c81fc00817
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.
181 lines
4.1 KiB
Makefile
181 lines
4.1 KiB
Makefile
# $FreeBSD$
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#
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COMMENT = Biology
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SUBDIR += abyss
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SUBDIR += artemis
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SUBDIR += avida
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SUBDIR += babel
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SUBDIR += bamtools
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SUBDIR += bcftools
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SUBDIR += bedtools
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SUBDIR += bioawk
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SUBDIR += biococoa
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SUBDIR += bolt-lmm
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SUBDIR += bowtie
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SUBDIR += bowtie2
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SUBDIR += bwa
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SUBDIR += canu
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SUBDIR += cd-hit
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SUBDIR += cdbfasta
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SUBDIR += checkm
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SUBDIR += clustal-omega
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SUBDIR += clustalw
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SUBDIR += cufflinks
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SUBDIR += cytoscape
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SUBDIR += ddocent
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SUBDIR += diamond
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SUBDIR += dsr-pdb
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SUBDIR += emboss
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SUBDIR += exonerate
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SUBDIR += fasta
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SUBDIR += fasta3
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SUBDIR += fastahack
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SUBDIR += fastdnaml
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SUBDIR += fastool
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SUBDIR += fastp
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SUBDIR += fastqc
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SUBDIR += fasttree
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SUBDIR += fastx-toolkit
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SUBDIR += figtree
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SUBDIR += fluctuate
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SUBDIR += freebayes
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SUBDIR += garlic
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SUBDIR += gatk
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SUBDIR += gcta
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SUBDIR += gemma
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SUBDIR += gff2ps
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SUBDIR += gmap
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SUBDIR += gperiodic
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SUBDIR += graphlan
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SUBDIR += grappa
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SUBDIR += groopm
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SUBDIR += haplohseq
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SUBDIR += hhsuite
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SUBDIR += hisat2
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SUBDIR += hmmer
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SUBDIR += htslib
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SUBDIR += hyphy
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SUBDIR += igv
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SUBDIR += infernal
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SUBDIR += iolib
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SUBDIR += iqtree
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SUBDIR += jalview
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SUBDIR += jellyfish
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SUBDIR += kallisto
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SUBDIR += lagan
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SUBDIR += lamarc
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SUBDIR += libbigwig
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SUBDIR += libgtextutils
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SUBDIR += libsbml
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SUBDIR += linux-foldingathome
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SUBDIR += mafft
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SUBDIR += mapm3
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SUBDIR += migrate
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SUBDIR += minimap2
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SUBDIR += molden
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SUBDIR += mopac
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SUBDIR += mothur
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SUBDIR += mrbayes
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SUBDIR += mummer
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SUBDIR += muscle
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SUBDIR += ncbi-blast+
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SUBDIR += ncbi-cxx-toolkit
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SUBDIR += ncbi-toolkit
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SUBDIR += ngs-sdk
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SUBDIR += p5-AcePerl
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SUBDIR += p5-Bio-ASN1-EntrezGene
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SUBDIR += p5-Bio-Cluster
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SUBDIR += p5-Bio-Coordinate
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SUBDIR += p5-Bio-DB-EMBL
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SUBDIR += p5-Bio-DB-NCBIHelper
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SUBDIR += p5-Bio-Das
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SUBDIR += p5-Bio-Das-Lite
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SUBDIR += p5-Bio-FeatureIO
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SUBDIR += p5-Bio-GFF3
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SUBDIR += p5-Bio-Glite
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SUBDIR += p5-Bio-Graphics
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SUBDIR += p5-Bio-MAGETAB
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SUBDIR += p5-Bio-NEXUS
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SUBDIR += p5-Bio-Phylo
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SUBDIR += p5-Bio-SCF
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SUBDIR += p5-Bio-Variation
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SUBDIR += p5-BioPerl
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SUBDIR += p5-BioPerl-Run
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SUBDIR += p5-TrimGalore
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SUBDIR += p5-transdecoder
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SUBDIR += paml
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SUBDIR += pbbam
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SUBDIR += pbcopper
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SUBDIR += pbseqan
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SUBDIR += pear-merger
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SUBDIR += phrap
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SUBDIR += phred
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SUBDIR += phylip
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SUBDIR += phyml
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SUBDIR += plink
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SUBDIR += primer3
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SUBDIR += prodigal
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SUBDIR += prodigy-lig
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SUBDIR += protomol
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SUBDIR += psi88
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SUBDIR += py-Genesis-PyAPI
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SUBDIR += py-biom-format
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SUBDIR += py-biopython
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SUBDIR += py-bx-python
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SUBDIR += py-cutadapt
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SUBDIR += py-dnaio
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SUBDIR += py-ete3
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SUBDIR += py-fastTSNE
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SUBDIR += py-gffutils
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SUBDIR += py-gtfparse
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SUBDIR += py-hits
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SUBDIR += py-loompy
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SUBDIR += py-macs2
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SUBDIR += py-multiqc
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SUBDIR += py-orange3-bioinformatics
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SUBDIR += py-orange3-single-cell
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SUBDIR += py-pandas-charm
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SUBDIR += py-pyfaidx
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SUBDIR += py-pysam
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SUBDIR += py-scikit-bio
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SUBDIR += py-xenaPython
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SUBDIR += pyfasta
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SUBDIR += python-nexus
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SUBDIR += rainbow
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SUBDIR += recombine
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SUBDIR += ruby-bio
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SUBDIR += rubygem-bio
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SUBDIR += samtools
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SUBDIR += scrm
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SUBDIR += seaview
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SUBDIR += seqan
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SUBDIR += seqan-apps
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SUBDIR += seqan1
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SUBDIR += seqio
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SUBDIR += seqtk
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SUBDIR += sim4
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SUBDIR += slclust
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SUBDIR += smithwaterman
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SUBDIR += stacks
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SUBDIR += star
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SUBDIR += stringtie
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SUBDIR += subread
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SUBDIR += tRNAscan-SE
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SUBDIR += tabixpp
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SUBDIR += tophat
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SUBDIR += treekin
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SUBDIR += treepuzzle
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SUBDIR += trimadap
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SUBDIR += trimmomatic
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SUBDIR += ugene
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SUBDIR += vcflib
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SUBDIR += vcftools
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SUBDIR += velvet
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SUBDIR += viennarna
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SUBDIR += vsearch
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SUBDIR += vt
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SUBDIR += wise
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.include <bsd.port.subdir.mk>
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