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This is a followup to the closed issue as noted in #291, which can be worked around using the nf-core pangenome workflow. I have separately confirmed this using the same data for the below. As noted below, this is likely due to the pggb wrapper script.
When I try to run a Docker-converted Singularity container:
The Illegal option -- is coming from the shell within the container for some reason. If I try running the latest container interactively, as follows, and check where the pggb path is:
$ singularity run $SINGULARITY_CACHEDIR/pggb_latest.sif
Singularity> which pggb
Illegal option --
Usage: /usr/bin/which [-a] args
Note the Illegal option --. What happens if I just try to invoke pggb?
Singularity> pggb
/usr/bin/env: 'bash': No such file or directory
No shell? What are we running.
Singularity> echo $0
/bin/bash
This is the path for the interactive shell if using singularity run, which doesn't match the error above when invoking pggb, so maybe it's the shebang line in the pggb script:
> pggb
/usr/bin/env: 'bash': No such file or directory
Singularity> /usr/bin/which pggb
/usr/local/bin/pggb
Singularity> head -n2 /usr/local/bin/pggb
#!/usr/bin/env bash
So there seems to be some confusion in the paths under singularity.
The text was updated successfully, but these errors were encountered:
This is a followup to the closed issue as noted in #291, which can be worked around using the nf-core pangenome workflow. I have separately confirmed this using the same data for the below. As noted below, this is likely due to the
pggb
wrapper script.When I try to run a Docker-converted Singularity container:
The
Illegal option --
is coming from the shell within the container for some reason. If I try running the latest container interactively, as follows, and check where thepggb
path is:Note the
Illegal option --
. What happens if I just try to invokepggb
?No shell? What are we running.
This is the path for the interactive shell if using
singularity run
, which doesn't match the error above when invokingpggb
, so maybe it's the shebang line in thepggb
script:So there seems to be some confusion in the paths under singularity.
The text was updated successfully, but these errors were encountered: