Date: Tue, 12 Oct 2021 16:43:26 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: cdf2ff2f68e6 - main - biology/bamutil: Utilities for working with SAM/BAM files Message-ID: <202110121643.19CGhQLX031101@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=cdf2ff2f68e6d4e78f85124aa5fbd8371adaebc2 commit cdf2ff2f68e6d4e78f85124aa5fbd8371adaebc2 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-10-12 16:40:35 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-10-12 16:40:35 +0000 biology/bamutil: Utilities for working with SAM/BAM files 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. --- biology/Makefile | 1 + biology/bamutil/Makefile | 26 ++++++++++++++++++++++ biology/bamutil/distinfo | 5 +++++ .../files/patch-libStatGen_Makefiles_Makefile.lib | 17 ++++++++++++++ .../patch-libStatGen_Makefiles_Makefile.toolchain | 13 +++++++++++ .../patch-libStatGen_vcf_VcfRecordGenotype.cpp | 11 +++++++++ biology/bamutil/pkg-descr | 6 +++++ 7 files changed, 79 insertions(+) diff --git a/biology/Makefile b/biology/Makefile index ba430926041c..c779368ef1d2 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -6,6 +6,7 @@ SUBDIR += avida SUBDIR += babel SUBDIR += bamtools + SUBDIR += bamutil SUBDIR += bbmap SUBDIR += bcftools SUBDIR += bedtools diff --git a/biology/bamutil/Makefile b/biology/bamutil/Makefile new file mode 100644 index 000000000000..1df27f50678d --- /dev/null +++ b/biology/bamutil/Makefile @@ -0,0 +1,26 @@ +PORTNAME= bamutil +DISTVERSIONPREFIX= v +DISTVERSION= 1.0.14 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Utilities for working with SAM/BAM files + +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 + +PLIST_FILES= bin/bam + +.include <bsd.port.mk> diff --git a/biology/bamutil/distinfo b/biology/bamutil/distinfo new file mode 100644 index 000000000000..4f76b5616521 --- /dev/null +++ b/biology/bamutil/distinfo @@ -0,0 +1,5 @@ +TIMESTAMP = 1634051641 +SHA256 (statgen-bamUtil-v1.0.14_GH0.tar.gz) = f5ec8d5e98a3797742106c3413a4ab1622d8787e38b29b3df4cddb59d77efda5 +SIZE (statgen-bamUtil-v1.0.14_GH0.tar.gz) = 1916953 +SHA256 (statgen-libStatGen-v1.0.14_GH0.tar.gz) = 70a504c5cc4838c6ac96cdd010644454615cc907df4e3794c999baf958fa734b +SIZE (statgen-libStatGen-v1.0.14_GH0.tar.gz) = 558924 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..6eb44e52fcb7 --- /dev/null +++ b/biology/bamutil/pkg-descr @@ -0,0 +1,6 @@ +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. + +WWW: https://github.com/statgen/bamUtil
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