diff --git a/biology/Makefile b/biology/Makefile index ba430926041c..c779368ef1d2 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,221 +1,222 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools + SUBDIR += bamutil SUBDIR += bbmap SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bfc SUBDIR += bioawk SUBDIR += biococoa SUBDIR += biolibc SUBDIR += biolibc-tools SUBDIR += bioparser SUBDIR += biosig SUBDIR += biosoup SUBDIR += biostar-tools SUBDIR += bolt-lmm SUBDIR += bowtie SUBDIR += bowtie2 SUBDIR += bwa SUBDIR += canu SUBDIR += cd-hit SUBDIR += cdbfasta SUBDIR += checkm SUBDIR += clustal-omega SUBDIR += clustalw SUBDIR += cufflinks SUBDIR += cytoscape SUBDIR += ddocent SUBDIR += diamond SUBDIR += dsr-pdb SUBDIR += edlib SUBDIR += emboss SUBDIR += erminej SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += flash SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gcta SUBDIR += gemma SUBDIR += generand SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += groopm SUBDIR += haplohseq SUBDIR += hhsuite SUBDIR += hisat2 SUBDIR += hmmer SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv SUBDIR += infernal SUBDIR += iolib SUBDIR += iqtree SUBDIR += jalview SUBDIR += jellyfish SUBDIR += kallisto SUBDIR += lamarc SUBDIR += libbigwig SUBDIR += libgtextutils SUBDIR += libneurosim SUBDIR += libnuml SUBDIR += libsbml SUBDIR += libsedml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += mmseqs2 SUBDIR += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-entrez-direct SUBDIR += ncbi-toolkit SUBDIR += ncbi-vdb SUBDIR += ngs-sdk SUBDIR += p5-AcePerl SUBDIR += p5-Bio-ASN1-EntrezGene SUBDIR += p5-Bio-Cluster SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-DB-EMBL SUBDIR += p5-Bio-DB-NCBIHelper SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite SUBDIR += p5-Bio-FeatureIO SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-MAGETAB SUBDIR += p5-Bio-NEXUS SUBDIR += p5-Bio-Phylo SUBDIR += p5-Bio-SCF SUBDIR += p5-Bio-Variation SUBDIR += p5-BioPerl SUBDIR += p5-BioPerl-Run SUBDIR += p5-TrimGalore SUBDIR += p5-transdecoder SUBDIR += paml SUBDIR += pbbam SUBDIR += pbseqan SUBDIR += peak-classifier SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phyml SUBDIR += picard-tools SUBDIR += plink SUBDIR += pooler SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-PySCeS SUBDIR += py-bigwig SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-crossmap SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-gffutils SUBDIR += py-goatools SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-libnuml SUBDIR += py-libsedml SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc SUBDIR += py-ont-fast5-api SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-python-libsbml SUBDIR += py-pywgsim SUBDIR += py-resdk SUBDIR += py-scikit-bio SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += rampler SUBDIR += readseq SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += rubygem-bio-executables SUBDIR += rubygem-bio-old-biofetch-emulator SUBDIR += rubygem-bio-shell SUBDIR += sam2pairwise SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqan3 SUBDIR += seqio SUBDIR += seqkit SUBDIR += seqtk SUBDIR += sigviewer SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += snpeff SUBDIR += spoa SUBDIR += sra-tools SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += taxonkit SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ucsc-userapps SUBDIR += ugene SUBDIR += unikmer SUBDIR += vcf-split SUBDIR += vcf2hap SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += vt SUBDIR += wise .include 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 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