Wally doesn't take option/ input

[min-codes]

Dear authors,

I downloaded the wally.sif but it doesn't seem to actually take options/ commands other than displaying the following when i execute it. Any suggestion will be much appreciated. Thanks!

Commands i tried:

$ .wally_v0.5.7.sif 
$ .wally_v0.5.7.sif region -R regions1.bed -g GRCh38.d1.vd1.fa 1T_WES.realn.bam

Output:

**********************************************************************
Program: Wally
This is free software, and you are welcome to redistribute it under
certain conditions (BSD License); for license details use '-l'.
This program comes with ABSOLUTELY NO WARRANTY; for details use '-w'.

Wally (Version: 0.5.7)
Contact: Tobias Rausch (rausch@embl.de)
**********************************************************************

Usage: wally <command> <arguments>

    region         plot genomic region
    matches        plot read or contig alignments
    dotplot        plot pairwise alignments
    hilbert        plot genomic region as hilbert curve

[tobiasrausch]

Should work like that:

singularity exec wally_v0.5.7.sif wally region

singularity exec wally_v0.5.7.sif wally matches

...

[min-codes]

Hi Tobias,

Thank you for the prompt response! It works now. I've also had to add -B option to singularity to 'mount' the file system correctly, if mount is the right word choice.

singularity exec -B /home/workdir/ wally_v0.5.7.sif wally region -p -R /home/workdir/regions1.bed -g /home/workdir/GRCh38.fa /home/workdir/1T_WES.realn.bam