* [gentoo-commits] proj/sci:master commit in: sci-biology/sailfish/
@ 2016-02-28 10:43 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2016-02-28 10:43 UTC (permalink / raw
To: gentoo-commits
commit: 6ec195fe065abff2e723c37351f5938e1e89bb2e
Author: mschubert <mschu.dev <AT> gmail <DOT> com>
AuthorDate: Sat Feb 27 19:56:31 2016 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 28 10:43:14 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ec195fe
sci-biology/sailfish: bump EAPI=6
sci-biology/sailfish/sailfish-0.9.1.ebuild | 2 +-
sci-biology/sailfish/sailfish-9999.ebuild | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/sailfish/sailfish-0.9.1.ebuild b/sci-biology/sailfish/sailfish-0.9.1.ebuild
index c17ea29..8a1b1c0 100644
--- a/sci-biology/sailfish/sailfish-0.9.1.ebuild
+++ b/sci-biology/sailfish/sailfish-0.9.1.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
inherit cmake-utils
diff --git a/sci-biology/sailfish/sailfish-9999.ebuild b/sci-biology/sailfish/sailfish-9999.ebuild
index 2d60e34..9024d1d 100644
--- a/sci-biology/sailfish/sailfish-9999.ebuild
+++ b/sci-biology/sailfish/sailfish-9999.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
inherit cmake-utils git-r3
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/sailfish/
@ 2018-04-21 16:22 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2018-04-21 16:22 UTC (permalink / raw
To: gentoo-commits
commit: 2e9f85acc8a4dfe99a06aeef66b0cc3eb4416799
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 21 16:21:46 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 21 16:21:46 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2e9f85ac
sci-biology/sailfish: drop KEYWORDS, version bump
This package automatically downloads 3rd-party sources
instead of just compiling.
https://github.com/kingsfordgroup/sailfish/issues/80
Package-Manager: Portage-2.3.28, Repoman-2.3.9
.../{sailfish-0.9.2.ebuild => sailfish-0.10.0.ebuild} | 19 ++++++++++---------
sci-biology/sailfish/sailfish-9999.ebuild | 18 ++++++++++++++----
2 files changed, 24 insertions(+), 13 deletions(-)
diff --git a/sci-biology/sailfish/sailfish-0.9.2.ebuild b/sci-biology/sailfish/sailfish-0.10.0.ebuild
similarity index 64%
rename from sci-biology/sailfish/sailfish-0.9.2.ebuild
rename to sci-biology/sailfish/sailfish-0.10.0.ebuild
index d4953a2a5..9d618076d 100644
--- a/sci-biology/sailfish/sailfish-0.9.2.ebuild
+++ b/sci-biology/sailfish/sailfish-0.10.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
-inherit cmake-utils
+inherit cmake-utils multilib
DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
HOMEPAGE="http://www.cs.cmu.edu/~ckingsf/software/sailfish/"
@@ -11,27 +11,28 @@ SRC_URI="https://github.com/kingsfordgroup/${PN}/archive/v${PV}.tar.gz -> ${P}.t
LICENSE="GPL-3+"
SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS=""
IUSE=""
PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch )
DEPEND="dev-libs/boost:0
dev-libs/jemalloc
- dev-cpp/tbb"
+ dev-cpp/tbb
+ sci-biology/jellyfish:2"
RDEPEND="${DEPEND}"
# a C++-11 compliant compiler is needs, aka >=gcc-4.7
-# TODO: disable
-# [ 7%] Performing download step (verify and extract) for 'libdivsufsort'
-#i
+# TODO: disable running wget/curl during src_compile
+# https://github.com/kingsfordgroup/sailfish/issues/80
# contains bundled RapMap
-# contains bundled libdivsufsort-master
+# contains bundled libdivsufsort
# contains bundled libgff
# contains bundled jellyfish-2.2.3
-# contains bundled sparsehash-sparsehash-2.0.2
+# contains bundled sparsehash-2.0.2
src_install() {
cmake-utils_src_install
rm -r "${ED}"/usr/tests || die
+ rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
}
diff --git a/sci-biology/sailfish/sailfish-9999.ebuild b/sci-biology/sailfish/sailfish-9999.ebuild
index 6c37b858e..f31f16197 100644
--- a/sci-biology/sailfish/sailfish-9999.ebuild
+++ b/sci-biology/sailfish/sailfish-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
-inherit cmake-utils git-r3
+inherit cmake-utils git-r3 multilib
DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
HOMEPAGE="http://www.cs.cmu.edu/~ckingsf/software/sailfish/"
@@ -14,14 +14,24 @@ LICENSE="GPL-3"
SLOT="0"
IUSE=""
-PATCHES=( "${FILESDIR}"/${PN}-0.9.1-no-boost-static.patch )
+PATCHES=( "${FILESDIR}"/${PN}-0.9.2-no-boost-static.patch )
DEPEND="dev-libs/boost:0
dev-libs/jemalloc
- dev-cpp/tbb"
+ dev-cpp/tbb
+ sci-biology/jellyfish:2"
RDEPEND="${DEPEND}"
+# TODO: disable running wget/curl during src_compile
+# https://github.com/kingsfordgroup/sailfish/issues/80
+# contains bundled RapMap
+# contains bundled libdivsufsort-master
+# contains bundled libgff
+# contains bundled jellyfish-2.2.3
+# contains bundled sparsehash-2.0.2
+
src_install() {
cmake-utils_src_install
rm -r "${ED}"/usr/tests || die
+ rm -f "${ED}"/usr/bin/jellyfish "${ED}"/usr/$(get_libdir)/libjellyfish || die
}
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/sailfish/
@ 2018-04-21 16:27 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2018-04-21 16:27 UTC (permalink / raw
To: gentoo-commits
commit: f3d840f23ecfc7a73bd21ed89eae5a5f9cca96f4
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 21 16:26:55 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 21 16:26:55 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f3d840f2
sci-biology/sailfish: fix filename with a patch
Anyway, it does not compile with gcc-7.3.0 at least.
Package-Manager: Portage-2.3.28, Repoman-2.3.9
sci-biology/sailfish/sailfish-0.10.0.ebuild | 4 ++--
sci-biology/sailfish/sailfish-9999.ebuild | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/sailfish/sailfish-0.10.0.ebuild b/sci-biology/sailfish/sailfish-0.10.0.ebuild
index 9d618076d..ee543e73e 100644
--- a/sci-biology/sailfish/sailfish-0.10.0.ebuild
+++ b/sci-biology/sailfish/sailfish-0.10.0.ebuild
@@ -14,7 +14,7 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch )
+PATCHES=( "${FILESDIR}"/${PN}-0.9.2-no-boost-static.patch )
DEPEND="dev-libs/boost:0
dev-libs/jemalloc
@@ -28,7 +28,7 @@ RDEPEND="${DEPEND}"
# contains bundled RapMap
# contains bundled libdivsufsort
# contains bundled libgff
-# contains bundled jellyfish-2.2.3
+# contains bundled jellyfish-2.2.5
# contains bundled sparsehash-2.0.2
src_install() {
diff --git a/sci-biology/sailfish/sailfish-9999.ebuild b/sci-biology/sailfish/sailfish-9999.ebuild
index f31f16197..17d35648d 100644
--- a/sci-biology/sailfish/sailfish-9999.ebuild
+++ b/sci-biology/sailfish/sailfish-9999.ebuild
@@ -27,7 +27,7 @@ RDEPEND="${DEPEND}"
# contains bundled RapMap
# contains bundled libdivsufsort-master
# contains bundled libgff
-# contains bundled jellyfish-2.2.3
+# contains bundled jellyfish-2.2.5
# contains bundled sparsehash-2.0.2
src_install() {
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/sailfish/
@ 2018-04-22 7:42 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2018-04-22 7:42 UTC (permalink / raw
To: gentoo-commits
commit: 93d4cefb6d4f6c5bc080280b117a31a5c7eb141d
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 22 07:42:25 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 22 07:42:25 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=93d4cefb
sci-biology/sailfish: update comments with URLs
Package-Manager: Portage-2.3.28, Repoman-2.3.9
sci-biology/sailfish/sailfish-0.10.0.ebuild | 4 ++--
sci-biology/sailfish/sailfish-9999.ebuild | 6 +++---
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/sci-biology/sailfish/sailfish-0.10.0.ebuild b/sci-biology/sailfish/sailfish-0.10.0.ebuild
index ee543e73e..228fcfdbb 100644
--- a/sci-biology/sailfish/sailfish-0.10.0.ebuild
+++ b/sci-biology/sailfish/sailfish-0.10.0.ebuild
@@ -25,9 +25,9 @@ RDEPEND="${DEPEND}"
# TODO: disable running wget/curl during src_compile
# https://github.com/kingsfordgroup/sailfish/issues/80
-# contains bundled RapMap
+# contains bundled RapMap https://github.com/COMBINE-lab/RapMap
# contains bundled libdivsufsort
-# contains bundled libgff
+# contains bundled libgff https://github.com/COMBINE-lab/libgff
# contains bundled jellyfish-2.2.5
# contains bundled sparsehash-2.0.2
diff --git a/sci-biology/sailfish/sailfish-9999.ebuild b/sci-biology/sailfish/sailfish-9999.ebuild
index 17d35648d..29a967af8 100644
--- a/sci-biology/sailfish/sailfish-9999.ebuild
+++ b/sci-biology/sailfish/sailfish-9999.ebuild
@@ -24,9 +24,9 @@ RDEPEND="${DEPEND}"
# TODO: disable running wget/curl during src_compile
# https://github.com/kingsfordgroup/sailfish/issues/80
-# contains bundled RapMap
-# contains bundled libdivsufsort-master
-# contains bundled libgff
+# contains bundled RapMap https://github.com/COMBINE-lab/RapMap
+# contains bundled libdivsufsort
+# contains bundled libgff https://github.com/COMBINE-lab/libgff
# contains bundled jellyfish-2.2.5
# contains bundled sparsehash-2.0.2
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/sailfish/
@ 2021-01-30 15:15 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-01-30 15:15 UTC (permalink / raw
To: gentoo-commits
commit: 7f1bbcfd235106e9681e937128532d1ebfefacb8
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Jan 30 15:15:18 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Jan 30 15:15:18 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f1bbcfd
sci-biology/sailfish: add bdep on unzip for unpack
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/sailfish/sailfish-0.10.0.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/sailfish/sailfish-0.10.0.ebuild b/sci-biology/sailfish/sailfish-0.10.0.ebuild
index 8ababe879..4aef4312e 100644
--- a/sci-biology/sailfish/sailfish-0.10.0.ebuild
+++ b/sci-biology/sailfish/sailfish-0.10.0.ebuild
@@ -23,6 +23,7 @@ DEPEND="
sci-biology/jellyfish:2
"
RDEPEND="${DEPEND}"
+BDEPEND="app-arch/unzip"
# a C++-11 compliant compiler is needs, aka >=gcc-4.7
# TODO: disable running wget/curl during src_compile
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/sailfish/
@ 2021-02-04 5:08 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-02-04 5:08 UTC (permalink / raw
To: gentoo-commits
commit: 9e1701c4483715ce8127247055278731d33a8079
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Feb 4 05:08:13 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Feb 4 05:08:13 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9e1701c4
sci-biology/sailfish: fix configure phase
does not compile at the moment though so no keywords yet
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/sailfish/sailfish-0.10.0.ebuild | 11 ++++++++++-
1 file changed, 10 insertions(+), 1 deletion(-)
diff --git a/sci-biology/sailfish/sailfish-0.10.0.ebuild b/sci-biology/sailfish/sailfish-0.10.0.ebuild
index 4aef4312e..8ba4d0cf7 100644
--- a/sci-biology/sailfish/sailfish-0.10.0.ebuild
+++ b/sci-biology/sailfish/sailfish-0.10.0.ebuild
@@ -8,7 +8,11 @@ inherit cmake multilib
DESCRIPTION="Rapid Mapping-based Isoform Quantification from RNA-Seq Reads"
HOMEPAGE="https://www.cs.cmu.edu/~ckingsf/software/sailfish/"
SRC_URI="https://github.com/kingsfordgroup/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
- https://github.com/COMBINE-lab/RapMap/archive/quasi-mph.zip"
+ https://github.com/COMBINE-lab/RapMap/archive/quasi-mph.zip
+ https://github.com/gmarcais/Jellyfish/releases/download/v2.2.5/jellyfish-2.2.5.tar.gz
+ https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz
+ https://github.com/Kingsford-Group/libgff/archive/v1.0.tar.gz
+"
LICENSE="GPL-3+"
SLOT="0"
@@ -45,10 +49,15 @@ src_unpack() {
mkdir -p "${S}/external"
cp "${DISTDIR}/quasi-mph.zip" "${S}/external/rapmap.zip" || die
mv "${WORKDIR}/RapMap-quasi-mph" "${S}/external/RapMap" || die
+ mv "${WORKDIR}/jellyfish-2.2.5" "${S}/external/jellyfish-2.2.5" || die
+ mv "${WORKDIR}/sparsehash-sparsehash-2.0.2" "${S}/external/sparsehash-sparsehash-2.0.2" || die
+ mv "${WORKDIR}/libgff-1.0" "${S}/external/libgff" || die
mkdir -p "${S}/external/install/lib"
cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort.so" "${S}/external/install/lib/" || die
cp "${EPREFIX}/usr/$(get_libdir)/libdivsufsort64.so" "${S}/external/install/lib/" || die
cp "${EPREFIX}/usr/$(get_libdir)/libjellyfish-2.0.so" "${S}/external/install/lib/" || die
+ mkdir -p "${S}/external/install/src/rapmap"
+ cp "${S}/external/RapMap/src/"* "${S}/external/install/src/rapmap" || die
}
src_prepare() {
^ permalink raw reply related [flat|nested] 6+ messages in thread
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