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

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

[Justin Lecher]

commit:     060a770920f2cd21994b2ff0efa7d263c3c70493
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 23 12:08:24 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep 23 12:08:24 2015 +0000
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 <jlec <AT> 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/

[Marius Brehler]

commit:     f1f6c31bb308f59777bb396827099ec71b4b35a1
Author:     Sergei Trofimovich <siarheit <AT> google <DOT> com>
AuthorDate: Sun Apr  3 15:34:21 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Sun Apr  3 17:43:47 2016 +0000
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 @@
     <email>sci-biology@gentoo.org</email>
     <name>Gentoo Biology Project</name>
   </maintainer>
+  <maintainer type="project">
+    <email>haskell@gentoo.org</email>
+    <name>Gentoo Haskell</name>
+  </maintainer>
+  <use>
+    <flag name='misc-haskell'>build abyss-samtobreak tool, pull in haskell toolchain</flag>
+  </use>
 </pkgmetadata>

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

[Martin Mokrejs]

commit:     e09e5ec884dd0210694529c19b81fab9c48a76bc
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Sep 11 21:54:18 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Sep 11 21:54:18 2018 +0000
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 000000000..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 000000000..47116e507
--- /dev/null
+++ b/sci-biology/abyss/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>haskell@gentoo.org</email>
+    <name>Gentoo Haskell</name>
+  </maintainer>
+  <use>
+    <flag name="misc-haskell">build abyss-samtobreak tool, pull in haskell toolchain</flag>
+  </use>
+  <upstream>
+    <remote-id type="github">bcgsc/abyss</remote-id>
+  </upstream>
+</pkgmetadata>

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

[Martin Mokrejs]

commit:     0e4eaa3b33984588d0d57ca68b0ea877c461c6ab
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Oct 29 13:56:23 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Oct 29 13:56:23 2018 +0000
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/

[Martin Mokrejs]

commit:     f0b1356038ad8ed9fcfd12298dd5e92749bc6a87
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Dec  6 10:59:50 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Dec  6 10:59:50 2018 +0000
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 <mmokrejs <AT> 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/

[Martin Mokrejs]

commit:     9eeb095bd6468b0ab9ac265d730eaf458afae83a
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Dec 10 13:28:09 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Dec 10 13:28:09 2018 +0000
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 <mmokrejs <AT> 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/

[Martin Mokrejs]

commit:     581b836c34e32d3e201b8cfc7a4377514d16e2e3
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Aug 15 07:51:31 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Aug 15 07:51:31 2019 +0000
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 <mmokrejs <AT> 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/

[Martin Mokrejs]

commit:     982e84f44b14e71d4bae96aab4d246a3f0ec0f6f
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Aug 20 13:22:28 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Aug 20 13:22:28 2019 +0000
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 <mmokrejs <AT> 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/

[Martin Mokrejs]

commit:     08f6cb388ea7db562f4f6a32e9cef76dfd62caff
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Sep 28 13:05:52 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Sep 28 13:05:52 2019 +0000
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 <mmokrejs <AT> 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/

[Martin Mokrejs]

commit:     05629a9dc997950a1bf3dfa002307decc492e4b7
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Thu Feb 20 15:15:16 2020 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Feb 20 15:16:22 2020 +0000
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 <mmokrejs <AT> 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/

[Horea Christian]

commit:     c7e35e6a3ba60f35a787c02b1472c867ed3e1e3f
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Dec 25 10:21:55 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Dec 25 10:21:55 2020 +0000
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 <chr <AT> 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/

[Aisha Tammy]

commit:     45d35292cee5f5b1f1f9c17d8fc343bdd99e7088
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Dec 31 16:22:46 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Thu Dec 31 16:50:12 2020 +0000
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 <andrewammerlaan <AT> riseup.net>
Closes: https://github.com/gentoo/sci/pull/1022
Signed-off-by: Aisha Tammy <gentoo <AT> 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/

[Martin Mokrejs]

commit:     85d646372a278f85c05c5c7c717b9e94fa967ddc
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Thu Apr  1 20:11:06 2021 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr  1 20:11:06 2021 +0000
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 <mmokrejs <AT> 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/

[Martin Mokrejs]

commit:     6c252245a4ab18f5d211723f9078682dfa06bd00
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Thu Apr 22 07:23:16 2021 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 22 07:23:16 2021 +0000
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 <mmokrejs <AT> 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 000000000..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
+}