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bcbio / bcbio-nextgen-vm

Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines
MIT License
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minimap2 support #191

Open fgvieira opened 4 years ago

fgvieira commented 4 years ago

Dear all,

bcbio-vm does not seem to support minimap2, even thought bcbio-nextgen does:

bcbio_vm.py install --cores 30 --tools --data --genomes hg19 --genomes hg38 --aligners bwa --aligners minimap2 --aligners star --aligners hisat2
usage: bcbio_vm.py install [-h]
                           [--genomes {GRCh37,hg19,hg38,hg38-noalt,mm10,mm9,rn6,rn5,canFam3,dm3,galGal4,phix,pseudomonas_aeruginosa_ucbpp_pa14,sacCer3,TAIR10,WBcel235,xenTro3,Zv9,GRCz10}]
                           [--aligners {bowtie,bowtie2,bwa,novoalign,rtg,snap,star,ucsc,seq,hisat2}]
                           [--datatarget {variation,rnaseq,smallrna,gemini,cadd,vep,dbnsfp,battenberg,kraken}]
                           [--data] [--tools] [--wrapper] [--image IMAGE]
                           [--cores CORES]
bcbio_vm.py install: error: argument --aligners: invalid choice: 'minimap2' (choose from 'bowtie', 'bowtie2', 'bwa', 'novoalign', 'rtg', 'snap', 'star', 'ucsc', 'seq', 'hisat2')

Is this intended? best,