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sdparekh / zUMIs

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
GNU General Public License v3.0
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Using singularity images as executable #340

Closed royfrancis closed 1 year ago

royfrancis commented 1 year ago

By default, STAR is specified in the yaml config as such

STAR_exec: STAR

But, if I have STAR as a singularity image run as 

singularity run star.sif STAR

I have tried adding singularity executable as an alias, but it doesn't seem to work

alias STAR="singularity run star.sif STAR"
./zUMIs/zUMIs.sh -y sample.yaml
which: no STAR in (<paths>)
One or more of your executables were not found. Please check back.

How would I specify to use this executable?

cziegenhain commented 1 year ago

Hi,

I have no experience with singularity. Have you tried writing: STAR_exec: singularity run star.sif STAR ?

royfrancis commented 1 year ago

I have tried that but it only pick up the first word even if it's all in quotes.

sdparekh commented 1 year ago

Hi, Have you tried running zUMIs with its conda environment (-c option)? I usually made a short shell script where I first load the singularity image for default binaries and run zUMIs with -c option.

royfrancis commented 1 year ago

That was giving me some errors. I managed to create a conda env based on the yaml file provided in #343. And that seems to work.