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STOmics / SAW

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Inconsistent names in help message from mapping #57

Closed ChangqingW closed 4 months ago

ChangqingW commented 1 year ago

With the latest image docker://stomics/saw:06.1.0, mapping prints a help message that refers to a program bcSTAR that does not exist in the image:

Singularity> mapping
Usage: STAR  [options]... --genomeDir REFERENCE   --readFilesIn R1.fq R2.fq
Spliced Transcripts Alignment to a Reference (c) Alexander Dobin, 2009-2019

For more details see:
<https://github.com/alexdobin/STAR>
<https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf>

To list all parameters, run bcSTAR --help . To list STOmics parameters, run bcSTAR --helpBcPara
Singularity> bcSTAR
bash: bcSTAR: command not found

Consider creating an alias in the image alias bcSTAR="mapping" or updating the help message.

TheSallyGardens commented 1 year ago

You need to import bcSTAR(/opt/saw_v6.1.0_software/pipeline/mapping/bcSTAR) into the environment variable.

ChangqingW commented 1 year ago

You need to import bcSTAR(/opt/saw_v6.1.0_software/pipeline/mapping/bcSTAR) into the environment variable.

Yes, but since mapping redirects to bcSTAR

Singularity> cat $(which mapping)
/opt/saw_v6.1.0_software/pipeline/mapping/bcSTAR $*

It is confusing for users to see mapping --help referring to bcSTAR, but bcSTAR is not available by default. I don't think this is mention in the user manual either?