Permissions issues with check_samplesheet.py

[slsevilla]

Description of the bug

Running the test data sends a permission error due to permissions on the python samplesheet check file check_samplesheet.py

Command used and terminal output

cruise run --mode local -profile test -preview

Error

Traceback (most recent call last):
  File "/data/CCBR_Pipeliner/Pipelines/CRUISE/v0.1/bin/cruise", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/data/CCBR_Pipeliner/Pipelines/CRUISE/v0.1/cruise/src/__main__.py", line 119, in main
    cli()
  File "/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/v0.2/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/v0.2/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/v0.2/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/v0.2/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/v0.2/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/CCBR_Pipeliner/Pipelines/CRUISE/v0.1/cruise/src/__main__.py", line 92, in run
    run_nextflow(
  File "/data/CCBR_Pipeliner/Pipelines/CRUISE/v0.1/cruise/src/util.py", line 157, in run_nextflow
    chmod_bins_exec()
  File "/data/CCBR_Pipeliner/Pipelines/CRUISE/v0.1/cruise/src/util.py", line 104, in chmod_bins_exec
    os.chmod(
PermissionError: [Errno 1] Operation not permitted: '/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CRUISE/.v0.1.0/cruise/bin/check_samplesheet.py'

Looking at permissions, there isn't global read access:

-rwxrwx--- 1 sovacoolkl CCBR 6440 Nov  1 15:18 /gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CRUISE/.v0.1.0/cruise/bin/check_samplesheet.py

### Relevant files

_No response_

### System information

_No response_

[kelly-sovacool]

Thanks for catching this, @slsevilla. I believe I've fixed the error, can you check that cruise run works for you now?

[slsevilla]

Hi - there's another permission issue within '/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CRUISE/.v0.1.0/cruise/bin/__pycache__':

[sevillas2@cn3102 test_data]$ cruise run --mode local -profile test -preview
Traceback (most recent call last):
  File "/data/CCBR_Pipeliner/Pipelines/CRUISE/v0.1/bin/cruise", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/data/CCBR_Pipeliner/Pipelines/CRUISE/v0.1/cruise/src/__main__.py", line 119, in main
    cli()
  File "/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/v0.2/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/v0.2/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/v0.2/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/v0.2/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/CCBR_Pipeliner/Pipelines/CHAMPAGNE/v0.2/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/data/CCBR_Pipeliner/Pipelines/CRUISE/v0.1/cruise/src/__main__.py", line 92, in run
    run_nextflow(
  File "/data/CCBR_Pipeliner/Pipelines/CRUISE/v0.1/cruise/src/util.py", line 157, in run_nextflow
    chmod_bins_exec()
  File "/data/CCBR_Pipeliner/Pipelines/CRUISE/v0.1/cruise/src/util.py", line 104, in chmod_bins_exec
    os.chmod(
PermissionError: [Errno 1] Operation not permitted: '/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CRUISE/.v0.1.0/cruise/bin/__pycache__'

Permissions on this:

ls -la '/gpfs/gsfs10/users/CCBR_Pipeliner/Pipelines/CRUISE/.v0.1.0/cruise/bin/__pycache__'
total 130
drwxrwxr-- 2 sovacoolkl CCBR 4096 Nov  2 10:38 .
drwxrwxr-- 3 sovacoolkl CCBR 4096 Nov  2 10:38 ..
-rw-rw-r-- 1 sovacoolkl CCBR 9103 Nov  2 10:38 check_samplesheet.cpython-311.pyc

[kelly-sovacool]

Ooh, this is a big problem since pycache files are made automatically when you run a python script, so the pycache will belong to whoever first called the script...

Surely this isn't a problem for other tools installed to shared locations e.g. /usr/local/bin/. I'll do some digging to figure out how to avoid this.

[kelly-sovacool]

Ok @slsevilla I think I've fixed it, can you try again?

[slsevilla]

Both the preview and slurm job submission ran successfully! Will monitor test run and update this issue.

[slsevilla]

Cleared permissions related issue getting pipeline kicked off!