diff options
Diffstat (limited to 'sci-biology/bedtools/files/bedtools-2.29.2-python.patch')
| -rw-r--r-- | sci-biology/bedtools/files/bedtools-2.29.2-python.patch | 41 |
1 files changed, 41 insertions, 0 deletions
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 |