specifying output folder for singularity

[SebastianHollizeck]

Hi,

i would love to use this through singularity in our HPC, but the issue is, that the program writes to the location of the python script, which errors out on the read-only filesystem singularity is based on.

I created a workaround with sandbox mode in singularity, but it would be amazing, if there was an option to specify the output location for the tool. So it can be more widely used.

Cheers,
Sebastian

[AAlhendi1707]

Same issue here

[pmitev]

I have changed line 17 in my container
from
filename = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'phylogicndt.log')
to
filename = os.path.join(os.getcwd(), 'phylogicndt.log')

which writes the logfile in the current directory instead...
I am not sure if this is the only place where the code will write in the installation folder, though...

[bio937]

@SebastianHollizeck @AAlhendi1707 @pmitev

I encountered the same issue while trying to run PhylogicNDT inside a singularity container.

After changing that one line of code suggested by @pmitev, now it works when using the --help argument. Previously, it will show: IOError: [Errno 30] Read-only file system: Thank you so much! @pmitev

I first created singularity sandbox and changed that line of code, then converted the sandbox to Singularity Image Format (.sif)