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yyoshiaki / VIRTUS

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
https://github.com/yyoshiaki/VIRTUS/wiki
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How to change location of output temporary directory from root to home partition? #29

Closed jlee110 closed 3 years ago

jlee110 commented 3 years ago

I'm using createindex.cwl to create indices but it fails due to space issue.

How would I change output temporary directory to /home where I do have plenty of space without having to resize my partitions.

Is it better to use STAR manually to generate indices like this? What parameters do you suggest?

STAR --runThreadN 12 --runMode genomeGenerate --outTmpDir tmp --genomeDir STAR_genome/ --genomeFastaFiles $ref_fa_dir --sjdbGTFfile $ref_gtf_dir --sjdbOverhang 100 --genomeChrBinNbits 15