bedbase tutorial feedback

[stolarczyk]

nice @joseverdezoto, I like the tutorial. I think it's clear and very helpful. Some minor remarks below:

• name of the software packages are inconsistently formatted -- code and not code
• after saying "we'll be using the dev version of bbconf that can be downloaded as follows" you do not actually install it
• but you install looper, which might be confusing. So either motivate this step (say why it's needed) or wait with installation to the step 4) where you submit the jobs with looper
• since the tutorial is quite long (as all the command outputs are included) maybe it will be worth creating a table of contents linking to the respective sections? This way we'll have a clear overview what's covered here. See PEP spec as an example of what I mean
• regarding your concern about sudo, I was able to run jupyter with: sudo jupyter notebook --allow-root, which solved the issue. Make sure you mention the possible sudo requirement in the text, though.
• in step 4) there is still links saying here. Use descriptive link text, like "try running refgenieserver"
• the --no-db-commit can be skipped since we'll make it a script, not a part of bedstat pipeline. So maybe run is as a whole for now? You're running it locally anyway right?
• it's enough to provide link to software packages when you first mention them. I caught that in the section describing iGD
• in the bedhost-related section you say that a development version of bedhost is required, that's not true
• I see that there are some dependency issues in bedhost I did not experience before (bedhost-starlette-itsdangerous) I'll look into that
• maybe we could use enumerating instead of headings like: "First/Second/Third part of the tutorial...". This will work nicely in combination with the table of contents above.

[nsheff]

@joseverdezoto what is the status on this issue?

[joseverdezoto]

All those suggested changes were made last week. There’s an issue at the very last step, when trying to run bedhost, but other than that it should be good to go. I think @stolarczyk is testing the whole tutorial workflow

[stolarczyk]

@joseverdezoto, the issue with bedhost serve -c bedbase_demo_PEPs/bedbase_configuration.yaml command stems from bbconf not making the config-sourced path in paths:pipelines_output relative to the config file itself. I think you assumed that it does. So the solution is to change the config you use -- prepend $HOME/bedbase_tutorial to the path in the config.

[stolarczyk]

Also, I'd put the BEDBASE config outside of the PEP directory, since it's not part of the PEP.

[joseverdezoto]

• @stolarczyk I'm not really sure I understand. I know that the bedbaseconfiguration file I've been using for testing points to an absolute path: $LABROOT/resources/regions/bedstat_output. Is the issue that as of now, we can only use absolute paths to the bedstat_output directory?
• In regards to the other suggestion, I placed the bedbase_config file inside that folder because I thought it wouldn't be very practical to have an extra .tar.gz file (with only 1 .yaml file) to download.

[joseverdezoto]

Update: I prepended $BEDBASEtutorial ($HOME/bedbase_tutorial) to the path in the config but I still get the error:

File "/home/jev4xy/.local/lib/python3.6/site-packages/starlette/routing.py", line 282, in __init__
    assert path == "" or path.startswith("/"), "Routed paths must start with '/'"
AssertionError: Routed paths must start with '/'

[stolarczyk]

It worked for me.

Are you sure the file you point to with -c arg in bedhost command is the updated file?

[stolarczyk]

maybe use $BEDBASEtutorial env var instead of the path path to the config in the call

[stolarczyk]

In regards to the other suggestion, I placed the bedbase_config file inside that folder because I thought it wouldn't be very practical to have an extra .tar.gz file (with only 1 .yaml file) to download

what about taring the config file and the PEP directory together (file outside the dir)?

[joseverdezoto]

Oops, I had forgotten to update the paths:pipelines_output path of the tutorial config. It's working now :)

[nsheff]

are these issues complete? please update status.

[joseverdezoto]

@nsheff yes, you should be able to run the tutorial in the example files and then open bedhost to explore the respective bedstat and bedbuncher outputs. Michal and I have succesfully tested the tutorial at this point.