* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/, sci-biology/salmon/files/
@ 2018-06-26 8:51 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2018-06-26 8:51 UTC (permalink / raw
To: gentoo-commits
commit: bf40c74c098f14730b400d26d37b2fc2c9c13589
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jun 26 08:39:13 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jun 26 08:39:13 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bf40c74c
sci-biology/salmon: fix tests
Thanks to @kiwifb
https://github.com/gentoo/sci/commit/a1d0487c37ba900c1f239f5d73f7d429f018359d#commitcomment-29493393
Package-Manager: Portage-2.3.40, Repoman-2.3.9
sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch | 10 ++++++++++
sci-biology/salmon/salmon-0.10.2.ebuild | 3 ++-
sci-biology/salmon/salmon-9999.ebuild | 3 ++-
3 files changed, 14 insertions(+), 2 deletions(-)
diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch
new file mode 100644
index 000000000..0a95757a8
--- /dev/null
+++ b/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch
@@ -0,0 +1,10 @@
+--- salmon-0.10.2/src/CMakeLists.txt.ori 2018-06-26 10:34:29.293225671 +0200
++++ salmon-0.10.2/src/CMakeLists.txt 2018-06-26 10:35:24.674730920 +0200
+@@ -335,6 +335,6 @@
+ )
+
+ include(InstallRequiredSystemLibraries)
+-add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${CMAKE_INSTALL_PREFIX} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake )
++add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake )
+ add_test( NAME salmon_read_test_fmd COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonFMD.cmake )
+ add_test( NAME salmon_read_test_quasi COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonQuasi.cmake )
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
index 90db2e1fe..84d73ea9e 100644
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -23,7 +23,8 @@ IUSE=""
PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch
"${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 )
+ "${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch
+ "${FILESDIR}"/salmon-0.10.2_fix_tests.patch )
RDEPEND="${DEPEND}"
# budled copies of:
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index 904c37654..0b19da725 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -22,7 +22,8 @@ IUSE=""
PATCHES=( "${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_lib_dir.patch
+ "${FILESDIR}"/salmon-0.10.2_fix_tests.patch )
# budled copies of:
# sci-biology/bwa-0.7.12.5
^ permalink raw reply related [flat|nested] 4+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/, sci-biology/salmon/files/
@ 2018-06-25 12:21 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2018-06-25 12:21 UTC (permalink / raw
To: gentoo-commits
commit: 44863d23a814e72b31f589ad412f35a024282766
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jun 25 12:21:16 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jun 25 12:21:16 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=44863d23
sci-biology/salmon: bring -9999 in sync with 0.10.2.ebuild
The -9999 won't work as the SRC_URI section is not respected,
hence is commented out.
Package-Manager: Portage-2.3.40, Repoman-2.3.9
.../salmon/files/salmon-9999-no-boost-static.patch | 18 -------------
sci-biology/salmon/salmon-9999.ebuild | 30 ++++++++--------------
2 files changed, 10 insertions(+), 38 deletions(-)
diff --git a/sci-biology/salmon/files/salmon-9999-no-boost-static.patch b/sci-biology/salmon/files/salmon-9999-no-boost-static.patch
deleted file mode 100644
index 1a9665251..000000000
--- a/sci-biology/salmon/files/salmon-9999-no-boost-static.patch
+++ /dev/null
@@ -1,18 +0,0 @@
---- salmon-9999/CMakeLists.txt 2018-06-25 10:51:47.179712781 +0200
-+++ salmon-9999/CMakeLists.txt 2018-06-25 10:52:47.951289159 +0200
-@@ -213,15 +213,6 @@
- set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
- endif ( DEFINED CUSTOM_BOOST_PATH )
-
--##
--# We want static, multithreaded boost libraries
--##
--if(CONDA_BUILD)
-- set (Boost_USE_STATIC_LIBS OFF)
--else ()
-- set (Boost_USE_STATIC_LIBS ON)
--endif(CONDA_BUILD)
--
- set (Boost_USE_MULTITHREADED ON)
- #set (Boost_USE_STATIC_RUNTIME OFF)
-
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index b5e748fd2..221418960 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -8,14 +8,21 @@ inherit multilib cmake-utils 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 -> ${PN}-0.10.2_RapMap.zip"
+#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}"/${P}-no-boost-static.patch
- "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch )
+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 )
# budled copies of:
# sci-biology/bwa-0.7.12.5
@@ -57,20 +64,3 @@ RDEPEND="${DEPEND}"
# see the many curl executions:
# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null
-#
-src_configure(){
- local mycmakeargs=(
- "-DBOOST_INCLUDEDIR=${EPREFIX}/usr/include/boost/"
- "-DBOOST_LIBRARYDIR=${EPREFIX}/usr/$(get_libdir)/"
- "-DTBB_INSTALL_DIR=${EPREFIX}/usr"
- "-DCMAKE_INSTALL_PREFIX=${EPREFIX}/usr"
- )
- # BUG: the configure step runs automatically curl download of 3rd-party stuff
- # https://github.com/COMBINE-lab/salmon/issues/19
- cmake-utils_src_configure
-}
-
-src_install() {
- cmake-utils_src_install
- rm -rf "${ED}"/usr/tests || die
-}
^ permalink raw reply related [flat|nested] 4+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/, sci-biology/salmon/files/
@ 2018-06-25 10:02 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2018-06-25 10:02 UTC (permalink / raw
To: gentoo-commits
commit: ed55a4e91d91312772ee71645ae280fba57ce4dc
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jun 25 10:01:47 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jun 25 10:01:47 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ed55a4e9
sci-biology/salmon: drop deps on static boost, some ebuild cleanup
Document zillions of cryptic dependencies of a lousy package
https://github.com/Kingsford-Group/libgff/issues/1
https://github.com/COMBINE-lab/salmon/issues/236
https://github.com/COMBINE-lab/salmon/issues/19
Incomplete install docs are deemed to be at:
http://salmon.readthedocs.io/en/latest/building.html#requirements-for-building-from-source
Try the command below to see yourself:
salmon-0.10.2 $ find . -type f | xargs grep curl 2>/dev/null
Thanks to @kiwifb for comments at
https://github.com/gentoo/sci/commit/a1d0487c37ba900c1f239f5d73f7d429f018359d
Package-Manager: Portage-2.3.40, Repoman-2.3.9
.../files/salmon-0.10.2-no-boost-static.patch | 18 +++++++++++++++
.../files/salmon-0.10.2_remove_curl_call.patch | 12 ++++++++++
.../files/salmon-0.3.2-no-boost-static.patch | 20 ----------------
.../salmon/files/salmon-9999-no-boost-static.patch | 18 +++++++++++++++
sci-biology/salmon/salmon-0.10.2.ebuild | 26 ++++++++++++++++++---
sci-biology/salmon/salmon-0.3.2.ebuild | 27 ----------------------
sci-biology/salmon/salmon-0.4.2.ebuild | 27 ----------------------
sci-biology/salmon/salmon-0.5.0.ebuild | 27 ----------------------
sci-biology/salmon/salmon-0.9.1.ebuild | 25 --------------------
sci-biology/salmon/salmon-9999.ebuild | 24 +++++++++++++++++--
10 files changed, 93 insertions(+), 131 deletions(-)
diff --git a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch
new file mode 100644
index 000000000..ac561d793
--- /dev/null
+++ b/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch
@@ -0,0 +1,18 @@
+--- salmon-0.10.2/CMakeLists.txt 2018-06-25 10:51:47.179712781 +0200
++++ salmon-0.10.2/CMakeLists.txt 2018-06-25 10:52:47.951289159 +0200
+@@ -213,15 +213,6 @@
+ set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
+ endif ( DEFINED CUSTOM_BOOST_PATH )
+
+-##
+-# We want static, multithreaded boost libraries
+-##
+-if(CONDA_BUILD)
+- set (Boost_USE_STATIC_LIBS OFF)
+-else ()
+- set (Boost_USE_STATIC_LIBS ON)
+-endif(CONDA_BUILD)
+-
+ set (Boost_USE_MULTITHREADED ON)
+ #set (Boost_USE_STATIC_RUNTIME OFF)
+
diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch
new file mode 100644
index 000000000..8eddc6e3a
--- /dev/null
+++ b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch
@@ -0,0 +1,12 @@
+--- salmon-9999/scripts/fetchRapMap.sh 2018-06-25 11:11:07.019798309 +0200
++++ salmon-9999/scripts/fetchRapMap.sh 2018-06-25 11:12:25.131824486 +0200
+@@ -29,7 +29,8 @@
+ EXPECTED_SHA256=c4ca27de299bee395b404d117d9d98ad9f0d6ee256ea1deb2890ea402893e688
+
+ mkdir -p ${EXTERNAL_DIR}
+-curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip
++# curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip
++cp ../../distdir/salmon-0.10.2_RapMap.zip ${EXTERNAL_DIR}/rapmap.zip
+
+ hashcheck=""
+ if exists sha256sum; then
diff --git a/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch
deleted file mode 100644
index 7ac3d0882..000000000
--- a/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-Do not force static and multithreaded boost libs, use what is available
-
-Patch by Michael Schubert
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -162,13 +162,6 @@ if ( DEFINED CUSTOM_BOOST_PATH )
- set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
- endif ( DEFINED CUSTOM_BOOST_PATH )
-
--##
--# We want static, multithreaded boost libraries
--##
--set (Boost_USE_STATIC_LIBS ON)
--set (Boost_USE_MULTITHREADED ON)
--#set (Boost_USE_STATIC_RUNTIME OFF)
--
- find_package (ZLIB)
- if (NOT ZLIB_FOUND)
- message (FATAL_ERROR "zlib must be installed before configuration & building can proceed")
diff --git a/sci-biology/salmon/files/salmon-9999-no-boost-static.patch b/sci-biology/salmon/files/salmon-9999-no-boost-static.patch
new file mode 100644
index 000000000..1a9665251
--- /dev/null
+++ b/sci-biology/salmon/files/salmon-9999-no-boost-static.patch
@@ -0,0 +1,18 @@
+--- salmon-9999/CMakeLists.txt 2018-06-25 10:51:47.179712781 +0200
++++ salmon-9999/CMakeLists.txt 2018-06-25 10:52:47.951289159 +0200
+@@ -213,15 +213,6 @@
+ set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
+ endif ( DEFINED CUSTOM_BOOST_PATH )
+
+-##
+-# We want static, multithreaded boost libraries
+-##
+-if(CONDA_BUILD)
+- set (Boost_USE_STATIC_LIBS OFF)
+-else ()
+- set (Boost_USE_STATIC_LIBS ON)
+-endif(CONDA_BUILD)
+-
+ set (Boost_USE_MULTITHREADED ON)
+ #set (Boost_USE_STATIC_RUNTIME OFF)
+
diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild
index f97a32f18..540225019 100644
--- a/sci-biology/salmon/salmon-0.10.2.ebuild
+++ b/sci-biology/salmon/salmon-0.10.2.ebuild
@@ -7,15 +7,35 @@ inherit cmake-utils
DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
+ https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
IUSE=""
-DEPEND="dev-libs/boost:0
- dev-libs/jemalloc
+PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch
+ "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch )
+
+RDEPEND="${DEPEND}"
+# budled copies of:
+# sci-biology/bwa-0.7.12.5
+# sci-biology/jellyfish
+# sci-biology/staden-1.14.8.1
+# sci-biology/gfftools
+#
+# libgff-1.1 from https://github.com/Kingsford-Group/libgff
+# actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz
+# https://github.com/Kingsford-Group/libgff/issues/1
+#
+# dev-libs/spdlog-0.16.1
+# cereal-1.2.2
+DEPEND="sys-libs/zlib
+ app-arch/bzip2
+ app-arch/xz-utils
+ dev-libs/boost:0[threads]
+ >=dev-libs/jemalloc-5.0.1
>=dev-cpp/tbb-2018.20180312"
RDEPEND="${DEPEND}"
diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild b/sci-biology/salmon/salmon-0.3.2.ebuild
deleted file mode 100644
index b9a50ebd1..000000000
--- a/sci-biology/salmon/salmon-0.3.2.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-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 -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch )
-
-DEPEND="dev-libs/boost:0
- dev-libs/jemalloc
- dev-cpp/tbb"
-RDEPEND="${DEPEND}"
-
-src_install() {
- cmake-utils_src_install
- rm -r "${ED}"/usr/tests || die
-}
diff --git a/sci-biology/salmon/salmon-0.4.2.ebuild b/sci-biology/salmon/salmon-0.4.2.ebuild
deleted file mode 100644
index 42ccf1e6c..000000000
--- a/sci-biology/salmon/salmon-0.4.2.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
-
-DEPEND="dev-libs/boost:0
- dev-libs/jemalloc
- dev-cpp/tbb"
-RDEPEND="${DEPEND}"
-
-src_install() {
- cmake-utils_src_install
- rm -r "${ED}"/usr/tests || die
-}
diff --git a/sci-biology/salmon/salmon-0.5.0.ebuild b/sci-biology/salmon/salmon-0.5.0.ebuild
deleted file mode 100644
index 42ccf1e6c..000000000
--- a/sci-biology/salmon/salmon-0.5.0.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
-
-DEPEND="dev-libs/boost:0
- dev-libs/jemalloc
- dev-cpp/tbb"
-RDEPEND="${DEPEND}"
-
-src_install() {
- cmake-utils_src_install
- rm -r "${ED}"/usr/tests || die
-}
diff --git a/sci-biology/salmon/salmon-0.9.1.ebuild b/sci-biology/salmon/salmon-0.9.1.ebuild
deleted file mode 100644
index 34a425403..000000000
--- a/sci-biology/salmon/salmon-0.9.1.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils
-
-DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
-HOMEPAGE="https://github.com/COMBINE-lab/salmon"
-SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="dev-libs/boost:0
- dev-libs/jemalloc
- dev-cpp/tbb"
-RDEPEND="${DEPEND}"
-
-src_install() {
- cmake-utils_src_install
- rm -r "${ED}"/usr/tests || die
-}
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index ab0f9c368..0083648fb 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -8,15 +8,35 @@ inherit multilib cmake-utils 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 -> ${PN}-0.10.2_RapMap.zip"
LICENSE="GPL-3"
SLOT="0"
IUSE=""
-DEPEND="dev-libs/boost:0
- dev-libs/jemalloc
+PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch
+ "${FILESDIR}"/salmon-0.10.2_remove_curl_call.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="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
^ permalink raw reply related [flat|nested] 4+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/, sci-biology/salmon/files/
@ 2016-02-28 10:43 Justin Lecher
0 siblings, 0 replies; 4+ messages in thread
From: Justin Lecher @ 2016-02-28 10:43 UTC (permalink / raw
To: gentoo-commits
commit: 1e1e01623ad2b04d0500d229995c50c3223dadcd
Author: mschubert <mschu.dev <AT> gmail <DOT> com>
AuthorDate: Sat Jan 23 21:38:55 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=1e1e0162
sci-biology/salmon: version bump 0.5/0.6, cleanup
Package-Manager: portage-2.2.20-prefix
.../salmon/files/salmon-0.3.2-no-boost-static.patch | 4 ++--
sci-biology/salmon/metadata.xml | 8 ++++----
sci-biology/salmon/salmon-0.3.2.ebuild | 12 +++++++++---
sci-biology/salmon/salmon-0.4.2.ebuild | 12 +++++++++---
.../salmon/{salmon-0.4.2.ebuild => salmon-0.5.0.ebuild} | 12 +++++++++---
.../salmon/{salmon-0.4.2.ebuild => salmon-0.6.0.ebuild} | 12 +++++++++---
sci-biology/salmon/salmon-9999.ebuild | 15 ++++++++++-----
7 files changed, 52 insertions(+), 23 deletions(-)
diff --git a/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch
index edc09e7..7ac3d08 100644
--- a/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch
+++ b/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch
@@ -2,8 +2,8 @@ Do not force static and multithreaded boost libs, use what is available
Patch by Michael Schubert
---- CMakeLists.txt
-+++ CMakeLists.txt
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
@@ -162,13 +162,6 @@ if ( DEFINED CUSTOM_BOOST_PATH )
set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH})
endif ( DEFINED CUSTOM_BOOST_PATH )
diff --git a/sci-biology/salmon/metadata.xml b/sci-biology/salmon/metadata.xml
index 1d04676..cb020ec 100644
--- a/sci-biology/salmon/metadata.xml
+++ b/sci-biology/salmon/metadata.xml
@@ -1,14 +1,14 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="person">
- <email>mschu.dev@gmail.com</email>
- <name>Michael Schubert</name>
- </maintainer>
<maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <maintainer type="person">
+ <email>mschu.dev@gmail.com</email>
+ <name>Michael Schubert</name>
+ </maintainer>
<upstream>
<remote-id type="github">COMBINE-lab/salmon</remote-id>
</upstream>
diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild b/sci-biology/salmon/salmon-0.3.2.ebuild
index 049344b..e64b220 100644
--- a/sci-biology/salmon/salmon-0.3.2.ebuild
+++ b/sci-biology/salmon/salmon-0.3.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -17,6 +17,12 @@ IUSE=""
PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch )
-DEPEND="dev-libs/boost
- dev-libs/jemalloc"
+DEPEND="dev-libs/boost:0
+ dev-libs/jemalloc
+ dev-cpp/tbb"
RDEPEND="${DEPEND}"
+
+src_install() {
+ cmake-utils_src_install
+ rm -r "${ED}"/usr/tests || die
+}
diff --git a/sci-biology/salmon/salmon-0.4.2.ebuild b/sci-biology/salmon/salmon-0.4.2.ebuild
index dffe77e..032fd4d 100644
--- a/sci-biology/salmon/salmon-0.4.2.ebuild
+++ b/sci-biology/salmon/salmon-0.4.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -17,6 +17,12 @@ IUSE=""
PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
-DEPEND="dev-libs/boost
- dev-libs/jemalloc"
+DEPEND="dev-libs/boost:0
+ dev-libs/jemalloc
+ dev-cpp/tbb"
RDEPEND="${DEPEND}"
+
+src_install() {
+ cmake-utils_src_install
+ rm -r "${ED}"/usr/tests || die
+}
diff --git a/sci-biology/salmon/salmon-0.4.2.ebuild b/sci-biology/salmon/salmon-0.5.0.ebuild
similarity index 73%
copy from sci-biology/salmon/salmon-0.4.2.ebuild
copy to sci-biology/salmon/salmon-0.5.0.ebuild
index dffe77e..032fd4d 100644
--- a/sci-biology/salmon/salmon-0.4.2.ebuild
+++ b/sci-biology/salmon/salmon-0.5.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -17,6 +17,12 @@ IUSE=""
PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
-DEPEND="dev-libs/boost
- dev-libs/jemalloc"
+DEPEND="dev-libs/boost:0
+ dev-libs/jemalloc
+ dev-cpp/tbb"
RDEPEND="${DEPEND}"
+
+src_install() {
+ cmake-utils_src_install
+ rm -r "${ED}"/usr/tests || die
+}
diff --git a/sci-biology/salmon/salmon-0.4.2.ebuild b/sci-biology/salmon/salmon-0.6.0.ebuild
similarity index 73%
copy from sci-biology/salmon/salmon-0.4.2.ebuild
copy to sci-biology/salmon/salmon-0.6.0.ebuild
index dffe77e..032fd4d 100644
--- a/sci-biology/salmon/salmon-0.4.2.ebuild
+++ b/sci-biology/salmon/salmon-0.6.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -17,6 +17,12 @@ IUSE=""
PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch )
-DEPEND="dev-libs/boost
- dev-libs/jemalloc"
+DEPEND="dev-libs/boost:0
+ dev-libs/jemalloc
+ dev-cpp/tbb"
RDEPEND="${DEPEND}"
+
+src_install() {
+ cmake-utils_src_install
+ rm -r "${ED}"/usr/tests || die
+}
diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild
index ab171cb..139e2ee 100644
--- a/sci-biology/salmon/salmon-9999.ebuild
+++ b/sci-biology/salmon/salmon-9999.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=5
-inherit git-r3 cmake-utils
+inherit cmake-utils git-r3
DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments"
HOMEPAGE="https://github.com/COMBINE-lab/salmon"
@@ -13,11 +13,16 @@ EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git"
LICENSE="GPL-3"
SLOT="0"
-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"
+DEPEND="dev-libs/boost:0
+ dev-libs/jemalloc
+ dev-cpp/tbb"
RDEPEND="${DEPEND}"
+
+src_install() {
+ cmake-utils_src_install
+ rm -r "${ED}"/usr/tests || die
+}
^ permalink raw reply related [flat|nested] 4+ messages in thread
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