Galaxy update errors

Question: Galaxy update errors

2.7 years ago by

SHAUN WEBB • 70 wrote:

I have recently updated Galaxy to the latest release and I am having a couple of issues.

When updating my mySQL database I got the following error:

OperationalError: (_mysql_exceptions.OperationalError) (1059, "Identifier name 'workflow_invocation_to_subworkflow_invocation_association_ibfk_1' is too long")

I am using mysql version 14.14. I know that mySQL has limits to the length of names, is there anyway to get around this without switching to postgres?

The server still starts and seems to (mostly) run without any issues.

Visualisations are not showing up correctly for bed and bam format. The tracks do not show any errors and appear to be "prepared" okay but they are just empty. BigWig files seem to be fine. I have followed the visualisation setup below to make sure everything is up to date but I must be missing something somewhere. https://wiki.galaxyproject.org/VisualizationSetup

Thanks for any help on either of these topics.

software error galaxy • 1.1k views

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modified 2.7 years ago by Dannon Baker ♦ 3.7k • written 2.7 years ago by SHAUN WEBB • 70

2.7 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

Thanks for reporting this Shaun. I'll take a look at the index length error -- we've fixed several of these in the past to accommodate mysql.

Regarding visualizations -- do you see any errors in the Galaxy log?

ADD COMMENT • link written 2.7 years ago by Dannon Baker ♦ 3.7k

Yes sorry, I should have posted this, thanks for your help.

89.242.178.50 - - [05/Mar/2016:07:51:23 +0100] "GET /galaxy/api/datasets/5853e7ef34c5f57a?data_type=data&chrom=chr1&low=231796608&high=247249718&mode=Auto&resolution=193163.8421875&hda_ldda=hda&filter_cols=%5B%5D HTTP/1.1" 500 - "http://bifx-core.bio.ed.ac.uk:8080/galaxy/visualization/trackster?dataset_id=5853e7ef34c5f57a&dbkey=hg18&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_5) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"

galaxy.webapps.galaxy.api.datasets ERROR 2016-03-05 07:51:23,754 Error in dataset API at listing contents: _open() got an unexpected

keyword argument 'index_filename': _open() got an unexpected keyword argument 'index_filename'

Traceback (most recent call last):

File "/storage/home/galaxy/production/fresh/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 66, in show rval = self._data( trans, dataset, **kwd )

File "/storage/home/galaxy/production/fresh/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 235, in _data ref_seq=region, mean_depth=mean_depth, **kwargs )

File "/storage/home/galaxy/production/fresh/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 191, in get_data data_file = self.open_data_file()

File "/storage/home/galaxy/production/fresh/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 350, in open_data_file index_filename=self.converted_dataset.file_name)

File "pysam/ctabix.pyx", line 302, in pysam.ctabix.TabixFile.__cinit__ (pysam/ctabix.c:3187)

File "pysam/ctabix.pyx", line 305, in pysam.ctabix.TabixFile._open (pysam/ctabix.c:3292)

TypeError: _open() got an unexpected keyword argument 'index_filename'

89.242.178.50 - - [05/Mar/2016:07:51:22 +0100] "GET /galaxy/api/datasets/5853e7ef34c5f57a?data_type=data&chrom=chr1&low=0&high=77265536&mode=Auto&resolution=193163.8421875&hda_ldda=hda&filter_cols=%5B%5D HTTP/1.1" 500 - "http://bifx-core.bio.ed.ac.uk:8080/galaxy/visualization/trackster?dataset_id=5853e7ef34c5f57a&dbkey=hg18&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_5) AppleWebKit/601.4.4 (KHTML, like Gecko) Version/9.0.3 Safari/601.4.4"

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by SHAUN WEBB • 70

If this is a new instance, can you try this patch for me?

ADD REPLY • link written 2.7 years ago by Dannon Baker ♦ 3.7k

It's not a new instance, if I try that on my test server I get the following error:

Traceback (most recent call last):
  File "/storage/home/galaxy/production/fresh/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 66, in show
    rval = self._data( trans, dataset, **kwd )
  File "/storage/home/galaxy/production/fresh/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 235, in _data
    ref_seq=region, mean_depth=mean_depth, **kwargs )
  File "/storage/home/galaxy/production/fresh/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 192, in get_data
    iterator = self.get_iterator( data_file, chrom, start, end, **kwargs )
  File "/storage/home/galaxy/production/fresh/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 360, in get_iterator
    iterator = data_file.fetch(reference=chrom, start=start, end=end)
  File "pysam/ctabix.pyx", line 430, in pysam.ctabix.TabixFile.fetch (pysam/ctabix.c:4601)
  File "pysam/cutils.pyx", line 106, in pysam.cutils.force_bytes (pysam/cutils.c:2170)
TypeError: Expected bytes, got unicode
92.22.36.82 - - [07/Mar/2016:13:53:58 +0100] "GET /galaxy/api/datasets/8fe017e0d9abe41f?data_type=data&chrom=chr1&low=46994482&high=70491723&mode=Auto&resolution=58743.102637205986&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - "http://bifx-core.bio.ed.ac.uk:8080/galaxy/visualization/trackster?dataset_id=5853e7ef34c5f57a&dbkey=hg18&hda_ldda=hda" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/48.0.2564.103 Safari/537.36"

ADD REPLY • link written 2.7 years ago by SHAUN WEBB • 70

https://github.com/galaxyproject/galaxy/pull/1897 should resolve this issue, without me needing to create a new version of pysam.

ADD REPLY • link written 2.7 years ago by Dannon Baker ♦ 3.7k

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