From peaks to genes - slighly outdated and possible tool error

[davelopez]

In general, the tutorial can be followed in 21.01 but some minor updates can be made as part of the next cofest:

These minor issues mainly affect the section related to the Workflow Editor:

• Some of the screenshots are a bit outdated.
• Instead of the new checkboxes for outputs, the asterisks are mentioned to hide intermediate steps in a workflow.
• There is a save icon to save the workflow without accessing the 'gear' icon (which is for the 'save as...' option).

Possible version incompatibility error?

I also faced an error when running the workflow at the Repeat workflow step. I can not tell if this is some problem with the datasets, the version of the tools, or my own clumsiness, but here is the error report after running the workflow on usegalaxy.org:

An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1/1.0.0.

std-err:

Exception while parsing command line:
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/intersect/33b3f3688db4/intersect/gops_intersect.py", line 35, in main
    chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
  File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-a4cb0f5781d6f9de5e288400a2ac9fa34202068e5723b723249629522600dc67/lib/python2.7/site-packages/galaxy/tools/util/galaxyops/__init__.py", line 29, in parse_cols_arg
    col_list = map( lambda x: int( x ) - 1, cols.split(",") )
  File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/mulled-v1-a4cb0f5781d6f9de5e288400a2ac9fa34202068e5723b723249629522600dc67/lib/python2.7/site-packages/galaxy/tools/util/galaxyops/__init__.py", line 29, in <lambda>
    col_list = map( lambda x: int( x ) - 1, cols.split(",") )
ValueError: invalid literal for int() with base 10: 'None'

Find regions of first interval file that overlap regions in a second interval file.
Interval files can either be BED or GFF format.

usage: /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/intersect/33b3f3688db4/intersect/gops_intersect.py interval_file_1 interval_file_2 out_file
    -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
    -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
    -m, --mincols=N: Require this much overlap (default 1bp)
    -p, --pieces: just print pieces of second set (after padding)
    -G, --gff1: input 1 is GFF format, meaning start and end coordinates are 1-based, closed interval
    -H, --gff2: input 2 is GFF format, meaning start and end coordinates are 1-based, closed interval

[rahmot]

I wanted to create this as a new issue then realized that @davelopez has done it earlier. I got stuck at Repeat workflow step. The Galaxy menu bar, Data Upload, and UCSC table browser screenshots are outdated.

[bebatut]

@rahmot What is your issue? For the screenshots, do you think you could update them?

[rahmot]

@bebatut yes, I would like to update the screenshots. How will I do that? When I was taken to the UCSC table browser, Galaxy logged me out and automatically created a new history for the Genes dataset.