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galaxyproject / tools-devteam

Contains a set of Galaxy Tools mostly written by the Galaxy Team.
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sam_bitwise_flag_filter - fix indent #587

Closed lecorguille closed 3 years ago

lecorguille commented 3 years ago

This MR should fix this issue:

File "/shared/ifbstor1/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/sam_bitwise_flag_filter/0b2424a404d9/sam_bitwise_flag_filter/sam_bitwise_flag_filter.py", line 111
infile = open ( options.input_sam, 'r')
^
TabError: inconsistent use of tabs and spaces in indentation
wm75 commented 3 years ago

Weird, just out of interest I ran the tool on usegalaxy.org now with a BAM file as input. It fails with:

Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/sam_bitwise_flag_filter/0b2424a404d9/sam_bitwise_flag_filter/sam_bitwise_flag_filter.py", line 148, in <module>
    if __name__ == "__main__": main()
  File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/sam_bitwise_flag_filter/0b2424a404d9/sam_bitwise_flag_filter/sam_bitwise_flag_filter.py", line 137, in main
    flags = int( fields[flag_col] )
IndexError: list index out of range

there, but that's past the indent problem I guess?

nsoranzo commented 3 years ago

The error in the CI logs doesn't make much sense to me, but it is reproducible. Planemo test passes locally.

@mvdbeek Any ideas? Maybe the pip cache is busted?

mvdbeek commented 3 years ago

This might be fixed in https://github.com/galaxyproject/planemo/pull/1145. I'll push a commit that will install planemo from that branch

mvdbeek commented 3 years ago

Arg, even with the new release:

Activating virtualenv at /home/runner/.planemo/gx_venv_3.7_release_20.09
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
planemo 0.74.3 requires bioblend>=0.14.0, but you have bioblend 0.13.0 which is incompatible.
planemo 0.74.3 requires gxformat2>=0.12.0, but you have gxformat2 0.11.3 which is incompatible.
bernt-matthias commented 3 years ago

And .. can you check if there is something in https://github.com/galaxyproject/tools-devteam/pull/555 that can be used?