diff --git a/biology/Makefile b/biology/Makefile index f97c311da9fe..294a87ca4e78 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -1,215 +1,216 @@ COMMENT = Biology SUBDIR += abyss SUBDIR += ad2vcf SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools 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 += libsbml 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-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/sam2pairwise/Makefile b/biology/sam2pairwise/Makefile new file mode 100644 index 000000000000..dd578353e5a9 --- /dev/null +++ b/biology/sam2pairwise/Makefile @@ -0,0 +1,20 @@ +PORTNAME= sam2pairwise +DISTVERSIONPREFIX= v +DISTVERSION= 1.0.0 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Show pairwise alignment for each read in a SAM file + +LICENSE= MIT +LICENSE_FILE= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/LICENSE + +USE_GITHUB= yes + +GH_ACCOUNT= mlafave + +WRKSRC_SUBDIR= src +ALL_TARGET= sam2pairwise +PLIST_FILES= bin/sam2pairwise + +.include diff --git a/biology/sam2pairwise/distinfo b/biology/sam2pairwise/distinfo new file mode 100644 index 000000000000..364e6c8bde7c --- /dev/null +++ b/biology/sam2pairwise/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1631041315 +SHA256 (mlafave-sam2pairwise-v1.0.0_GH0.tar.gz) = 899d3db071cc248870bbedbdb39784de4c54c9a7888bc408022e809ace47ec0e +SIZE (mlafave-sam2pairwise-v1.0.0_GH0.tar.gz) = 10013 diff --git a/biology/sam2pairwise/files/patch-Makefile b/biology/sam2pairwise/files/patch-Makefile new file mode 100644 index 000000000000..56ed56b8a857 --- /dev/null +++ b/biology/sam2pairwise/files/patch-Makefile @@ -0,0 +1,39 @@ +--- Makefile.orig 2014-08-22 20:02:24 UTC ++++ Makefile +@@ -1,8 +1,19 @@ +-CXX = g++ +-CC = g++ ++CXX ?= g++ ++LD = ${CXX} + +-sam2pairwise: sam2pairwise.o isolate_md.o shift_cigar.o shift_md.o translate_cigar.o translate_md.o ++OBJS = sam2pairwise.o isolate_md.o shift_cigar.o shift_md.o \ ++ translate_cigar.o translate_md.o + ++PREFIX ?= /usr/local ++DESTDIR ?= . ++INSTALL ?= install ++MKDIR ?= mkdir ++ ++all: sam2pairwise ++ ++sam2pairwise: ${OBJS} ++ ${CXX} ${OBJS} -o sam2pairwise ++ + isolate_md.o: isolate_md.cc isolate_md.hh + + shift_cigar.o: shift_cigar.cc shift_cigar.hh +@@ -15,6 +26,11 @@ translate_md.o: translate_md.cc translate_md.hh + + sam2pairwise.o: sam2pairwise.cc isolate_md.hh shift_cigar.hh shift_md.hh translate_cigar.hh translate_md.hh + +-clobber: +- rm -f *.o core sam2pairwise ++.PHONY: install clean + ++install: ++ ${MKDIR} -p ${DESTDIR}${PREFIX}/bin ++ ${INSTALL} -c sam2pairwise ${DESTDIR}${PREFIX}/bin ++ ++clean: ++ rm -f *.o core sam2pairwise diff --git a/biology/sam2pairwise/pkg-descr b/biology/sam2pairwise/pkg-descr new file mode 100644 index 000000000000..800de1d7998e --- /dev/null +++ b/biology/sam2pairwise/pkg-descr @@ -0,0 +1,4 @@ +sam2pairwise takes a SAM file and uses the CIGAR and MD tag to +reconstruct the pairwise alignment of each read. + +WWW: https://github.com/mlafave/sam2pairwise