gentoo resync : 20.03.2022

3 files changed, 247 insertions, 0 deletions

diff --git a/sci-biology/STAR/Manifest b/sci-biology/STAR/Manifest
index 3fb4a0879865..8f7c05fc8c7f 100644
--- a/sci-biology/STAR/Manifest
+++ b/sci-biology/STAR/Manifest
@@ -1,4 +1,7 @@
 AUX STAR-2.5.3a-fix-build-system.patch 5318 BLAKE2B 28a839eb61a5b1adef804249328c7917dca2ec765f00a48b90aa42d7da3ca393f7726b7aafdb6d0429a55fe696bd51b0e06d85ef6e50a3a4f5874c731b194f1e SHA512 412bdf74c50869f470f3d7452d3799e92a45da198e50ecad63688e4c24444a25f044d464e462e19ba41c5abf590865e43542cd1b60a1f3948bf357be468e8441
+AUX STAR-2.7.10a-fix-build-system.patch 7176 BLAKE2B 24a14d2d8af26565a3a7f754e9633c54c2cdaf72bf4e3b4fe3390a3790be16620117f576abf82d91e8816478fc1a012e7424ab6d93bb6161b975acd08627d3f0 SHA512 4d854336b2e0c61ca1ac604cded7f08e484974e1ec6d78928e5eb21eb7adb0ae3f6ec9deb3dc050dcffe1732f9076f2b4cddad7aa18ccad20f9232c9e11d1856
 DIST STAR-2.5.3a.tar.gz 9857460 BLAKE2B 32cc633862e6e81f5a5bdfc59986dca74e8adc4970a11a06c501065c5ad9cb37fc788f8e67ab2353292e683c8c385778cd0ffee69c0b15803796dbc445013a43 SHA512 8bd86ad384f2c0331fd701873b02641301f4205a5ff0fceeb800d425da42c53b6c61a74500d37fee7fc13a5bff10e1fb44b9142811883b8f5cd012f51f1f9fdf
+DIST STAR-2.7.10a.tar.gz 12270915 BLAKE2B 51a9cf2c838cfeb313df9e5024b53cd5a89088f08ac88c8dc57a9e08cd3ba394e46ffe86a8ff3b9484b25b681ecd960098c06d879e772d21afe8cc2d0d35175d SHA512 19a5f3c25d147bcd96cf68249d275dad7fd11425031a40c97c7ae15846f55839ced897d541ed60b426a6bf089d968ac86625af774db3950dc459035ac2b659c9
 EBUILD STAR-2.5.3a.ebuild 881 BLAKE2B 692466b512aaa3da2e2323f90576d47c2f5e694a4ac8ee8ce2d887435a1ef964dcab9adbdb3c3f88b43cc5463b258635be0f2b542485ee16bc9ec32b655fcf65 SHA512 9b8a80c19b0da8e697c913a8401c08a71a07511477c71b1dd20748e5487e8bb5ab870c37058d49abc27a5ac56722e98b2d784431c19f7173275b82f41f9a2663
+EBUILD STAR-2.7.10a.ebuild 970 BLAKE2B 63bc2b4656d4e672faf819f83bd2a930851e0b5c2d1ff422c5a72b655d5c68515a317675c59df2ff9256e4653351f1f180d9c94dbd256c89810d31ca3940b9ad SHA512 76841ebb6bb3a7c15da15c2124287959938beeb1c6e1a5fa362c476283b51dca49bcca83be9e10d5f39702f23b01ee131f8ab2f568b986e529fc006e65a25ffb
 MISC metadata.xml 341 BLAKE2B 5cf54dcbc5013bbebd80edd8d03456553ec6f7f52527d076f921916ebe9b862c97aae6f641741b81ac44cfc84356ca13e19dd3be2b63c075923a701c22e695c1 SHA512 888d00d5873390206f21aa9daaf78fc8c3f9b88e528c38ca7696779b221fd21acc6beadf543c14e16f74cb600cab479bc3f9bba8625214480583f369e6ea67a8
diff --git a/sci-biology/STAR/STAR-2.7.10a.ebuild b/sci-biology/STAR/STAR-2.7.10a.ebuild
new file mode 100644
index 000000000000..7239efcfe45c
--- /dev/null
+++ b/sci-biology/STAR/STAR-2.7.10a.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+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}"
+BDEPEND="virtual/pkgconfig"
+
+PATCHES=( "${FILESDIR}"/${PN}-2.7.10a-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_prepare() {
+	default
+
+	# remove bundled htslib
+	rm -r source/htslib || die
+}
+
+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-2.7.10a-fix-build-system.patch b/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch
new file mode 100644
index 000000000000..0f06c94fb109
--- /dev/null
+++ b/sci-biology/STAR/files/STAR-2.7.10a-fix-build-system.patch
@@ -0,0 +1,195 @@
+--- a/source/bam_cat.c
++++ b/source/bam_cat.c
+@@ -52,8 +52,8 @@
+ #include <stdlib.h>
+ #include <unistd.h>
+ 
+-#include "htslib/htslib/bgzf.h"
+-#include "htslib/htslib/sam.h"
++#include <htslib/bgzf.h>
++#include <htslib/sam.h>
+ #include <cstring>
+ 
+ #define BUF_SIZE 0x10000
+--- a/source/bam_cat.h
++++ b/source/bam_cat.h
+@@ -1,7 +1,7 @@
+ #ifndef CODE_bam_cat
+ #define CODE_bam_cat
+ 
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+ 
+ int bam_cat(int nfn, char * const *fn, const bam_hdr_t *h, const char* outbam);
+ 
+--- a/source/BAMfunctions.cpp
++++ b/source/BAMfunctions.cpp
+@@ -1,5 +1,5 @@
+ #include "BAMfunctions.h"
+-#include "htslib/htslib/kstring.h"
++#include <htslib/kstring.h>
+ 
+ 
+ string bam_cigarString (bam1_t *b) {//output CIGAR string
+--- a/source/bamRemoveDuplicates.cpp
++++ b/source/bamRemoveDuplicates.cpp
+@@ -1,7 +1,7 @@
+ #include <unordered_map>
+ #include "bamRemoveDuplicates.h"
+ #include <iostream>
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+ #include "IncludeDefine.h"
+ #include SAMTOOLS_BGZF_H
+ #include "ErrorWarning.h"
+--- a/source/IncludeDefine.h
++++ b/source/IncludeDefine.h
+@@ -30,8 +30,8 @@
+ #define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ )
+ 
+ //external libs
+-#define SAMTOOLS_BGZF_H "htslib/htslib/bgzf.h"
+-#define SAMTOOLS_SAM_H  "htslib/htslib/sam.h"
++#define SAMTOOLS_BGZF_H <htslib/bgzf.h>
++#define SAMTOOLS_SAM_H  <htslib/sam.h>
+ 
+ using namespace std;
+ 
+--- a/source/Makefile
++++ b/source/Makefile
+@@ -12,11 +12,7 @@
+ CXX ?= g++
+ 
+ # pre-defined flags
+-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
+-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)
++LIBS := -pthread -lhts -lz
+ 
+ DATE_FMT = --iso-8601=seconds
+ ifdef SOURCE_DATE_EPOCH
+@@ -27,7 +23,7 @@
+ 
+ BUILD_PLACE ?= $(HOSTNAME):$(shell pwd)
+ 
+-COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(BUILD_DATE) $(BUILD_PLACE)"'
++COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE=""'
+ 
+ 
+ GIT_CHECK := $(shell git status 1> /dev/null 2> /dev/null && echo 0)
+@@ -41,13 +37,13 @@
+ 
+ # Defaults, can be overridden by make arguments or environment
+ CXXFLAGS ?= -pipe -Wall -Wextra
+-CFLAGS ?= -pipe -Wall -Wextra -O3
++CFLAGS ?= -pipe -Wall -Wextra
+ CXXFLAGS_SIMD ?= -mavx2
+ 
+ # Unconditionally set essential flags and optimization options
+ CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE) $(GIT_BRANCH_COMMIT_DIFF)
+-CXXFLAGS_main := -O3 $(CXXFLAGS_common)
+-CXXFLAGS_gdb := -O0 -g3 $(CXXFLAGS_common)
++CXXFLAGS_main := $(CXXFLAGS_common)
++CXXFLAGS_gdb := $(CXXFLAGS_common)
+ 
+ ##########################################################################################################
+ OBJECTS = SoloFeature_collapseUMI_Graph.o SoloFeature_collapseUMIall_multiMappers.o ParametersClip_initialize.o ClipMate_clip.o ClipCR4.o opal/opal.o ClipMate_clipChunk.o ClipMate_initialize.o \
+@@ -130,7 +126,7 @@
+ ifneq ($(MAKECMDGOALS),clean_solo)
+ ifneq ($(MAKECMDGOALS),STARforMac)
+ ifneq ($(MAKECMDGOALS),STARforMacGDB)
+-Depend.list: $(SOURCES) parametersDefault.xxd htslib
++Depend.list: $(SOURCES) parametersDefault.xxd
+ 	echo $(SOURCES)
+ 	'rm' -f ./Depend.list
+ 	$(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
+@@ -142,57 +138,43 @@
+ endif
+ endif
+ 
+-htslib : htslib/libhts.a
+-
+-htslib/libhts.a :
+-	$(MAKE) -C htslib lib-static
+-
+ parametersDefault.xxd: parametersDefault
+ 	xxd -i parametersDefault > parametersDefault.xxd
+ 
+ STAR$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
+-STAR$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
+ STAR$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ STARstatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
+-STARstatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
+ STARstatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ STARlong$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
+-STARlong$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
+ STARlong$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ STARlongStatic$(SFX) : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
+-STARlongStatic$(SFX) : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
+ STARlongStatic$(SFX) : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(LDFLAGS) -o STARlong$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ 
+ 
+ POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS)
+-POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
+ POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(LDFLAGS) -o STAR$(SFX) $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ 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) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ 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) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ 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) $(LDFLAGS) -o STAR $(CXXFLAGS) $(OBJECTS) $(LIBS)
+ 
+ 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) $(LDFLAGS) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LIBS)
+--- a/source/signalFromBAM.h
++++ b/source/signalFromBAM.h
+@@ -1,6 +1,6 @@
+ #ifndef CODE_signalFromBAM
+ #define CODE_signalFromBAM
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+ #include  <fstream>
+ #include <string>
+ #include "Stats.h"
+--- a/source/STAR.cpp
++++ b/source/STAR.cpp
+@@ -29,7 +29,7 @@
+ 
+ #include "twoPassRunPass1.h"
+ 
+-#include "htslib/htslib/sam.h"
++#include <htslib/sam.h>
+ #include "parametersDefault.xxd"
+ 
+ void usage(int usageType) {