sci-biology/abyss/metadata.xml | 18
2 files changed, 72 insertions(+)
diff --git a/sci-biology/abyss/abyss-2.1.1.ebuild
b/sci-biology/abyss/abyss-2.1.1.ebuild
new file mode 100644
index 0..ccce937c7
--- /dev/null
+++ b/sci-biology/abyss/abyss-2.1.1.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end
sequence assembler"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/";
+SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp misc-haskell"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-cpp/sparsehash
+ dev-libs/boost:=
+ misc-haskell? (
+ dev-libs/gmp:0=
+ virtual/libffi:0=
+ )
+ mpi? ( sys-cluster/openmpi )"
+DEPEND="${RDEPEND}
+ misc-haskell? (
+ dev-lang/ghc
+ )"
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+pkg_pretend() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+src_prepare() {
+ default
+ sed -i -e "s/-Werror//" configure.ac || die #365195
+ sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
+ eautoreconf
+}
+
+src_configure() {
+ # disable building haskell tool Misc/samtobreak
+ # unless request by user: bug #534412
+ use misc-haskell || export ac_cv_prog_ac_ct_GHC=
+
+ econf $(use_enable openmp)
+}
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
new file mode 100644
index 0..47116e507
--- /dev/null
+++ b/sci-biology/abyss/metadata.xml
@@ -0,0 +1,18 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+
+sci-biol...@gentoo.org
+Gentoo Biology Project
+
+
+hask...@gentoo.org
+Gentoo Haskell
+
+
+build abyss-samtobreak tool, pull in haskell
toolchain
+
+
+bcgsc/abyss
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/, sci-biology/abyss/files/
commit: 1ee6452972e294f0825ef450ec0f53cda42cb65f
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Tue Jan 10 00:20:33 2017 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Jan 10 00:20:33 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1ee64529
sci-biology/abyss: removing old, 2.0.2 in main repo already
sci-biology/abyss/abyss-1.9.0.ebuild | 53 --
.../abyss/files/abyss-1.9.0-ac_prog_ar.patch | 18
sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch| 34 --
sci-biology/abyss/metadata.xml | 15 --
4 files changed, 120 deletions(-)
diff --git a/sci-biology/abyss/abyss-1.9.0.ebuild
b/sci-biology/abyss/abyss-1.9.0.ebuild
deleted file mode 100644
index c32b477..000
--- a/sci-biology/abyss/abyss-1.9.0.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=6
-
-inherit autotools toolchain-funcs
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end
sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/";
-SRC_URI="https://github.com/bcgsc/abyss/archive/1.9.0.tar.gz -> ${P}.tar.gz"
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-cpp/sparsehash
- dev-libs/boost
- misc-haskell? ( dev-libs/gmp:0=
- virtual/libffi:0=
- )
- mpi? ( virtual/mpi )
-"
-DEPEND="${RDEPEND}
- misc-haskell? ( dev-lang/ghc
- dev-haskell/mmap )
-"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-PATCHES=(
- "${FILESDIR}"/${P}-ac_prog_ar.patch
- "${FILESDIR}"/${P}-gcc-6.patch
-)
-
-src_prepare() {
- default
- tc-export AR
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- eautoreconf
-}
-
-src_configure() {
- # disable building haskell tool Misc/samtobreak
- # unless request by user: bug #534412
- use misc-haskell || export ac_cv_prog_ac_ct_GHC=
-
- econf $(use_enable openmp)
-}
diff --git a/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch
b/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch
deleted file mode 100644
index 158e9b1..000
--- a/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch
+++ /dev/null
@@ -1,18 +0,0 @@
- configure.ac | 4
- 1 file changed, 4 insertions(+)
-
-diff --git a/configure.ac b/configure.ac
-index 9d4bb66..aa94364 100644
a/configure.ac
-+++ b/configure.ac
-@@ -12,6 +12,10 @@ AC_PROG_CPP
- AC_PROG_CXX
- AC_PROG_INSTALL
- AC_PROG_RANLIB
-+AN_MAKEVAR([AR], [AC_PROG_AR])
-+AN_PROGRAM([ar], [AC_PROG_AR])
-+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
-+AC_PROG_AR
- AC_CHECK_TOOL(GHC, ghc)
- AM_CONDITIONAL([HAVE_GHC], [test "$GHC"])
-
diff --git a/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch
b/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch
deleted file mode 100644
index 49a30f9..000
--- a/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-diff --git a/DataBase/db-csv.cc b/DataBase/db-csv.cc
-index 05cac19..48e3b44 100644
a/DataBase/db-csv.cc
-+++ b/DataBase/db-csv.cc
-@@ -18,11 +18,11 @@ static const char TABLE_LIST[] =
- typedef vector vs;
-
- static bool existFile(const char* f)
- {
- ifstream file(f);
-- return file;
-+ return bool(file);
- }
-
- template
- static bool existTable(
- D& db, const string& t)
-diff --git a/SimpleGraph/SimpleGraph.cpp b/SimpleGraph/SimpleGraph.cpp
-index 373ec70..0a9ebd3 100644
a/SimpleGraph/SimpleGraph.cpp
-+++ b/SimpleGraph/SimpleGraph.cpp
-@@ -645,11 +645,11 @@ static void* worker(void* pArg)
- for (;;) {
- /** Lock the input stream. */
- static pthread_mutex_t inMutex = PTHREAD_MUTEX_INITIALIZER;
- pthread_mutex_lock(&inMutex);
- EstimateRecord er;
-- bool good = (*arg.in) >> er;
-+ bool good = bool((*arg.in) >> er);
- pthread_mutex_unlock(&inMutex);
- if (!good)
- break;
-
- // Flip the anterior distance estimates.
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
deleted file mode 100644
index c0c84f0..000
--- a/sci-biology/abyss/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd";>
-
-
-sci-biol...@gentoo.org
-Gentoo Biology Project
-
-
-hask...@gentoo.org
-Gentoo Haskell
-
-
-build abyss-samtobreak tool, pull in haskell
toolchain
-
-
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/files/, sci-biology/abyss/
commit: b81e4c632efa6b2d53c8750b84deb2b315c86dd0
Author: Sergei Trofimovich inbox ru>
AuthorDate: Fri Sep 23 13:16:56 2016 +
Commit: Marius Brehler linux sungazer de>
CommitDate: Fri Sep 23 13:16:56 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b81e4c63
sci-biology/abyss: tweak for gcc-6, bug #594254 (#681)
Build failed as:
```
In file included from AssemblyAlgorithms.cpp:4:0:
../DataLayer/FastaReader.h: In member function ‘FastaReader::operator
void*() const’:
../DataLayer/FastaReader.h:49:35: error: cannot convert ‘std::istream {aka
std::basic_istream}’ to ‘void*’ ...
operator void*() const { return m_in; }
^~~~
```
In the following source:
```c++
static bool existFile(const char* f)
{
ifstream file(f);
return file;
}
```
c++98 provides file->operator void*()
c++11 provides file->explicit operator bool()
Hence the failure on c++11.
The change adds explicit casts around istream.
Reported-by: Toralf Förster
Bug: https://bugs.gentoo.org/594254
Package-Manager: portage-2.3.0
sci-biology/abyss/abyss-1.9.0.ebuild| 1 +
sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch | 34 +
2 files changed, 35 insertions(+)
diff --git a/sci-biology/abyss/abyss-1.9.0.ebuild
b/sci-biology/abyss/abyss-1.9.0.ebuild
index b2de141..c32b477 100644
--- a/sci-biology/abyss/abyss-1.9.0.ebuild
+++ b/sci-biology/abyss/abyss-1.9.0.ebuild
@@ -33,6 +33,7 @@ DEPEND="${RDEPEND}
PATCHES=(
"${FILESDIR}"/${P}-ac_prog_ar.patch
+ "${FILESDIR}"/${P}-gcc-6.patch
)
src_prepare() {
diff --git a/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch
b/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch
new file mode 100644
index 000..49a30f9
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch
@@ -0,0 +1,34 @@
+diff --git a/DataBase/db-csv.cc b/DataBase/db-csv.cc
+index 05cac19..48e3b44 100644
+--- a/DataBase/db-csv.cc
b/DataBase/db-csv.cc
+@@ -18,11 +18,11 @@ static const char TABLE_LIST[] =
+ typedef vector vs;
+
+ static bool existFile(const char* f)
+ {
+ ifstream file(f);
+- return file;
++ return bool(file);
+ }
+
+ template
+ static bool existTable(
+ D& db, const string& t)
+diff --git a/SimpleGraph/SimpleGraph.cpp b/SimpleGraph/SimpleGraph.cpp
+index 373ec70..0a9ebd3 100644
+--- a/SimpleGraph/SimpleGraph.cpp
b/SimpleGraph/SimpleGraph.cpp
+@@ -645,11 +645,11 @@ static void* worker(void* pArg)
+ for (;;) {
+ /** Lock the input stream. */
+ static pthread_mutex_t inMutex = PTHREAD_MUTEX_INITIALIZER;
+ pthread_mutex_lock(&inMutex);
+ EstimateRecord er;
+- bool good = (*arg.in) >> er;
++ bool good = bool((*arg.in) >> er);
+ pthread_mutex_unlock(&inMutex);
+ if (!good)
+ break;
+
+ // Flip the anterior distance estimates.
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/, sci-biology/abyss/files/
commit: 76c8aa5fabb5f1ae43d4fdf831bcf94b7e6e09a6
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Thu Jun 30 22:02:59 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jun 30 22:02:59 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=76c8aa5f
sci-biology/abyss: version bump, update SRC_URI
Package-Manager: portage-2.2.28
sci-biology/abyss/abyss-1.9.0.ebuild | 52 ++
.../abyss/files/abyss-1.9.0-ac_prog_ar.patch | 18
sci-biology/abyss/metadata.xml | 15 +++
3 files changed, 85 insertions(+)
diff --git a/sci-biology/abyss/abyss-1.9.0.ebuild
b/sci-biology/abyss/abyss-1.9.0.ebuild
new file mode 100644
index 000..b2de141
--- /dev/null
+++ b/sci-biology/abyss/abyss-1.9.0.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end
sequence assembler"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/";
+SRC_URI="https://github.com/bcgsc/abyss/archive/1.9.0.tar.gz -> ${P}.tar.gz"
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp misc-haskell"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-cpp/sparsehash
+ dev-libs/boost
+ misc-haskell? ( dev-libs/gmp:0=
+ virtual/libffi:0=
+ )
+ mpi? ( virtual/mpi )
+"
+DEPEND="${RDEPEND}
+ misc-haskell? ( dev-lang/ghc
+ dev-haskell/mmap )
+"
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+PATCHES=(
+ "${FILESDIR}"/${P}-ac_prog_ar.patch
+)
+
+src_prepare() {
+ default
+ tc-export AR
+ sed -i -e "s/-Werror//" configure.ac || die #365195
+ sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
+ eautoreconf
+}
+
+src_configure() {
+ # disable building haskell tool Misc/samtobreak
+ # unless request by user: bug #534412
+ use misc-haskell || export ac_cv_prog_ac_ct_GHC=
+
+ econf $(use_enable openmp)
+}
diff --git a/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch
b/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch
new file mode 100644
index 000..158e9b1
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.9.0-ac_prog_ar.patch
@@ -0,0 +1,18 @@
+ configure.ac | 4
+ 1 file changed, 4 insertions(+)
+
+diff --git a/configure.ac b/configure.ac
+index 9d4bb66..aa94364 100644
+--- a/configure.ac
b/configure.ac
+@@ -12,6 +12,10 @@ AC_PROG_CPP
+ AC_PROG_CXX
+ AC_PROG_INSTALL
+ AC_PROG_RANLIB
++AN_MAKEVAR([AR], [AC_PROG_AR])
++AN_PROGRAM([ar], [AC_PROG_AR])
++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
++AC_PROG_AR
+ AC_CHECK_TOOL(GHC, ghc)
+ AM_CONDITIONAL([HAVE_GHC], [test "$GHC"])
+
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
new file mode 100644
index 000..c0c84f0
--- /dev/null
+++ b/sci-biology/abyss/metadata.xml
@@ -0,0 +1,15 @@
+
+http://www.gentoo.org/dtd/metadata.dtd";>
+
+
+sci-biol...@gentoo.org
+Gentoo Biology Project
+
+
+hask...@gentoo.org
+Gentoo Haskell
+
+
+build abyss-samtobreak tool, pull in haskell
toolchain
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/files/, sci-biology/abyss/
commit: 9c102d9aebd555a1db337e89911a198ba8274b55
Author: David Seifert gentoo org>
AuthorDate: Sun Apr 3 18:04:28 2016 +
Commit: Marius Brehler linux sungazer de>
CommitDate: Sun Apr 3 18:04:28 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9c102d9a
sci-biology/abyss: moved to main tree
sci-biology/abyss/abyss-1.3.3-r1.ebuild| 42 ---
sci-biology/abyss/abyss-1.3.4-r1.ebuild| 47 -
sci-biology/abyss/abyss-1.3.6-r1.ebuild| 59 --
.../abyss/files/abyss-1.3.3-ac_prog_ar.patch | 18 ---
sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch | 15 --
sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch | 40 ---
sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch | 15 --
sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch | 40 ---
.../abyss/files/abyss-1.3.6-ac_prog_ar.patch | 18 ---
sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch | 15 --
sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch | 40 ---
sci-biology/abyss/metadata.xml | 15 --
12 files changed, 364 deletions(-)
diff --git a/sci-biology/abyss/abyss-1.3.3-r1.ebuild
b/sci-biology/abyss/abyss-1.3.3-r1.ebuild
deleted file mode 100644
index 76f15b4..000
--- a/sci-biology/abyss/abyss-1.3.3-r1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit autotools eutils toolchain-funcs
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end
sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/";
-SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz";
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- dev-cpp/sparsehash
- mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-src_prepare() {
- tc-export AR
- epatch \
- "${FILESDIR}"/${P}-gcc-4.7.patch \
- "${FILESDIR}"/${P}-ac_prog_ar.patch \
- "${FILESDIR}"/${P}-samtoafg.patch
-
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- eautoreconf
-}
-
-src_configure() {
- econf \
- --docdir="${EPREFIX}/usr/share/doc/${PF}" \
- $(use_enable openmp)
-}
diff --git a/sci-biology/abyss/abyss-1.3.4-r1.ebuild
b/sci-biology/abyss/abyss-1.3.4-r1.ebuild
deleted file mode 100644
index 762d49a..000
--- a/sci-biology/abyss/abyss-1.3.4-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end
sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/";
-SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz";
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
- dev-cpp/sparsehash
- mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-PATCHES=(
- "${FILESDIR}"/${P}-gcc-4.7.patch
- "${FILESDIR}"/${PN}-1.3.3-ac_prog_ar.patch
- "${FILESDIR}"/${P}-samtoafg.patch
- )
-
-src_prepare() {
- tc-export AR
- sed -i -e "s/-Werror//" configure.ac || die #365195
- sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
- autotools-utils_src_prepare
-}
-
-src_configure() {
- local myeconfargs=(
- --docdir="${EPREFIX}/usr/share/doc/${PF}"
- $(use_enable openmp)
- )
- autotools-utils_src_configure
-}
diff --git a/sci-biology/abyss/abyss-1.3.6-r1.ebuild
b/sci-biology/abyss/abyss-1.3.6-r1.ebuild
deleted file mode 100644
index a449c72..000
--- a/sci-biology/abyss/abyss-1.3.6-r1.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end
sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/";
-SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz";
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp misc-haskell"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-cpp/sparsehash
- dev-libs/boost
- misc-haskell? ( dev-libs/gmp:0=
- virtual/libffi:0=
- )
- mpi? ( virtual/mpi )
-"
-DEPEND="${RDEPEND}
- misc-haskell? ( dev-lang/ghc
- dev-haskell/mmap )
-"
-
-# tod
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: f1f6c31bb308f59777bb396827099ec71b4b35a1
Author: Sergei Trofimovich google com>
AuthorDate: Sun Apr 3 15:34:21 2016 +
Commit: Marius Brehler linux sungazer de>
CommitDate: Sun Apr 3 17:43:47 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f1f6c31b
sci-biology/abyss: fix automagic haskell deps, bug #534412
It's a ::gentoo change a50e1769e82e28dedb16083ac9136f17f9af2297
Reported-by: Toralf Förster
Bug: https://bugs.gentoo.org/534412
Package-Manager: portage-2.2.28
sci-biology/abyss/abyss-1.3.6-r1.ebuild | 19 +++
sci-biology/abyss/metadata.xml | 7 +++
2 files changed, 22 insertions(+), 4 deletions(-)
diff --git a/sci-biology/abyss/abyss-1.3.6-r1.ebuild
b/sci-biology/abyss/abyss-1.3.6-r1.ebuild
index f002a95..a449c72 100644
--- a/sci-biology/abyss/abyss-1.3.6-r1.ebuild
+++ b/sci-biology/abyss/abyss-1.3.6-r1.ebuild
@@ -14,14 +14,21 @@ SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz";
LICENSE="abyss"
SLOT="0"
-IUSE="+mpi openmp"
+IUSE="+mpi openmp misc-haskell"
KEYWORDS="~amd64 ~x86"
-DEPEND="
+RDEPEND="
dev-cpp/sparsehash
dev-libs/boost
- mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
+ misc-haskell? ( dev-libs/gmp:0=
+ virtual/libffi:0=
+ )
+ mpi? ( virtual/mpi )
+"
+DEPEND="${RDEPEND}
+ misc-haskell? ( dev-lang/ghc
+ dev-haskell/mmap )
+"
# todo: --enable-maxk=N configure option
# todo: fix automagic mpi toggling
@@ -40,6 +47,10 @@ src_prepare() {
}
src_configure() {
+ # disable building haskell tool Misc/samtobreak
+ # unless request by user: bug #534412
+ use misc-haskell || export ac_cv_prog_ac_ct_GHC=
+
local myeconfargs=(
--docdir="${EPREFIX}/usr/share/doc/${PF}"
$(use_enable openmp)
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
index 959160f..c0c84f0 100644
--- a/sci-biology/abyss/metadata.xml
+++ b/sci-biology/abyss/metadata.xml
@@ -5,4 +5,11 @@
sci-biol...@gentoo.org
Gentoo Biology Project
+
+hask...@gentoo.org
+Gentoo Haskell
+
+
+build abyss-samtobreak tool, pull in haskell
toolchain
+
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: 060a770920f2cd21994b2ff0efa7d263c3c70493 Author: Justin Lecher gentoo org> AuthorDate: Wed Sep 23 12:08:24 2015 + Commit: Justin Lecher gentoo org> CommitDate: Wed Sep 23 12:08:24 2015 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=060a7709 sci-biology/abyss: Bump to EAPI=5 Package-Manager: portage-2.2.21 Signed-off-by: Justin Lecher gentoo.org> sci-biology/abyss/abyss-1.3.3-r1.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/abyss/abyss-1.3.3-r1.ebuild b/sci-biology/abyss/abyss-1.3.3-r1.ebuild index 5afbdd0..76f15b4 100644 --- a/sci-biology/abyss/abyss-1.3.3-r1.ebuild +++ b/sci-biology/abyss/abyss-1.3.3-r1.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Id$ -EAPI="4" +EAPI=5 inherit autotools eutils toolchain-funcs
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/, sci-biology/abyss/files/
commit: 4c3880bfe25f6b81461523e3f1f38b43614d51b9
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Sat May 23 21:51:58 2015 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat May 23 21:51:58 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4c3880bf
sci-biology/amos: bring in upstream patch to cope with secondary alignments
from 'bwa mem -M'
Package-Manager: portage-2.2.18
sci-biology/abyss/ChangeLog| 17
sci-biology/abyss/abyss-1.3.3-r1.ebuild| 42 +++
sci-biology/abyss/abyss-1.3.4-r1.ebuild| 47 +
sci-biology/abyss/abyss-1.3.6-r1.ebuild| 48 ++
.../abyss/files/abyss-1.3.3-ac_prog_ar.patch | 18
sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch | 15 +++
sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch | 40 ++
sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch | 15 +++
sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch | 40 ++
.../abyss/files/abyss-1.3.6-ac_prog_ar.patch | 18
sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch | 15 +++
sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch | 40 ++
sci-biology/abyss/metadata.xml | 5 +++
13 files changed, 360 insertions(+)
diff --git a/sci-biology/abyss/ChangeLog b/sci-biology/abyss/ChangeLog
new file mode 100644
index 000..c680959
--- /dev/null
+++ b/sci-biology/abyss/ChangeLog
@@ -0,0 +1,17 @@
+# ChangeLog for sci-biology/abyss
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*abyss-1.3.3-r1 (23 May 2015)
+*abyss-1.3.4-r1 (23 May 2015)
+*abyss-1.3.6-r1 (23 May 2015)
+
+ 23 May 2015; Martin Mokrejs
+ +abyss-1.3.3-r1.ebuild, +abyss-1.3.4-r1.ebuild, +abyss-1.3.6-r1.ebuild,
+ +files/abyss-1.3.3-ac_prog_ar.patch, +files/abyss-1.3.3-gcc-4.7.patch,
+ +files/abyss-1.3.3-samtoafg.patch, +files/abyss-1.3.4-gcc-4.7.patch,
+ +files/abyss-1.3.4-samtoafg.patch, +files/abyss-1.3.6-ac_prog_ar.patch,
+ +files/abyss-1.3.6-gcc-4.7.patch, +files/abyss-1.3.6-samtoafg.patch,
+ +metadata.xml:
+ sci-biology/amos: bring in upstream patch to cope with secondary alignments
+ from 'bwa mem -M'
diff --git a/sci-biology/abyss/abyss-1.3.3-r1.ebuild
b/sci-biology/abyss/abyss-1.3.3-r1.ebuild
new file mode 100644
index 000..b727861
--- /dev/null
+++ b/sci-biology/abyss/abyss-1.3.3-r1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.3.ebuild,v 1.5
2013/08/11 14:55:22 jlec Exp $
+
+EAPI="4"
+
+inherit autotools eutils toolchain-funcs
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end
sequence assembler"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/";
+SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz";
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+ dev-cpp/sparsehash
+ mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+src_prepare() {
+ tc-export AR
+ epatch \
+ "${FILESDIR}"/${P}-gcc-4.7.patch \
+ "${FILESDIR}"/${P}-ac_prog_ar.patch \
+ "${FILESDIR}"/${P}-samtoafg.patch
+
+ sed -i -e "s/-Werror//" configure.ac || die #365195
+ sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
+ eautoreconf
+}
+
+src_configure() {
+ econf \
+ --docdir="${EPREFIX}/usr/share/doc/${PF}" \
+ $(use_enable openmp)
+}
diff --git a/sci-biology/abyss/abyss-1.3.4-r1.ebuild
b/sci-biology/abyss/abyss-1.3.4-r1.ebuild
new file mode 100644
index 000..48d7671
--- /dev/null
+++ b/sci-biology/abyss/abyss-1.3.4-r1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.4.ebuild,v 1.3
2013/08/11 14:55:22 jlec Exp $
+
+EAPI=5
+
+AUTOTOOLS_AUTORECONF=true
+
+inherit autotools-utils
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end
sequence assembler"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/";
+SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz";
+
+LICENSE="abyss"
+SLOT="0"
+IUSE="+mpi openmp"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+ dev-cpp/sparsehash
+ mpi? ( virtual/mpi )"
+RDEPEND="${DEPEND}"
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+PATCHES=(
+ "${FILESDIR}"/${P}-gcc-4.7.patch
+ "${FILESDIR}"/${PN}-1.3.3-ac_prog_ar.patch
+ "${FILESDIR}"/${P}-samtoafg.patch
+ )
+
+src_prepare() {
+ tc-export AR
+ sed -i -e "s/-Werror//" configure.ac || die #365195
+
