summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat (limited to 'sci-biology')
-rw-r--r--sci-biology/STAR/Manifest1
-rw-r--r--sci-biology/STAR/STAR-2.5.3a.ebuild42
-rw-r--r--sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch123
3 files changed, 0 insertions, 166 deletions
diff --git a/sci-biology/STAR/Manifest b/sci-biology/STAR/Manifest
index d8457898903..d97c61cb21c 100644
--- a/sci-biology/STAR/Manifest
+++ b/sci-biology/STAR/Manifest
@@ -1,2 +1 @@
-DIST STAR-2.5.3a.tar.gz 9857460 BLAKE2B 32cc633862e6e81f5a5bdfc59986dca74e8adc4970a11a06c501065c5ad9cb37fc788f8e67ab2353292e683c8c385778cd0ffee69c0b15803796dbc445013a43 SHA512 8bd86ad384f2c0331fd701873b02641301f4205a5ff0fceeb800d425da42c53b6c61a74500d37fee7fc13a5bff10e1fb44b9142811883b8f5cd012f51f1f9fdf
DIST STAR-2.7.10a.tar.gz 12270915 BLAKE2B 51a9cf2c838cfeb313df9e5024b53cd5a89088f08ac88c8dc57a9e08cd3ba394e46ffe86a8ff3b9484b25b681ecd960098c06d879e772d21afe8cc2d0d35175d SHA512 19a5f3c25d147bcd96cf68249d275dad7fd11425031a40c97c7ae15846f55839ced897d541ed60b426a6bf089d968ac86625af774db3950dc459035ac2b659c9
diff --git a/sci-biology/STAR/STAR-2.5.3a.ebuild b/sci-biology/STAR/STAR-2.5.3a.ebuild
deleted file mode 100644
index 73743cbb4e5..00000000000
--- a/sci-biology/STAR/STAR-2.5.3a.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays"
-HOMEPAGE="https://github.com/alexdobin/STAR"
-SRC_URI="https://github.com/alexdobin/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="sci-libs/htslib:="
-DEPEND="${RDEPEND}
- virtual/pkgconfig"
-
-PATCHES=( "${FILESDIR}"/${PN}-2.5.3a-fix-build-system.patch )
-DOCS=( README.md CHANGES.md RELEASEnotes.md doc/STARmanual.pdf )
-
-pkg_pretend() {
- [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
-}
-
-pkg_setup() {
- [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
-}
-
-src_configure() {
- tc-export CC CXX PKG_CONFIG
-}
-
-src_compile() {
- emake -C source STAR
-}
-
-src_install() {
- dobin source/STAR
- einstalldocs
-}
diff --git a/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch b/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch
deleted file mode 100644
index 8e504fa429e..00000000000
--- a/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch
+++ /dev/null
@@ -1,123 +0,0 @@
-* unbundle htslib
-* honour all user flags
-* use pkg-config for linking
-
---- a/source/Makefile
-+++ b/source/Makefile
-@@ -8,24 +8,12 @@
- LDFLAGSextra ?=
- CXXFLAGSextra ?=
-
--# user may define the compiler
--CXX ?= g++
--
- # pre-defined flags
--LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz -lrt
--LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
--LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
--LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
--LDFLAGS_gdb := $(LDFLAGS_shared)
--
- COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'
-
--CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE)
--CXXFLAGS_main := -O3 $(CXXFLAGS_common)
--CXXFLAGS_gdb := -O0 -g $(CXXFLAGS_common)
--
--CFLAGS := -O3 -pipe -Wall -Wextra $(CFLAGS)
--
-+CFLAGS_common = -Wall -Wextra -pthread `$(PKG_CONFIG) --cflags htslib` `$(PKG_CONFIG) --cflags zlib`
-+CXXFLAGS_common = $(CFLAGS_common) -std=c++11 -fopenmp $(COMPTIMEPLACE)
-+LIBS_common = -pthread `$(PKG_CONFIG) --libs htslib` `$(PKG_CONFIG) --libs zlib` -lrt
-
- ##########################################################################################################
-
-@@ -54,10 +42,10 @@
-
-
- %.o : %.cpp
-- $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $<
-+ $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_common) $<
-
- %.o : %.c
-- $(CXX) -c $(CPPFLAGS) $(CFLAGS) $<
-+ $(CXX) -c $(CPPFLAGS) $(CFLAGS) $(CFLAGS_common) $<
-
- all: STAR
-
-@@ -84,7 +72,7 @@
- ifneq ($(MAKECMDGOALS),CLEAN)
- ifneq ($(MAKECMDGOALS),STARforMac)
- ifneq ($(MAKECMDGOALS),STARforMacGDB)
--Depend.list: $(SOURCES) parametersDefault.xxd htslib
-+Depend.list: $(SOURCES) parametersDefault.xxd
- echo $(SOURCES)
- /bin/rm -f ./Depend.list
- $(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
-@@ -95,57 +83,34 @@
- endif
- endif
-
--htslib : htslib/libhts.a
--
--htslib/libhts.a :
-- $(MAKE) -C htslib lib-static
--
- parametersDefault.xxd: parametersDefault
- xxd -i parametersDefault > parametersDefault.xxd
-
--STAR : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
--STAR : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
- STAR : Depend.list parametersDefault.xxd $(OBJECTS)
-- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
-
--POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS)
--POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
- POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS)
-- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
-
--STARstatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
--STARstatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
- STARstatic : Depend.list parametersDefault.xxd $(OBJECTS)
-- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
-
--STARlong : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
--STARlong : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
- STARlong : Depend.list parametersDefault.xxd $(OBJECTS)
-- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
-
--STARlongStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
--STARlongStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
- STARlongStatic : Depend.list parametersDefault.xxd $(OBJECTS)
-- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
-
--gdb : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) $(CXXFLAGS)
--gdb : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
- gdb : Depend.list parametersDefault.xxd $(OBJECTS)
-- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
-
--gdb-long : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
--gdb-long : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
- gdb-long : Depend.list parametersDefault.xxd $(OBJECTS)
-- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
-
--STARforMacStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
--STARforMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
- STARforMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
-- $(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
-
--STARlongForMacStatic : CXXFLAGS := -D'COMPILE_FOR_LONG_READS' $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
--STARlongForMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
- STARlongForMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
-- $(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
-+ $(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
-
-