Singularity Read-only file system Error about big-scape HOT 3 CLOSED

Hi again,

Thanks for the answer. I have been able to modify the docker image and run BiG-SCAPE in singularity. I am posting the steps for others to access the solution or provide a better one.

• curl -q https://git.wageningenur.nl/medema-group/BiG-SCAPE/raw/master/run_bigscape > run_bigscape
• singularity pull bigscape.sif docker://docker-registry.wur.nl/medema-group/big-scape:1.1.2
• singularity build --sandbox BiGSCAPE bigscape.sif
• vim BiGSCAPE/usr/src/BiG-SCAPE/ArrowerSVG.py # Comment the lines [657, 663:665]
• singularity build bigscape_mod.sif BiGSCAPE

Once I have the modified image:

singularity run bigscape_mod.sif -i 00-Data/AntiSMASHgbk/ -o 01-BigScape -c 16 --include_gbk_str '*'

from big-scape.

Hi,
sorry for commenting on this closed issue, but I just observed, that those lines which should be commented out to avoid the issue are still not commented out in the recent release (1.1.7). Am I missing something?
Thanks for your time!

from big-scape.

I think commenting/removing the following lines (around line 663 of ArrowerSVG.py) should do it:

    if len(new_color_domains) > 0:
        #if len(new_color_domains) < 10:
            #print("   Saving new color names for domains " + ", ".join(new_color_domains.keys()))
        #else:
            #print("   Saving new color names for 10+ domains")
            
        with open(domains_color_file, "a") as color_domains_handle:
            for new_names in new_color_domains:
                color_domains_handle.write(new_names + "\t" + ",".join([str(ncdom) for ncdom in new_color_domains[new_names]]) + "\n")

cheers

from big-scape.