gentoo resync : 25.08.2020

3 files changed, 136 insertions, 0 deletions

diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch
new file mode 100644
index 000000000000..573e88993bc9
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.29.2-buildsystem.patch
@@ -0,0 +1,82 @@
+--- a/Makefile
++++ b/Makefile
+@@ -4,44 +4,29 @@
+ # (c) 2009 Aaron Quinlan
+ # ==========================
+ 
+-SHELL := /bin/bash -e
++SHELL := bash -e
+ 
+ VERSION_FILE=./src/utils/version/version_git.h
+ RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
+ 
+ 
+ # define our object and binary directories
+-ifeq ($(VERBOSE),1)
+ CCPREFIX =
+-else
+-CCPREFIX = @
+-endif
+ 
+ OBJ_DIR	= obj
+ BIN_DIR	= bin
+ SRC_DIR	= src
+ 
+-CXX     = g++
+-
+-ifeq ($(DEBUG),1)
+-BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
+-BT_CXXFLAGS = -Wconversion -Wall -Wextra -g -O0
+-else
+ BT_CPPFLAGS = -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
+-BT_CXXFLAGS = -g -Wall -O2
+-endif
++BT_CXXFLAGS = -Wall
+ 
+ # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
+-ifeq ($(USE_RAND),1)
+-BT_CXXFLAGS += -DUSE_RAND
+-else
+ BT_CXXFLAGS += -std=c++11
+-endif
+ 
+ BT_LDFLAGS =
+ BT_LIBS    = -lz -lm -lbz2 -llzma -lpthread
+ 
+-prefix ?= /usr/local
++prefix = $(EPREFIX)/usr
+ 
+ SUBDIRS = $(SRC_DIR)/annotateBed \
+ 		  $(SRC_DIR)/bamToBed \
+@@ -204,7 +189,7 @@
+ 
+ # make the "obj/" and "bin/" directories, if they don't exist
+ $(OBJ_DIR) $(BIN_DIR):
+-	@mkdir -p $@
++	mkdir -p $@
+ 
+ 
+ # Usually HTSlib's configure script has not been used (detected via config.mk
+--- a/src/utils/htslib/Makefile
++++ b/src/utils/htslib/Makefile
+@@ -22,20 +22,13 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+ 
+-CC     = gcc
+-AR     = ar
+-RANLIB = ranlib
+-
+ # Default libraries to link if configure is not used
+ htslib_default_libs = -lz -lm -lbz2 -llzma
+ 
+-CPPFLAGS =
+ # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+ # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
+ #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
+-CFLAGS   = -g -Wall -O2
+ EXTRA_CFLAGS_PIC = -fpic
+-LDFLAGS  =
+ LIBS     = $(htslib_default_libs)
+ 
+ prefix      = /usr/local
diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-python.patch b/sci-biology/bedtools/files/bedtools-2.29.2-python.patch
new file mode 100644
index 000000000000..9576a78bd1dd
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.29.2-python.patch
@@ -0,0 +1,41 @@
+--- a/Makefile
++++ b/Makefile
+@@ -183,7 +168,7 @@
+ 
+ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
+ 	@echo "- Creating executables for old CLI."
+-	@python scripts/makeBashScripts.py
++	$(EPYTHON) scripts/makeBashScripts.py
+ 	@chmod +x bin/*
+ 	@echo "done."
+ 
+--- a/src/utils/BamTools/Makefile.frag
++++ b/src/utils/BamTools/Makefile.frag
+@@ -1,4 +1,4 @@
+ src/utils/BamTools/include/BamAlignment.mapping.hpp: src/utils/BamTools/mapping/BamAlignment.py src/utils/BamTools/mapping/BamAlignment.map
+ 
+ src/utils/BamTools/include/%.mapping.hpp: src/utils/BamTools/mapping/%.py src/utils/BamTools/mapping/%.map
+-	python $^ > $@
++	$(EPYTHON) $^ > $@
+--- a/test/bigchroms/test-bigchroms.sh
++++ b/test/bigchroms/test-bigchroms.sh
+@@ -28,7 +28,7 @@
+ rm obs
+ 
+ if [[ "$BT_NO_BIG_FILES" != "" ]]; then
+-python make-big-chrom.py
++${EPYTHON} make-big-chrom.py
+ 
+ echo -e "    bigchroms.t03...big get fasta \c"
+ $BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs
+--- a/test/fisher/cmp.sh
++++ b/test/fisher/cmp.sh
+@@ -3,7 +3,7 @@
+ echo "fisher,shuffled"
+ 
+ for i in $(seq 1000); do
+-    fisher=$(python ./sim.py | tail -1 | cut -f 2)
++    fisher=$(${EPYTHON} ./sim.py | tail -1 | cut -f 2)
+     shuffle=$(bash shuf.sh)
+     echo "$fisher,$shuffle"
+ done
diff --git a/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch b/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch
new file mode 100644
index 000000000000..7cc0e23de2d4
--- /dev/null
+++ b/sci-biology/bedtools/files/bedtools-2.29.2-samtools-1.10.patch
@@ -0,0 +1,13 @@
+--- a/test/intersect/new_test-intersect.sh
++++ b/test/intersect/new_test-intersect.sh
+@@ -975,8 +975,8 @@
+ #  Test intersect preserve the text header in bam
+ ############################################################
+ echo -e "    intersect.new.t78...\c"
+-echo -e "@HD     VN:1.5  SO:coordinate" > exp
+-echo "@HD     VN:1.5  SO:coordinate" | samtools view -b  | $BT intersect -a /dev/stdin -b b.bed | samtools view -H >obs
++echo -e "@HD	VN:1.5	SO:coordinate" > exp
++echo "@HD	VN:1.5	SO:coordinate" | samtools view --no-PG -b | $BT intersect -a /dev/stdin -b b.bed | samtools view --no-PG -H >obs
+ check exp obs
+ rm exp obs
+ [[ $FAILURES -eq 0 ]] || exit 1;