diff options
Diffstat (limited to 'sci-biology/samtools/files/samtools-1.3.1-buildsystem.patch')
| -rw-r--r-- | sci-biology/samtools/files/samtools-1.3.1-buildsystem.patch | 75 |
1 files changed, 75 insertions, 0 deletions
diff --git a/sci-biology/samtools/files/samtools-1.3.1-buildsystem.patch b/sci-biology/samtools/files/samtools-1.3.1-buildsystem.patch new file mode 100644 index 000000000..bd0f20c7c --- /dev/null +++ b/sci-biology/samtools/files/samtools-1.3.1-buildsystem.patch @@ -0,0 +1,75 @@ +--- samtools-1.3.1/Makefile.ori 2016-04-22 11:51:16.000000000 +0200 ++++ samtools-1.3.1/Makefile 2017-02-16 23:41:19.819951687 +0100 +@@ -21,9 +21,9 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc ++CC ?= gcc + CPPFLAGS = +-CFLAGS = -g -Wall -O2 ++CFLAGS ?= -g -Wall -O2 + LDFLAGS = + LIBS = + +@@ -197,8 +203,8 @@ + # For tests that might use it, set $REF_PATH explicitly to use only reference + # areas within the test suite (or set it to ':' to use no reference areas). + # (regression.sh sets $REF_PATH to a subdirectory itself.) +-check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) +- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) ++check test: samtools $(BUILT_TEST_PROGRAMS) ++ REF_PATH=: test/test.pl --exec bgzip=bgzip + test/merge/test_bam_translate test/merge/test_bam_translate.tmp + test/merge/test_rtrans_build + test/merge/test_trans_tbl_init +@@ -210,28 +216,28 @@ + test/split/test_parse_args + + +-test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB) ++test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o sam_opts.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB) ++test/merge/test_rtrans_build: test/merge/test_rtrans_build.o sam_opts.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB) ++test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o sam_opts.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB) ++test/split/test_count_rg: test/split/test_count_rg.o test/test.o sam_opts.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB) ++test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o sam_opts.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB) ++test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o sam_opts.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB) ++test/split/test_parse_args: test/split/test_parse_args.o test/test.o sam_opts.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o sam_opts.o $(HTSLIB_LIB) $(ALL_LIBS) + +-test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) ++test/vcf-miniview: test/vcf-miniview.o + $(CC) -pthread $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) + + test_test_h = test/test.h $(htslib_sam_h) +@@ -258,10 +264,10 @@ + misc/maq2sam-long: misc/maq2sam-long.o + $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS) + +-misc/md5fa: misc/md5fa.o $(HTSLIB) ++misc/md5fa: misc/md5fa.o + $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS) + +-misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB) ++misc/md5sum-lite: misc/md5sum-lite.o + $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS) + + misc/wgsim: misc/wgsim.o |