Hello,
I am trying to create a small teaching environment and I was hesitating to use either IGV or Galaxy and as I am planning to use galaxy for other steps as well it would be a nice combination.
When loading the fasta file obtained from: https://www.ncbi.nlm.nih.gov/nuccore/J01636 it seems to work ok, cannot visualise the sequence and the 3 reading frames but not sure yet if this is possible?
When loading the gff file I get the following error:
Traceback (most recent call last): File "/galaxy-central/lib/galaxy/datatypes/converters/interval_to_fli.py", line 20, in from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed, GFFReaderWrapper, read_unordered_gtf ImportError: No module named galaxy.datatypes.util.gff_util Close
The original docker file that I use as a spin of from the original docker file is located:
https://gitlab.com/wurssb/ibiosystems/tree/master/docker
And the error must have been resolved at https://github.com/galaxyproject/tools-devteam/pull/335 but perhaps I am missing some fundamental binaries due to docker?
The next step would be to visualise bam files with 1x, 10x and 100x read coverage to teach them on the coverage impact
just double checking: the fasta file you want the visualize is the 'genome' sequence? If so, it is best to add the (nucleotide) sequence as a twobit file (see: https://galaxyproject.org/visualization-setup/#optional-but-highly-recommended-get-genome-data )
Regards, Hans-Rudolf
It is indeed a fasta file of ±7kb its an example operon
wrt the gff file: does it work with another (eg smaller, simpler) gff file?
Regards, Hans-Rudolf
The current gff file is only 26 lines but ill try a single gene
well, it looks like, I have just been running into a similar issue as part of upgrading to release v17.01
see: http://dev.list.galaxyproject.org/Convert-BED-to-Feature-Location-Index-breaks-when-preserve-python-environment-legacy-only-tp4670669.html
...and in your case, you probably need to add "CONVERTER_gff_to_fli_0"
I hope this fixes your problem as well. Regards, Hans-Rudolf