* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2021-01-19 15:29 Andrew Ammerlaan
0 siblings, 0 replies; 18+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 15:29 UTC (permalink / raw
To: gentoo-commits
commit: 89b29b2a57824d3a32051c4f8aa2eae6eb21bfab
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 15:28:59 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 15:28:59 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=89b29b2a
sci-biology/salmon: add version 1.4.0
Closes: https://github.com/gentoo/sci/pull/1013
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/salmon/salmon-1.4.0.ebuild | 40 +++++++++++++++++
sci-biology/salmon/salmon-9999.ebuild | 81 ++++++++++------------------------
2 files changed, 63 insertions(+), 58 deletions(-)
diff --git a/sci-biology/salmon/salmon-1.4.0.ebuild b/sci-biology/salmon/salmon-1.4.0.ebuild
new file mode 100644
index 000000000..858ff642b
--- /dev/null
+++ b/sci-biology/salmon/salmon-1.4.0.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
+HOMEPAGE="https://github.com/COMBINE-lab/salmon"
+SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+
+RDEPEND="
+ dev-libs/boost:=[threads]
+ sys-libs/zlib
+"
+
+DEPEND="${RDEPEND}
+ app-arch/bzip2
+ app-arch/xz-utils
+ >=dev-libs/jemalloc-5.0.1
+ >=dev-cpp/tbb-2018.20180312
+ sci-biology/pufferfish
+ sci-libs/staden-io
+ sci-libs/libgff
+ dev-libs/cereal
+"
+
+BDEPEND="
+ app-arch/unzip
+ net-misc/curl
+"
+
+PATCHES=(
+ "${FILESDIR}/${P}-do-not-fetch-pufferfish.patch"
+ "${FILESDIR}/${P}-allow-newer-boost.patch"
+)
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index 8862ff790..b7d02edd7 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -1,69 +1,34 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-inherit multilib cmake-utils git-r3
+inherit cmake git-r3
DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
HOMEPAGE="https://github.com/COMBINE-lab/salmon"
EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git"
-#SRC_URI="https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip
-# https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz
-# https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz
-# https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz
-# https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz
-# https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz"
LICENSE="GPL-3"
SLOT="0"
-IUSE=""
-PATCHES=( "${FILESDIR}"/salmon-0.10.2-no-boost-static.patch
- "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch
- "${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch
- "${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch
- "${FILESDIR}"/salmon-0.10.2_fix_tests.patch
- "${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch )
-
-# budled copies of:
-# sci-biology/bwa-0.7.12.5
-# sci-biology/jellyfish
-# sci-biology/staden-1.14.8.1
-# sci-biology/gfftools
-#
-# libgff-1.1 from https://github.com/Kingsford-Group/libgff
-# actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
-# https://github.com/Kingsford-Group/libgff/issues/1
-#
-# dev-libs/spdlog-0.16.1
-# cereal-1.2.2
-DEPEND="net-misc/curl
- app-arch/unzip
- sys-libs/zlib
- app-arch/bzip2
- app-arch/xz-utils
- dev-libs/boost:0[threads]
- >=dev-libs/jemalloc-5.0.1
- >=dev-cpp/tbb-2018.20180312"
-RDEPEND="${DEPEND}"
-
-# https://github.com/COMBINE-lab/salmon/issues/19
-#
-# contains bundled copies of https://github.com/jemalloc/jemalloc
-# https://github.com/gabime/spdlog
-# https://github.com/efficient/libcuckoo
-# https://github.com/greg7mdp/sparsepp
-# https://github.com/COMBINE-lab/RapMap , actually runs curl to fetch it
-# https://github.com/Kingsford-Group/libgff
-# sci-libs/io_lib
-#
-# https://github.com/COMBINE-lab/salmon/issues/19#issuecomment-144721158
-# modified bwa copy
-#
-# and maybe more
-
-# See https://github.com/COMBINE-lab/salmon/issues/236 for Cmake tweaks needed by Debian
-
-# see the many curl executions:
-# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null
+RDEPEND="
+ dev-libs/boost:=[threads]
+ sys-libs/zlib
+"
+
+DEPEND="${RDEPEND}
+ app-arch/bzip2
+ app-arch/xz-utils
+ >=dev-libs/jemalloc-5.0.1
+ >=dev-cpp/tbb-2018.20180312
+ sci-biology/pufferfish
+ sci-libs/staden-io
+ sci-libs/libgff
+ dev-libs/cereal
+"
+
+BDEPEND="
+ app-arch/unzip
+ net-misc/curl
+"
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2022-01-23 13:32 Andrew Ammerlaan
0 siblings, 0 replies; 18+ messages in thread
From: Andrew Ammerlaan @ 2022-01-23 13:32 UTC (permalink / raw
To: gentoo-commits
commit: 34e6a206c9459aeff470972b4f4dd7915ee8dcd9
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 23 13:14:15 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sun Jan 23 13:14:15 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=34e6a206
sci-biology/salmon: drop live
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/salmon/salmon-9999.ebuild | 32 --------------------------------
1 file changed, 32 deletions(-)
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
deleted file mode 100644
index 89ca690c6..000000000
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake git-r3
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git"
-
-LICENSE="GPL-3"
-SLOT="0"
-
-RDEPEND="
- dev-libs/boost:=[threads(-)]
- sys-libs/zlib
-"
-
-DEPEND="${RDEPEND}
- app-arch/bzip2
- app-arch/xz-utils
- >=dev-libs/jemalloc-5.0.1
- >=dev-cpp/tbb-2018.20180312
- sci-biology/pufferfish
- dev-libs/cereal
-"
-
-BDEPEND="
- app-arch/unzip
- net-misc/curl
-"
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2022-01-15 14:14 Andrew Ammerlaan
0 siblings, 0 replies; 18+ messages in thread
From: Andrew Ammerlaan @ 2022-01-15 14:14 UTC (permalink / raw
To: gentoo-commits
commit: 509cb4055d987fb9812743711caa87af2b8a88ca
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 15 14:14:38 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat Jan 15 14:14:38 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=509cb405
sci-biology/salmon: drop unavailable flag
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/salmon/salmon-0.10.2.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
index 7e58d41fb..c3ef9e50a 100644
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -48,7 +48,7 @@ DEPEND="
sys-libs/zlib
app-arch/bzip2
app-arch/xz-utils
- dev-libs/boost:0[threads(-)]
+ dev-libs/boost:0=
dev-libs/libdivsufsort
sci-biology/bwa
>=dev-libs/jemalloc-5.0.1
^ permalink raw reply related [flat|nested] 18+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2021-08-31 9:45 Andrew Ammerlaan
0 siblings, 0 replies; 18+ messages in thread
From: Andrew Ammerlaan @ 2021-08-31 9:45 UTC (permalink / raw
To: gentoo-commits
commit: 7ec26f243df0dc5a5c03295335a772e38d795ebb
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Aug 31 09:40:40 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Aug 31 09:40:40 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7ec26f24
sci-biology/salmon: add MissingUseDepDefault
Package-Manager: Portage-3.0.22, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/salmon/salmon-0.10.2.ebuild | 2 +-
sci-biology/salmon/salmon-1.4.0.ebuild | 2 +-
sci-biology/salmon/salmon-9999.ebuild | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
index 671309ed0..b5bd8bdfe 100644
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -48,7 +48,7 @@ DEPEND="
sys-libs/zlib
app-arch/bzip2
app-arch/xz-utils
- dev-libs/boost:0[threads]
+ dev-libs/boost:0[threads(-)]
dev-libs/libdivsufsort
sci-biology/bwa
>=dev-libs/jemalloc-5.0.1
diff --git a/sci-biology/salmon/salmon-1.4.0.ebuild b/sci-biology/salmon/salmon-1.4.0.ebuild
index 0338e5ebe..420cb2ae2 100644
--- a/sci-biology/salmon/salmon-1.4.0.ebuild
+++ b/sci-biology/salmon/salmon-1.4.0.ebuild
@@ -14,7 +14,7 @@ SLOT="0"
KEYWORDS=""
RDEPEND="
- dev-libs/boost:=[threads]
+ dev-libs/boost:=[threads(-)]
sys-libs/zlib
"
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index da5a220c8..89ca690c6 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -13,7 +13,7 @@ LICENSE="GPL-3"
SLOT="0"
RDEPEND="
- dev-libs/boost:=[threads]
+ dev-libs/boost:=[threads(-)]
sys-libs/zlib
"
^ permalink raw reply related [flat|nested] 18+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2021-03-22 13:46 Andrew Ammerlaan
0 siblings, 0 replies; 18+ messages in thread
From: Andrew Ammerlaan @ 2021-03-22 13:46 UTC (permalink / raw
To: gentoo-commits
commit: 459e5c7233c8d8e9aae0946e5fef3279fdcd0ba2
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Mar 22 13:46:22 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Mar 22 13:46:22 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=459e5c72
sci-biology/salmon: fix library path
https://github.com/gentoo/sci/issues/1058
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/salmon/salmon-0.10.2.ebuild | 16 +++++++++++++++-
1 file changed, 15 insertions(+), 1 deletion(-)
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
index 914ab0e69..671309ed0 100644
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-inherit cmake
+inherit cmake multilib
DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
HOMEPAGE="https://github.com/COMBINE-lab/salmon"
@@ -49,6 +49,8 @@ DEPEND="
app-arch/bzip2
app-arch/xz-utils
dev-libs/boost:0[threads]
+ dev-libs/libdivsufsort
+ sci-biology/bwa
>=dev-libs/jemalloc-5.0.1
>=dev-cpp/tbb-2018.20180312
"
@@ -57,3 +59,15 @@ BDEPEND="
net-misc/curl
app-arch/unzip
"
+
+src_prepare() {
+ # use system libs
+ sed -i \
+ -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a%/usr/$(get_libdir)/libstaden-read.so%g" \
+ -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort.a%/usr/$(get_libdir)/libdivsufsort.so%g" \
+ -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort64.a%/usr/$(get_libdir)/libdivsufsort64.so%g" \
+ -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libbwa.a%/usr/$(get_libdir)/libbwa.so%g" \
+ src/CMakeLists.txt || die
+
+ cmake_src_prepare
+}
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2021-01-26 21:10 Andrew Ammerlaan
0 siblings, 0 replies; 18+ messages in thread
From: Andrew Ammerlaan @ 2021-01-26 21:10 UTC (permalink / raw
To: gentoo-commits
commit: 8a24647b19039e4a4e392688f98cbfcea24d302d
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 26 21:10:14 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 26 21:10:14 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8a24647b
sci-biology/salmon: cmake-utils --> cmake EAPI bump
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/salmon/salmon-0.10.2.ebuild | 24 ++++++++++++++----------
1 file changed, 14 insertions(+), 10 deletions(-)
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
index a4d6a40e1..914ab0e69 100644
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -1,9 +1,9 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-inherit cmake-utils
+inherit cmake
DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
HOMEPAGE="https://github.com/COMBINE-lab/salmon"
@@ -44,12 +44,16 @@ RDEPEND="${DEPEND}"
# see the many curl executions:
# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null
#
-DEPEND="net-misc/curl
- app-arch/unzip
- sys-libs/zlib
- app-arch/bzip2
- app-arch/xz-utils
- dev-libs/boost:0[threads]
- >=dev-libs/jemalloc-5.0.1
- >=dev-cpp/tbb-2018.20180312"
+DEPEND="
+ sys-libs/zlib
+ app-arch/bzip2
+ app-arch/xz-utils
+ dev-libs/boost:0[threads]
+ >=dev-libs/jemalloc-5.0.1
+ >=dev-cpp/tbb-2018.20180312
+"
RDEPEND="${DEPEND}"
+BDEPEND="
+ net-misc/curl
+ app-arch/unzip
+"
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2021-01-19 17:10 Andrew Ammerlaan
0 siblings, 0 replies; 18+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 17:10 UTC (permalink / raw
To: gentoo-commits
commit: 5d4336a74e71bccf810d38c2010ec5990c6b4f30
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 17:10:48 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 17:10:48 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5d4336a7
sci-biology/salmon: remove missing deps packaged in pufferfish
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/salmon/salmon-9999.ebuild | 2 --
1 file changed, 2 deletions(-)
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index b7d02edd7..da5a220c8 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -23,8 +23,6 @@ DEPEND="${RDEPEND}
>=dev-libs/jemalloc-5.0.1
>=dev-cpp/tbb-2018.20180312
sci-biology/pufferfish
- sci-libs/staden-io
- sci-libs/libgff
dev-libs/cereal
"
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2021-01-19 15:45 Andrew Ammerlaan
0 siblings, 0 replies; 18+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 15:45 UTC (permalink / raw
To: gentoo-commits
commit: a488fcefd25cebb552bbd2ac239e4c88e2382cda
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 15:45:25 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 15:45:25 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a488fcef
sci-biology/salmon: remove non-existing deps included in pufferfish
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/salmon/salmon-1.4.0.ebuild | 2 --
1 file changed, 2 deletions(-)
diff --git a/sci-biology/salmon/salmon-1.4.0.ebuild b/sci-biology/salmon/salmon-1.4.0.ebuild
index 858ff642b..0338e5ebe 100644
--- a/sci-biology/salmon/salmon-1.4.0.ebuild
+++ b/sci-biology/salmon/salmon-1.4.0.ebuild
@@ -24,8 +24,6 @@ DEPEND="${RDEPEND}
>=dev-libs/jemalloc-5.0.1
>=dev-cpp/tbb-2018.20180312
sci-biology/pufferfish
- sci-libs/staden-io
- sci-libs/libgff
dev-libs/cereal
"
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2021-01-06 9:42 Andrew Ammerlaan
0 siblings, 0 replies; 18+ messages in thread
From: Andrew Ammerlaan @ 2021-01-06 9:42 UTC (permalink / raw
To: gentoo-commits
commit: 87c089260eee3eddbcc4d48c160318c6d6d54cb9
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Jan 6 09:33:46 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Jan 6 09:33:46 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=87c08926
sci-biology/salmon: drop keywords not available in bzip2 dep
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/salmon/salmon-0.10.2.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
index 088fea331..a4d6a40e1 100644
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -17,7 +17,7 @@ SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86"
IUSE=""
PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2018-06-25 20:22 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2018-06-25 20:22 UTC (permalink / raw
To: gentoo-commits
commit: 92c5061f6b2bb7bd14c0727b5c69df87b433f472
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jun 25 20:22:36 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jun 25 20:22:36 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=92c5061f
sci-biology/salmon: add missing DEPENDency on app-arch/unzip
https://github.com/COMBINE-lab/salmon/issues/181#issuecomment-367800400
Package-Manager: Portage-2.3.40, Repoman-2.3.9
sci-biology/salmon/salmon-0.10.2.ebuild | 1 +
sci-biology/salmon/salmon-9999.ebuild | 1 +
2 files changed, 2 insertions(+)
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
index b3bdc6d53..90db2e1fe 100644
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -43,6 +43,7 @@ RDEPEND="${DEPEND}"
# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null
#
DEPEND="net-misc/curl
+ app-arch/unzip
sys-libs/zlib
app-arch/bzip2
app-arch/xz-utils
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index 221418960..904c37654 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -37,6 +37,7 @@ PATCHES=( "${FILESDIR}"/salmon-0.10.2-no-boost-static.patch
# dev-libs/spdlog-0.16.1
# cereal-1.2.2
DEPEND="net-misc/curl
+ app-arch/unzip
sys-libs/zlib
app-arch/bzip2
app-arch/xz-utils
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2018-06-24 16:30 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2018-06-24 16:30 UTC (permalink / raw
To: gentoo-commits
commit: a2507a4b3b03f1f72898e2304baaa7b1780516fe
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jun 24 16:29:54 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jun 24 16:29:54 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a2507a4b
sci-biology/salmon: bump version of required dev-cpp/tbb
Package-Manager: Portage-2.3.40, Repoman-2.3.9
sci-biology/salmon/salmon-0.10.2.ebuild | 2 +-
sci-biology/salmon/salmon-9999.ebuild | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
index 34a425403..f97a32f18 100644
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -16,7 +16,7 @@ IUSE=""
DEPEND="dev-libs/boost:0
dev-libs/jemalloc
- dev-cpp/tbb"
+ >=dev-cpp/tbb-2018.20180312"
RDEPEND="${DEPEND}"
src_install() {
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index faf91aaa8..ab0f9c368 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -15,7 +15,7 @@ IUSE=""
DEPEND="dev-libs/boost:0
dev-libs/jemalloc
- dev-cpp/tbb"
+ >=dev-cpp/tbb-2018.20180312"
RDEPEND="${DEPEND}"
# https://github.com/COMBINE-lab/salmon/issues/19
#
@@ -35,7 +35,7 @@ RDEPEND="${DEPEND}"
# See https://github.com/COMBINE-lab/salmon/issues/236 for Cmake tweaks needed by Debian
src_configure(){
local mycmakeargs=(
- "-DBOOST_INCLUDEDIR=${EPREFIX}/usr/include/"
+ "-DBOOST_INCLUDEDIR=${EPREFIX}/usr/include/boost/"
"-DBOOST_LIBRARYDIR=${EPREFIX}/usr/$(get_libdir)/"
"-DTBB_INSTALL_DIR=${EPREFIX}/usr"
"-DCMAKE_INSTALL_PREFIX=${EPREFIX}/usr"
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2018-06-24 16:30 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2018-06-24 16:30 UTC (permalink / raw
To: gentoo-commits
commit: 594a1b96b0ddfda0c68ddc46f14e3e6db0961856
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jun 24 16:05:15 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jun 24 16:05:15 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=594a1b96
sci-biology/salmon: add URL link
Package-Manager: Portage-2.3.40, Repoman-2.3.9
sci-biology/salmon/salmon-9999.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index d370710b6..faf91aaa8 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -32,6 +32,7 @@ RDEPEND="${DEPEND}"
#
# and maybe more
+# See https://github.com/COMBINE-lab/salmon/issues/236 for Cmake tweaks needed by Debian
src_configure(){
local mycmakeargs=(
"-DBOOST_INCLUDEDIR=${EPREFIX}/usr/include/"
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2018-06-24 14:01 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2018-06-24 14:01 UTC (permalink / raw
To: gentoo-commits
commit: a1d0487c37ba900c1f239f5d73f7d429f018359d
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jun 24 14:01:12 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jun 24 14:01:12 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a1d0487c
sci-biology/salmon: version bump, attempts to get boost picked up
cmake does not detect boost for me although the errors speak of pthread
and not boost. Older version could probably be dropped soon.
Package-Manager: Portage-2.3.40, Repoman-2.3.9
.../salmon/{salmon-0.3.2.ebuild => salmon-0.10.2.ebuild} | 4 +---
sci-biology/salmon/salmon-0.3.2.ebuild | 2 +-
sci-biology/salmon/salmon-0.4.2.ebuild | 2 +-
sci-biology/salmon/salmon-0.5.0.ebuild | 2 +-
sci-biology/salmon/salmon-9999.ebuild | 10 +++++-----
5 files changed, 9 insertions(+), 11 deletions(-)
diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
similarity index 85%
copy from sci-biology/salmon/salmon-0.3.2.ebuild
copy to sci-biology/salmon/salmon-0.10.2.ebuild
index 6f5be90fb..34a425403 100644
--- a/sci-biology/salmon/salmon-0.3.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -14,8 +14,6 @@ SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""
-PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch )
-
DEPEND="dev-libs/boost:0
dev-libs/jemalloc
dev-cpp/tbb"
diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild b/sci-biology/salmon/salmon-0.3.2.ebuild
index 6f5be90fb..b9a50ebd1 100644
--- a/sci-biology/salmon/salmon-0.3.2.ebuild
+++ b/sci-biology/salmon/salmon-0.3.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
diff --git a/sci-biology/salmon/salmon-0.4.2.ebuild b/sci-biology/salmon/salmon-0.4.2.ebuild
index f88310f95..42ccf1e6c 100644
--- a/sci-biology/salmon/salmon-0.4.2.ebuild
+++ b/sci-biology/salmon/salmon-0.4.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
diff --git a/sci-biology/salmon/salmon-0.5.0.ebuild b/sci-biology/salmon/salmon-0.5.0.ebuild
index f88310f95..42ccf1e6c 100644
--- a/sci-biology/salmon/salmon-0.5.0.ebuild
+++ b/sci-biology/salmon/salmon-0.5.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index 4f48644c6..d370710b6 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -3,11 +3,10 @@
EAPI=6
-inherit cmake-utils git-r3
+inherit multilib cmake-utils git-r3
DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI=""
EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git"
LICENSE="GPL-3"
@@ -24,7 +23,7 @@ RDEPEND="${DEPEND}"
# https://github.com/gabime/spdlog
# https://github.com/efficient/libcuckoo
# https://github.com/greg7mdp/sparsepp
-# https://github.com/COMBINE-lab/RapMap
+# https://github.com/COMBINE-lab/RapMap , actually runs curl to fetch it
# https://github.com/Kingsford-Group/libgff
# sci-libs/io_lib
#
@@ -35,11 +34,12 @@ RDEPEND="${DEPEND}"
src_configure(){
local mycmakeargs=(
- "-DBOOST_ROOT=${EPREFIX}/usr"
+ "-DBOOST_INCLUDEDIR=${EPREFIX}/usr/include/"
+ "-DBOOST_LIBRARYDIR=${EPREFIX}/usr/$(get_libdir)/"
"-DTBB_INSTALL_DIR=${EPREFIX}/usr"
"-DCMAKE_INSTALL_PREFIX=${EPREFIX}/usr"
)
- # BUG: the configure step run automatically curl download of 3rd-party stuff
+ # BUG: the configure step runs automatically curl download of 3rd-party stuff
# https://github.com/COMBINE-lab/salmon/issues/19
cmake-utils_src_configure
}
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2018-04-21 17:17 Martin Mokrejs
0 siblings, 0 replies; 18+ messages in thread
From: Martin Mokrejs @ 2018-04-21 17:17 UTC (permalink / raw
To: gentoo-commits
commit: 5bcbca87122d15ab6ae31547021b65c872cef1c5
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 21 17:17:12 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 21 17:17:12 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5bcbca87
sci-biology/salmon: document install procedure issues
The building procedure is still a mess.
https://github.com/COMBINE-lab/salmon/issues/19
Package-Manager: Portage-2.3.28, Repoman-2.3.9
.../{salmon-0.6.0.ebuild => salmon-0.9.1.ebuild} | 4 +--
sci-biology/salmon/salmon-9999.ebuild | 29 +++++++++++++++++++---
2 files changed, 27 insertions(+), 6 deletions(-)
diff --git a/sci-biology/salmon/salmon-0.6.0.ebuild b/sci-biology/salmon/salmon-0.9.1.ebuild
similarity index 84%
rename from sci-biology/salmon/salmon-0.6.0.ebuild
rename to sci-biology/salmon/salmon-0.9.1.ebuild
index f88310f95..34a425403 100644
--- a/sci-biology/salmon/salmon-0.6.0.ebuild
+++ b/sci-biology/salmon/salmon-0.9.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -14,8 +14,6 @@ SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""
-PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
-
DEPEND="dev-libs/boost:0
dev-libs/jemalloc
dev-cpp/tbb"
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index 4acc02e71..4f48644c6 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -14,12 +14,35 @@ LICENSE="GPL-3"
SLOT="0"
IUSE=""
-PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
-
DEPEND="dev-libs/boost:0
dev-libs/jemalloc
dev-cpp/tbb"
RDEPEND="${DEPEND}"
+# https://github.com/COMBINE-lab/salmon/issues/19
+#
+# contains bundled copies of https://github.com/jemalloc/jemalloc
+# https://github.com/gabime/spdlog
+# https://github.com/efficient/libcuckoo
+# https://github.com/greg7mdp/sparsepp
+# https://github.com/COMBINE-lab/RapMap
+# https://github.com/Kingsford-Group/libgff
+# sci-libs/io_lib
+#
+# https://github.com/COMBINE-lab/salmon/issues/19#issuecomment-144721158
+# modified bwa copy
+#
+# and maybe more
+
+src_configure(){
+ local mycmakeargs=(
+ "-DBOOST_ROOT=${EPREFIX}/usr"
+ "-DTBB_INSTALL_DIR=${EPREFIX}/usr"
+ "-DCMAKE_INSTALL_PREFIX=${EPREFIX}/usr"
+ )
+ # BUG: the configure step run automatically curl download of 3rd-party stuff
+ # https://github.com/COMBINE-lab/salmon/issues/19
+ cmake-utils_src_configure
+}
src_install() {
cmake-utils_src_install
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2016-02-28 10:43 Justin Lecher
0 siblings, 0 replies; 18+ messages in thread
From: Justin Lecher @ 2016-02-28 10:43 UTC (permalink / raw
To: gentoo-commits
commit: a13c0868e6c317818d24a273d9ad1c12aae7930c
Author: mschubert <mschu.dev <AT> gmail <DOT> com>
AuthorDate: Sat Feb 27 20:03:05 2016 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 28 10:25:28 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a13c0868
sci-biology/salmon: bump EAPI=6
sci-biology/salmon/salmon-0.3.2.ebuild | 2 +-
sci-biology/salmon/salmon-0.4.2.ebuild | 2 +-
sci-biology/salmon/salmon-0.5.0.ebuild | 2 +-
sci-biology/salmon/salmon-0.6.0.ebuild | 2 +-
sci-biology/salmon/salmon-9999.ebuild | 2 +-
5 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild b/sci-biology/salmon/salmon-0.3.2.ebuild
index e64b220..782bd27 100644
--- a/sci-biology/salmon/salmon-0.3.2.ebuild
+++ b/sci-biology/salmon/salmon-0.3.2.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/salmon/salmon-0.4.2.ebuild b/sci-biology/salmon/salmon-0.4.2.ebuild
index 032fd4d..444be82 100644
--- a/sci-biology/salmon/salmon-0.4.2.ebuild
+++ b/sci-biology/salmon/salmon-0.4.2.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/salmon/salmon-0.5.0.ebuild b/sci-biology/salmon/salmon-0.5.0.ebuild
index 032fd4d..444be82 100644
--- a/sci-biology/salmon/salmon-0.5.0.ebuild
+++ b/sci-biology/salmon/salmon-0.5.0.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/salmon/salmon-0.6.0.ebuild b/sci-biology/salmon/salmon-0.6.0.ebuild
index 032fd4d..444be82 100644
--- a/sci-biology/salmon/salmon-0.6.0.ebuild
+++ b/sci-biology/salmon/salmon-0.6.0.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/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index 139e2ee..de56a06 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-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] 18+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2015-08-20 23:29 Christoph Junghans
0 siblings, 0 replies; 18+ messages in thread
From: Christoph Junghans @ 2015-08-20 23:29 UTC (permalink / raw
To: gentoo-commits
commit: 3a7ee875a11fd87e5f21cf122dbf2923d6d166de
Author: layman <layman <AT> localhost>
AuthorDate: Sun Aug 16 13:17:38 2015 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Mon Aug 17 10:01:00 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a7ee875
sci-biology/salmon: fix deps & version bump to 0.4.2
Package-Manager: portage-2.2.20-prefix
sci-biology/salmon/ChangeLog | 6 ++++++
sci-biology/salmon/salmon-0.3.2.ebuild | 4 ++++
sci-biology/salmon/{salmon-0.3.2.ebuild => salmon-0.4.2.ebuild} | 6 +++++-
sci-biology/salmon/salmon-9999.ebuild | 4 ++++
4 files changed, 19 insertions(+), 1 deletion(-)
diff --git a/sci-biology/salmon/ChangeLog b/sci-biology/salmon/ChangeLog
index 5b870c4..e398b16 100644
--- a/sci-biology/salmon/ChangeLog
+++ b/sci-biology/salmon/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*salmon-0.4.2 (16 Aug 2015)
+
+ 16 Aug 2015; Michael Schubert <mschu.dev@gmail.com> +salmon-0.4.2.ebuild,
+ salmon-0.3.2.ebuild, salmon-9999.ebuild:
+ sci-biology/salmon: fix deps & version bump to 0.4.2
+
05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
sci-biology/salmon: Add github to remote-id in metadata.xml
diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild b/sci-biology/salmon/salmon-0.3.2.ebuild
index 0a6409e..3ea1980 100644
--- a/sci-biology/salmon/salmon-0.3.2.ebuild
+++ b/sci-biology/salmon/salmon-0.3.2.ebuild
@@ -16,3 +16,7 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""
PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch )
+
+DEPEND="dev-libs/boost
+ dev-libs/jemalloc"
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild b/sci-biology/salmon/salmon-0.4.2.ebuild
similarity index 78%
copy from sci-biology/salmon/salmon-0.3.2.ebuild
copy to sci-biology/salmon/salmon-0.4.2.ebuild
index 0a6409e..c1021a6 100644
--- a/sci-biology/salmon/salmon-0.3.2.ebuild
+++ b/sci-biology/salmon/salmon-0.4.2.ebuild
@@ -15,4 +15,8 @@ SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""
-PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch )
+PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
+
+DEPEND="dev-libs/boost
+ dev-libs/jemalloc"
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index 5e80cc2..8ec7814 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -17,3 +17,7 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""
PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
+
+DEPEND="dev-libs/boost
+ dev-libs/jemalloc"
+RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2015-06-05 11:20 Justin Lecher
0 siblings, 0 replies; 18+ messages in thread
From: Justin Lecher @ 2015-06-05 11:20 UTC (permalink / raw
To: gentoo-commits
commit: 1c6458f7f5121cbc7bfa07cb004164a3ad3d3a17
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 5 11:12:24 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 5 11:12:24 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1c6458f7
sci-biology/salmon: Add github to remote-id in metadata.xml
Package-Manager: portage-2.2.20
sci-biology/salmon/ChangeLog | 3 +++
sci-biology/salmon/metadata.xml | 3 +++
2 files changed, 6 insertions(+)
diff --git a/sci-biology/salmon/ChangeLog b/sci-biology/salmon/ChangeLog
index b897449..5b870c4 100644
--- a/sci-biology/salmon/ChangeLog
+++ b/sci-biology/salmon/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
+ sci-biology/salmon: Add github to remote-id in metadata.xml
+
23 May 2015; Michael Schubert <mschu.dev@gmail.com>
files/salmon-0.3.2-no-boost-static.patch:
sci-biology/salmon: clean patch
diff --git a/sci-biology/salmon/metadata.xml b/sci-biology/salmon/metadata.xml
index b7551a6..c72510b 100644
--- a/sci-biology/salmon/metadata.xml
+++ b/sci-biology/salmon/metadata.xml
@@ -6,4 +6,7 @@
<email>mschu.dev@gmail.com</email>
<name>Michael Schubert</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">COMBINE-lab/salmon</remote-id>
+ </upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 18+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/
@ 2015-05-24 8:14 Justin Lecher
0 siblings, 0 replies; 18+ messages in thread
From: Justin Lecher @ 2015-05-24 8:14 UTC (permalink / raw
To: gentoo-commits
commit: 51078384acfa96d516c961d2b7720c5e3a6ab9b0
Author: layman <layman <AT> localhost>
AuthorDate: Thu May 21 18:42:04 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu May 21 18:42:04 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=51078384
sci-biology/salmon: streamline ebuild
Package-Manager: portage-2.2.14-prefix
sci-biology/salmon/ChangeLog | 4 ++++
sci-biology/salmon/salmon-0.3.2.ebuild | 7 +------
sci-biology/salmon/salmon-9999.ebuild | 7 +------
3 files changed, 6 insertions(+), 12 deletions(-)
diff --git a/sci-biology/salmon/ChangeLog b/sci-biology/salmon/ChangeLog
index 83c1c81..e3d76fd 100644
--- a/sci-biology/salmon/ChangeLog
+++ b/sci-biology/salmon/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 21 May 2015; Michael Schubert <mschu.dev@gmail.com> salmon-0.3.2.ebuild,
+ salmon-9999.ebuild:
+ sci-biology/salmon: streamline ebuild
+
*salmon-0.3.2 (21 May 2015)
*salmon-9999 (21 May 2015)
diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild b/sci-biology/salmon/salmon-0.3.2.ebuild
index 59ab07e..0a6409e 100644
--- a/sci-biology/salmon/salmon-0.3.2.ebuild
+++ b/sci-biology/salmon/salmon-0.3.2.ebuild
@@ -15,9 +15,4 @@ SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_prepare() {
- epatch "${FILESDIR}/${P}-no-boost-static.patch"
-}
+PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch )
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index e631316..5e80cc2 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -16,9 +16,4 @@ SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""
-DEPEND=""
-RDEPEND="${DEPEND}"
-
-src_prepare() {
- epatch "${FILESDIR}/${PN}-0.3.2-no-boost-static.patch"
-}
+PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
^ permalink raw reply related [flat|nested] 18+ messages in thread
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