diff options
Diffstat (limited to 'biology/bamutil')
| -rw-r--r-- | biology/bamutil/Makefile | 29 | ||||
| -rw-r--r-- | biology/bamutil/distinfo | 5 | ||||
| -rw-r--r-- | biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.lib | 17 | ||||
| -rw-r--r-- | biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.toolchain | 13 | ||||
| -rw-r--r-- | biology/bamutil/files/patch-libStatGen_vcf_VcfRecordGenotype.cpp | 11 | ||||
| -rw-r--r-- | biology/bamutil/pkg-descr | 4 |
6 files changed, 79 insertions, 0 deletions
diff --git a/biology/bamutil/Makefile b/biology/bamutil/Makefile new file mode 100644 index 000000000000..485df533807e --- /dev/null +++ b/biology/bamutil/Makefile @@ -0,0 +1,29 @@ +PORTNAME= bamutil +DISTVERSIONPREFIX= v +DISTVERSION= 1.0.15 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Utilities for working with SAM/BAM files +WWW= https://github.com/statgen/bamUtil + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/copyrights/COPYING + +USES= gmake +USE_GITHUB= yes + +GH_ACCOUNT= statgen +GH_PROJECT= bamUtil + +# Build needs access to libStatGen Makefiles, so can't install separately +GH_TUPLE= statgen:libStatGen:v${DISTVERSION}:statgen/libStatGen + +MAKE_ENV= LIB_PATH_GENERAL=${WRKSRC}/libStatGen +MAKE_ENV+= INSTALLDIR=${STAGEDIR}${PREFIX}/bin + +CONFLICTS_INSTALL= bam + +PLIST_FILES= bin/bam + +.include <bsd.port.mk> diff --git a/biology/bamutil/distinfo b/biology/bamutil/distinfo new file mode 100644 index 000000000000..919bfb6a8cd4 --- /dev/null +++ b/biology/bamutil/distinfo @@ -0,0 +1,5 @@ +TIMESTAMP = 1634754069 +SHA256 (statgen-bamUtil-v1.0.15_GH0.tar.gz) = 24ac4bdb81eded6e33f60dba85ec3d32ebdb06d42f75df775c2632bbfbd8cce9 +SIZE (statgen-bamUtil-v1.0.15_GH0.tar.gz) = 1929150 +SHA256 (statgen-libStatGen-v1.0.15_GH0.tar.gz) = 075dcd891409c48d76c0c66186c0cc479bc3cd50bba093e7f318e1d1d19961ff +SIZE (statgen-libStatGen-v1.0.15_GH0.tar.gz) = 560782 diff --git a/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.lib b/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.lib new file mode 100644 index 000000000000..7f8d5a434e94 --- /dev/null +++ b/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.lib @@ -0,0 +1,17 @@ +--- libStatGen/Makefiles/Makefile.lib.orig 2021-10-12 15:28:34 UTC ++++ libStatGen/Makefiles/Makefile.lib +@@ -34,11 +34,11 @@ profile: $(STAT_GEN_LIB_PROFILE) + # To build the library, build the objects + # Then add them to the library + $(STAT_GEN_LIB_OPT): $(OBJECTS_OPT) +- ar -cru $@ $(OBJECTS_OPT) ++ ar -cr $@ $(OBJECTS_OPT) + $(STAT_GEN_LIB_DEBUG): $(OBJECTS_DEBUG) +- ar -cru $@ $(OBJECTS_DEBUG) ++ ar -cr $@ $(OBJECTS_DEBUG) + $(STAT_GEN_LIB_PROFILE): $(OBJECTS_PROFILE) +- ar -cru $@ $(OBJECTS_PROFILE) ++ ar -cr $@ $(OBJECTS_PROFILE) + + UNAME=$(shell uname) + diff --git a/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.toolchain b/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.toolchain new file mode 100644 index 000000000000..447be2125380 --- /dev/null +++ b/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.toolchain @@ -0,0 +1,13 @@ +--- libStatGen/Makefiles/Makefile.toolchain.orig 2021-10-12 15:09:29 UTC ++++ libStatGen/Makefiles/Makefile.toolchain +@@ -51,8 +51,8 @@ endif + + # CPP0X=-std=c++0x + +-CXX = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)g++ $(CPP0X) +-CC = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)gcc ++CXX = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)c++ $(CPP0X) ++CC = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)cc + LD = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ld + AR = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ar + RANLIB = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ranlib diff --git a/biology/bamutil/files/patch-libStatGen_vcf_VcfRecordGenotype.cpp b/biology/bamutil/files/patch-libStatGen_vcf_VcfRecordGenotype.cpp new file mode 100644 index 000000000000..db31c78ab9d7 --- /dev/null +++ b/biology/bamutil/files/patch-libStatGen_vcf_VcfRecordGenotype.cpp @@ -0,0 +1,11 @@ +--- libStatGen/vcf/VcfRecordGenotype.cpp.orig 2021-10-12 15:13:03 UTC ++++ libStatGen/vcf/VcfRecordGenotype.cpp +@@ -176,7 +176,7 @@ bool VcfRecordGenotype::setString(const std::string& k + if(sampleNum >= mySamples.size()) + { + // Out of range sample index. +- return(NULL); ++ return(false); + } + // Set the field in the sample. + return(mySamples.get(sampleNum).setString(key, value)); diff --git a/biology/bamutil/pkg-descr b/biology/bamutil/pkg-descr new file mode 100644 index 000000000000..e914877c3721 --- /dev/null +++ b/biology/bamutil/pkg-descr @@ -0,0 +1,4 @@ +Utilities for working on SAM/BAM files from The Center for Statistical +Genetics at the University of Michigan School of Public Health. It +includes numerous functions such as splitting, merging, trimming reads, +filtering, validation, diff, etc. |