Index: head/biology/Makefile =================================================================== --- head/biology/Makefile (revision 537982) +++ head/biology/Makefile (revision 537983) @@ -1,180 +1,181 @@ # $FreeBSD$ # COMMENT = Biology SUBDIR += abyss SUBDIR += artemis SUBDIR += avida SUBDIR += babel SUBDIR += bamtools SUBDIR += bcftools SUBDIR += bedtools + SUBDIR += bioawk SUBDIR += biococoa 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 += emboss SUBDIR += exonerate SUBDIR += fasta SUBDIR += fasta3 SUBDIR += fastahack SUBDIR += fastdnaml SUBDIR += fastool SUBDIR += fastp SUBDIR += fastqc SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += figtree SUBDIR += fluctuate SUBDIR += freebayes SUBDIR += garlic SUBDIR += gatk SUBDIR += gcta SUBDIR += gemma SUBDIR += gff2ps SUBDIR += gmap SUBDIR += gperiodic SUBDIR += graphlan SUBDIR += grappa 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 += lagan SUBDIR += lamarc SUBDIR += libbigwig SUBDIR += libgtextutils SUBDIR += libsbml SUBDIR += linux-foldingathome SUBDIR += mafft SUBDIR += mapm3 SUBDIR += migrate SUBDIR += minimap2 SUBDIR += molden SUBDIR += mopac SUBDIR += mothur SUBDIR += mrbayes SUBDIR += mummer SUBDIR += muscle SUBDIR += ncbi-blast+ SUBDIR += ncbi-cxx-toolkit SUBDIR += ncbi-toolkit 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 += pbcopper SUBDIR += pbseqan SUBDIR += pear-merger SUBDIR += phrap SUBDIR += phred SUBDIR += phylip SUBDIR += phyml SUBDIR += plink SUBDIR += primer3 SUBDIR += prodigal SUBDIR += prodigy-lig SUBDIR += protomol SUBDIR += psi88 SUBDIR += py-Genesis-PyAPI SUBDIR += py-biom-format SUBDIR += py-biopython SUBDIR += py-bx-python SUBDIR += py-cutadapt SUBDIR += py-dnaio SUBDIR += py-ete3 SUBDIR += py-fastTSNE SUBDIR += py-gffutils SUBDIR += py-gtfparse SUBDIR += py-hits SUBDIR += py-loompy SUBDIR += py-macs2 SUBDIR += py-multiqc SUBDIR += py-orange3-bioinformatics SUBDIR += py-orange3-single-cell SUBDIR += py-pandas-charm SUBDIR += py-pyfaidx SUBDIR += py-pysam SUBDIR += py-scikit-bio SUBDIR += py-xenaPython SUBDIR += pyfasta SUBDIR += python-nexus SUBDIR += rainbow SUBDIR += recombine SUBDIR += ruby-bio SUBDIR += rubygem-bio SUBDIR += samtools SUBDIR += scrm SUBDIR += seaview SUBDIR += seqan SUBDIR += seqan-apps SUBDIR += seqan1 SUBDIR += seqio SUBDIR += seqtk SUBDIR += sim4 SUBDIR += slclust SUBDIR += smithwaterman SUBDIR += stacks SUBDIR += star SUBDIR += stringtie SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += tophat SUBDIR += treekin SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcflib SUBDIR += vcftools SUBDIR += velvet SUBDIR += viennarna SUBDIR += vsearch SUBDIR += vt SUBDIR += wise .include Index: head/biology/bioawk/Makefile =================================================================== --- head/biology/bioawk/Makefile (nonexistent) +++ head/biology/bioawk/Makefile (revision 537983) @@ -0,0 +1,24 @@ +# $FreeBSD$ + +PORTNAME= bioawk +DISTVERSIONPREFIX= v +DISTVERSION= 1.0-7 +DISTVERSIONSUFFIX= -gfd40150 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= BWK awk modified for biological data + +LICENSE= BSD3CLAUSE + +USE_GITHUB= yes + +GH_ACCOUNT= lh3 + +MAKE_JOBS_UNSAFE= yes +ALL_TARGET= bioawk +INSTALL_TARGET= install-strip + +PLIST_FILES= bin/bioawk + +.include Property changes on: head/biology/bioawk/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/bioawk/distinfo =================================================================== --- head/biology/bioawk/distinfo (nonexistent) +++ head/biology/bioawk/distinfo (revision 537983) @@ -0,0 +1,3 @@ +TIMESTAMP = 1591283068 +SHA256 (lh3-bioawk-v1.0-7-gfd40150_GH0.tar.gz) = 4510ee9493d0acef846e66f7b370c83e6e731954437ef6128a2e0b1fa8a38874 +SIZE (lh3-bioawk-v1.0-7-gfd40150_GH0.tar.gz) = 72209 Property changes on: head/biology/bioawk/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/bioawk/files/patch-Makefile =================================================================== --- head/biology/bioawk/files/patch-Makefile (nonexistent) +++ head/biology/bioawk/files/patch-Makefile (revision 537983) @@ -0,0 +1,43 @@ +--- Makefile.orig 2017-09-11 13:43:01 UTC ++++ Makefile +@@ -22,14 +22,20 @@ + # THIS SOFTWARE. + # ****************************************************************/ + +-CFLAGS = -g -Wall -O2 ++CFLAGS ?= -g -Wall -O2 + +-CC = gcc ++CC ?= gcc + +-YACC = bison -y ++# YACC = bison -y + YACC = yacc + YFLAGS = -d + ++MKDIR ?= mkdir ++INSTALL ?= install ++DESTDIR ?= . ++PREFIX ?= /usr/local ++STRIP ?= strip ++ + OFILES = b.o main.o parse.o proctab.o tran.o lib.o run.o lex.o addon.o + + SOURCE = awk.h ytab.c ytab.h proto.h awkgram.y lex.c b.c main.c \ +@@ -61,5 +67,15 @@ maketab: ytab.h maketab.c + names: + @echo $(LISTING) + ++.PHONY: intall-strip install clean ++ ++install-strip: install ++ ${STRIP} ${DESTDIR}${PREFIX}/bin/bioawk ++ ++install: ++ ${MKDIR} -p ${DESTDIR}${PREFIX}/bin ++ ${INSTALL} -c bioawk ${DESTDIR}${PREFIX}/bin ++ + clean: +- rm -fr a.out *.o *.obj maketab maketab.exe *.bb *.bbg *.da *.gcov *.gcno *.gcda awk bioawk ytab.* proctab.c *.dSYM ++ rm -fr a.out *.o *.obj maketab maketab.exe *.bb *.bbg *.da *.gcov \ ++ *.gcno *.gcda awk bioawk ytab.* proctab.c *.dSYM Property changes on: head/biology/bioawk/files/patch-Makefile ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/biology/bioawk/pkg-descr =================================================================== --- head/biology/bioawk/pkg-descr (nonexistent) +++ head/biology/bioawk/pkg-descr (revision 537983) @@ -0,0 +1,8 @@ +Bioawk is an extension to Brian Kernighan's awk, adding the support of several +common biological data formats, including optionally gzip'ed BED, GFF, SAM, +VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few +built-in functions and an command line option to use TAB as the input/output +delimiter. When the new functionality is not used, bioawk is intended to behave +exactly the same as the original BWK awk. + +WWW: https://github.com/lh3/bioawk Property changes on: head/biology/bioawk/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property