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bgruening / galaxytools

:microscope::books: Galaxy Tool wrappers
MIT License
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Update salmon v1.9.0 #1266

Closed gallardoalba closed 1 year ago

gallardoalba commented 1 year ago

This PR updates salmon. In addition it improves index generation by enabling decoy-aware transcriptome, according with https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode

gallardoalba commented 1 year ago

Not sure why it is failing, I didn't modify the .shed.xml file @bgruening

bgruening commented 1 year ago

I see a broken XML in alevin. Planemo lint will show you.

gallardoalba commented 1 year ago

I see a broken XML in alevin. Planemo lint will show you.

Ah, thanks a lot!

gallardoalba commented 1 year ago

Dot not merge, I need to fix an error.

gallardoalba commented 1 year ago

Now should be fine.

gallardoalba commented 1 year ago

This is the current error, but it is strange because also the non-modified XML file seems to fail:

Traceback (most recent call last): 
File "/home/laptop/Galaxy/galaxy/lib/galaxy/jobs/runners/__init__.py", line 629, in _finish_or_resubmit_job job_wrapper.finish( 
File "/home/laptop/Galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 1853, in finish self._finish_dataset(output_name, dataset, job, context, final_job_state, remote_metadata_directory) File "/home/laptop/Galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 1671, in _finish_dataset dataset.datatype.set_meta(dataset, overwrite=False) 
File "/home/laptop/Galaxy/galaxy/lib/galaxy/datatypes/tabular.py", line 1613, in set_meta for line in dataset_fh: File "/home/laptop/miniconda3/envs/_galaxy_/lib/python3.8/codecs.py", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0x80 in position 1: invalid start byte
gallardoalba commented 1 year ago

This is the error:Timed out after 900.25 seconds waiting on tool test run, but I don't think is a tool problem @bgruening

bgruening commented 1 year ago

It could mean that Galaxy has been waiting for conda for too long and that the dependencies are conflicting ... I restarted lets see..

gallardoalba commented 1 year ago

It could mean that Galaxy has been waiting for conda for too long and that the dependencies are conflicting ... I restarted lets see..

It seems to be fixed. I read that Alevin will be replaced very soon by Alevin-fry very soon.

bgruening commented 1 year ago

Ist alevin fry the single cell component?

gallardoalba commented 1 year ago

Ist alevin fry the single cell component?

Yes, according the developers, despite Alevin will be maintained for a while, it will be replaced by Alevin-fry.

bgruening commented 1 year ago

Ok good to know. Maybe we can replace this tool here at some point.