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    Anne Fouilloux
    @annefou
    Is there any Galaxy training/tutorial for bioblend? Or do we just refer users to the bioblend usage documentation?
    Anne Fouilloux
    @annefou
    No I didn't! This is what I was looking for. Thank you!
    Nicola Soranzo
    @nsoranzo
    @annefou I'm going to teach that (but with tutorial from https://github.com/nsoranzo/bioblend-tutorial/ ) at BCC2020 (if it's not cancelled).
    Anne Fouilloux
    @annefou
    Awesome! I think it is close to the workflow we have. I have created a jupyterhub instance with access to climate data and need to communicate with Galaxy climate. The only problem I have so far is to upload data larger then 2GB in Galaxy from my Jupyter instance. I did not manage to use upload_from_ftp. Do you have an example with it in your tutorial?
    Nicola Soranzo
    @nsoranzo
    Mmmh, I don't think so
    Simon Bray
    @simonbray
    I'm wondering how to rerun failed jobs in a workflow
    This looks promising but I'm not sure what to give as the 'action' parameter: https://github.com/galaxyproject/bioblend/blob/master/bioblend/galaxy/invocations/__init__.py#L120
    Nicola Soranzo
    @nsoranzo
    Simon Bray
    @simonbray
    Oh yeah, I remember reading this issue
    Is it actually possible? It's not totally clear from reading that.
    Nicola Soranzo
    @nsoranzo
    In other words, there is no Galaxy API yet
    Simon Bray
    @simonbray
    Okay, thanks
    Nicola Soranzo
    @nsoranzo
    Heads-up: Unless anyone objects, I'm going to drop BioBlend support for Galaxy releases <=17.05: galaxyproject/bioblend#326
    Thomas N Lawson
    @Tomnl
    Hi all. I have been having some problems using BioBlend on workflows that contain tools with optional files (galaxyproject/bioblend#327). Has anybody else experienced anything similar?
    Tim Dudgeon
    @tdudgeon
    How do you hide a dataset (or all datasets in a collection) with bioblend?
    Tim Dudgeon
    @tdudgeon
    Thanks. Why didn't I see that!
    Nicola Soranzo
    @nsoranzo
    NP
    Nicola Soranzo
    @nsoranzo
    Björn Grüning
    @bgruening
    Cool, congrats!
    Simon Bray
    @simonbray
    :tada:
    Marius van den Beek
    @mvdbeek
    Nice, thanks a lot @nsoranzo!
    ashraf_borg
    @amkibriya
    Hi All, I'm managing a local server for our group. I'm having problems using the library_upload_dir.py script to automatically upload data to a Galaxy library. Does someone have experience with that? Particularly where exactlyt do I get the "library id" for this script? The one from the web-url (formed like Ff2dbxxxxxx1b3e ) gives Malformed library ID error by this script.
    I'm asking here, since it the script uses the bioblend to communicate with the galaxy server :)
    Nicola Soranzo
    @nsoranzo
    That's a library folder ID (all those starting with "F")
    You can also use ephemeris for data library upload
    (which wraps BioBlend in a script)
    Nicola Soranzo
    @nsoranzo
    Hi all, just a quick heads-up about 2 recent changes in the BioBlend repository on GitHub:
    • We changed the default branch from master to main
    • We moved the Continuous Integration (CI) from TravisCI to GitHub workflows (thanks to Oleg Zharkov!)
    Nolan Woods
    @innovate-invent
    Why the change from master to main?
    Nicola Soranzo
    @nsoranzo
    @innovate-invent galaxyproject/galaxy#10850
    Nolan Woods
    @innovate-invent
    Huh, I wasn't aware git was on that bandwagon
    Andrew Mcgregor
    @Mcgregor381
    @simonbray
    Simon Bray
    @simonbray
    Hello
    (You can also send me a PM if you want?)
    Nicola Soranzo
    @nsoranzo
    Forgot to mention here that BioBlend 0.15.0 was released about 3 weeks ago, see https://github.com/galaxyproject/bioblend/releases/tag/v0.15.0 for the Changelog. As usual, it's available also on PyPI and Bioconda.
    Björn Grüning
    @bgruening
    :100:
    Nicola Soranzo
    @nsoranzo
    @mvdbeek (or any other with experience with this) Do you think it would make sense to add Py3 type annotations to the BioBlend API?
    Marius van den Beek
    @mvdbeek
    I think overall that's a good idea, but if I had to prioritize time and effort I’d explore in how far bioblend can take advantage of the openapi schema to do some semi-automated typing ?
    Nicola Soranzo
    @nsoranzo
    For now I'll create an issue :)
    Simon Bray
    @simonbray:matrix.org
    [m]
    Hello, it seems there's no way in bioblend to (un)publish a dataset, is that correct? The relevant API seems to be https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/history_contents.py#L579, not sure if there is another way
    dkolbe
    @dkolbe
    Hi - I'm running workflows using invoke_workflow and need to set some explicit parameters in the code rather in the workflow UI. Using the params={TOOL_ID: PARAM_DICT, ...} (deprecated I know) is working well when the step in question is in the top-level workflow, but not when it is nested in a subworkflow (bioblend v0.15). In a subworkflow, the parameter gets set to things like "ltgalaxy.tools.parameters.basic.RuntimeValue object at 0x7fd582cefed0gt". I noticed this function has a new parameters_normalized option in the pre-release dev code that explicitly mentions subworkflows - is this likely to solve my issue? Or should I investigate other fixes? Identify the step ID and switching to the newer params format?
    Nicola Soranzo
    @nsoranzo
    @simonbray:matrix.org Do you have any suggestion here? ^
    Simon Bray
    @simonbray:matrix.org
    [m]
    @dkolbe your issue sounds similar to this one: galaxyproject/bioblend#321
    so I think it might help. Do you get the same error message as reported in that issue?
    dkolbe
    @dkolbe
    No, actually I don't get an error at all, just the parameter getting set to a python object description rather than my variable's value. However, I'm connecting to a notably old Galaxy server version - 18.09, so there may be significant differences in handling on that end? (Clinical use means stuff gets frozen in place once it's approved; we are planning a current server build this year. Some of the other improvements should give me support for variables as input parameters; just had been hoping to get stuff done in the meantime.)
    Simon Bray
    @simonbray:matrix.org
    [m]
    I'm not sure I have any good ideas but maybe this issue is related: galaxyproject/galaxy#2007
    dkolbe
    @dkolbe
    I seem to have gotten it working for now with some combination of explicitly specifying the step ids and using the current dev codebase. This note was helpful on how to describe subworkflow params galaxyproject/bioblend#322
    Björn Grüning
    @bgruening
    @dkolbe glad its working.
    If you have some time, please feel free to spin up a PR with docs improvements