b0a76db7a108bdaa7d25442f6a20dcfdf2c67839 braney Mon Dec 7 13:45:51 2015 -0800 start using htslib for BAM, CRAM, and vcf/tabix support #14717 diff --git src/inc/common.mk src/inc/common.mk index 561b53b..c2aca37 100644 --- src/inc/common.mk +++ src/inc/common.mk @@ -206,31 +206,31 @@ # MySQL version 5.6 libraries, but no 'librt' on Mac OSX ifeq (${FULLWARN},hgwdev) MYSQLLIBS += /usr/lib/gcc/x86_64-redhat-linux/4.4.4/libstdc++.a /usr/lib/debug/usr/lib64/librt.a else ifeq ($(UNAME_S),Darwin) MYSQLLIBS += -lstdc++ else MYSQLLIBS += -lstdc++ -lrt endif endif L+=${PNGLIB} HG_INC+=${PNGINCL} # autodetect UCSC installation of htslib: -ifeq (${HTSDIR},"NOTNOW") +ifeq (${HTSDIR},) HTSDIR = /hive/groups/browser/htslib ifneq ($(wildcard ${HTSDIR}),) ifeq (${USE_HTS},) USE_HTS=1 USE_TABIX=1 USE_SAMTABIX=1 SAMTABIXDIR = /hive/groups/browser/htslib SAMTABIXLIB=/hive/groups/browser/htslib/libhts.a HG_DEFS+=-DUSE_HTS endif endif endif # autodetect UCSC installation of samtabix: