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  • Jan 31 2019 17:58
    jorgemachucav starred galaxyproject/tools-iuc
  • Jan 31 2019 17:45
    bebatut opened #2270
  • Jan 31 2019 16:18
    cpreviti synchronize #2267
  • Jan 31 2019 14:15
    cpreviti synchronize #2267
  • Jan 31 2019 12:42
    bernt-matthias review_requested #2269
  • Jan 31 2019 12:42
    bernt-matthias edited #2269
  • Jan 31 2019 12:41
    bernt-matthias edited #2269
  • Jan 31 2019 12:40
    bernt-matthias synchronize #2269
  • Jan 31 2019 12:13
    cpreviti commented #2267
  • Jan 31 2019 12:07
    nsoranzo commented #2267
  • Jan 31 2019 12:01
    cpreviti synchronize #2267
  • Jan 31 2019 11:21
    cpreviti synchronize #2267
  • Jan 31 2019 09:47
    cpreviti synchronize #2267
  • Jan 31 2019 09:27
    cpreviti synchronize #2267
  • Jan 30 2019 20:38
    bernt-matthias commented #2131
  • Jan 30 2019 20:19
    hepcat72 commented #2239
  • Jan 30 2019 19:50
    lparsons commented #2239
  • Jan 30 2019 18:36
    bgruening commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2268
  • Jan 30 2019 15:23
    nsoranzo commented #2267
M Bernt
@bernt-matthias:matrix.org
[m]

Tunc Kayikcioglu: I think that is basically the way to go.

Problem is that you can (probably) not simply add a new column to an existing data table because either admins would need to update old entries (adding some mock value to the new column) or Galaxy would need a way to return a default value if a column is accessed that does not exist in the requested row (I'm not sure if this actually works .. but I doubt it).

So, you can't propagate to old versions.

What we did before is to create a new datatable that contains the new version column.

Tunc Kayikcioglu
@kayikci:matrix.org
[m]
Thanks a lot for your reply. Yes, so there is now indeed a new table named "abc_versioned.table" in addition to "abc.table", this does not seem to mess up with the old versions already installed on the system. However, this does not block the users of the old tool from mistakenly providing a the new version of the DB.
M Bernt
@bernt-matthias:matrix.org
[m]
with "old tool" you mean the data manager?
Btw. is this for metaphlan? .. Asking because I also just stumbled over this galaxyproject/tools-iuc#5050 .. Seems to be a quite annoying tool since with v4 of the tool old data can't be downloaded (e.g. mpa_v30_CHOCOPhlAn_201901).
M Bernt
@bernt-matthias:matrix.org
[m]

with "old tool" you mean the data manager?

If we deprecate it, then nobody can add new entries to the select ..

kayikci
@kayikci:matrix.org
[m]
Yes, my question is about metaphlan. Its v4 downloads DB from biobakery4 URL, v3 from biobakery3 URL. As such, it should not be possible to simply pull the old DB by passing its name as a string anymore.
M Bernt
@bernt-matthias:matrix.org
[m]
I guess this is a bug, otherwise the --mpa3 parameter does not make much sense .. or?
1 reply
M Bernt
@bernt-matthias:matrix.org
[m]

Just checked. The --mpa3 flag allows you to use old databases (I had a user error report who wanted to use metaphlan4 with an old database .. and new databases can't be downloaded at the moment since the new data manager has not been deployed to the toolshed).

So my suggestion would be to ask upstream if they plan to make the old databases available. Then we would need to create a new data table supporting the version .. and trigger --mpa3 if a v3 database is selected.

Alternatively, we could decide to not support --mpa3 and only use the v4 DB (which still would require the new data table .. be safe for the future).

If you like we can continue elsewhere .. e.g. in an issue/PR .. if you like. Just ping me.

M Bernt
@bernt-matthias:matrix.org
[m]
Hi IUC .. I just disabled "rebase merge" in the repo settings .. as a preparation for galaxyproject/tools-iuc#5047
M Bernt
@bernt-matthias:matrix.org
[m]
Now that this is merged I would like to triple check that this works. Is there an easy way to test if failing deployment triggers a message to the PR. I could simply invalidate the TTS API key (but I can not reset it later .. since I do not know it). Does anyone has a PR to merge these days?
Marius
@mvdbeek:matrix.org
[m]
Could I get a 👍️ on galaxyproject/tools-iuc#5062 ? Trying to get the weekly tests to finish again
CristĂłbal Gallardo
@gallardoalba:matrix.org
[m]
Hi all, I found a problem when trying to extract elements from a collection consisted in heterogeneous datatypes; does somebody knows why the collection from is history https://assembly.usegalaxy.eu/u/gallardoalba/h/unnamed-history is not recognised by https://assembly.usegalaxy.eu/root?tool_id=__EXTRACT_DATASET__? Thanks a lot!
CristĂłbal Gallardo
@gallardoalba:matrix.org
[m]
Hi all! It would be great if somebody could review the PR for including IsoformSwitchAnalyzeR galaxyproject/tools-iuc#5009, thanks a lot!
CristĂłbal Gallardo
@gallardoalba:matrix.org
[m]
The object_name_linter function of lintr that evaluates if the names are snake case or symbols seems to be very problematic in some cases, do you think it is fine to disable it from the lintr workflow?
Nicola Soranzo
@nsoranzo:matrix.org
[m]
Can someone with privileges change the default branch of https://github.com/planemo-autoupdate/tools-iuc to main ? I think that's what causing the planemo autoupdate GitHub workflows to fail for tools-iuc
2 replies
Simon Bray: maybe? ^
M Bernt
@bernt-matthias:matrix.org
[m]

No idea CristĂłbal Gallardo why the collection is not shown. Just checked on my 22.01 and 22.05 instances with a collection containing a fasta and a txt .. without any problems.

Can you try with such a toy example?

Or download the collection and reupload (maybe also to another galaxy) ..

1 reply
Hi all, I found a problem when trying to extract elements from a collection consisted in heterogeneous datatypes; ...
CristĂłbal Gallardo
@gallardoalba:matrix.org
[m]
Ah! Thanks a lot!
Marius
@mvdbeek:matrix.org
[m]
Should we have a Expression Tools or Workflow Tools category on the tool shed ?
I think we should export the existing pick_value expression tool to the IUC, and I really can't think of a matching category (plus some of the other existing expression tools are rather odd fits in the text manipulation category)
Lucille Delisle
@lldelisle
I have a technical question (do not hesitate to reply in a thread so we don't loose Marius' question). I would like to preview the help of a tool which includes images. How can I specify the path of the image to have it displayed with planemo serve?
Marius
@mvdbeek:matrix.org
[m]
I'd look at working tools, like bedtools
(To just verify it's not the serve that is broken)

The image itself is embedded with

.. image:: $PATH_TO_IMAGES/flank-glyph.png

.. class:: warningmark

and the images are in static/images

Lucille Delisle
@lldelisle
Yes but when I run planemo serve with pygenometracks I don't see the image while I see it here: https://usegalaxy.org/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fpygenometracks%2FpygenomeTracks%2F3.7%2Bgalaxy0&version=3.7%20galaxy0
(I ran planemo serve which took version 22.05)
4 replies
Marius
@mvdbeek:matrix.org
[m]
I remember now, we have a special route handling for tools installed from the toolshed, and those tools when served by planemo are just local tools
You could enhance planemo to copy those images into static/images when running a managed instance
Lucille Delisle
@lldelisle
Which static/images should it be copied to?
Marius
@mvdbeek:matrix.org
[m]
in the galaxy root
Lucille Delisle
@lldelisle
OK let me try
Lucille Delisle
@lldelisle
The following image definitions are all supported.  The former $PATH_TO_IMAGES is no longer
        required, and is now ignored.
        .. image:: https://raw.github.com/galaxy/some_image.png
        .. image:: $PATH_TO_IMAGES/some_image.png
        .. image:: /static/images/some_image.gif
        .. image:: some_image.jpg
        .. image:: /deep/some_image.png
This is super interesting and should be somewhere in tools-iuc.
Lucille Delisle
@lldelisle
I managed to do it manually... I just need to implement it into planemo...
M Bernt
@bernt-matthias:matrix.org
[m]

Huh:

The job was not started because recent account payments have failed or your spending limit needs to be increased. Please check the 'Billing & plans' section in your settings.

https://github.com/galaxyproject/tools-iuc/actions/runs/4008074858

Michelle Savage
@michellesavage:matrix.org
[m]
M Bernt: maybe a github third-party webhook app (for instance, Jenkins) needs updated billing? That is just a guess.
bgruening
@bgruening:matrix.org
[m]
did our academic account run out?
Marius
@mvdbeek:matrix.org
[m]
Seems to be running again, maybe an intermittent problem ?
M Bernt
@bernt-matthias:matrix.org
[m]
Seems so
Greg Von Kuster
@gvonkuster:matrix.org
[m]
I've seen recent activity with the iuc-owned amrfinderplus data manager tool https://toolshed.g2.bx.psu.edu/view/iuc/amrfinderplus_data_manager_build/eea0c38a9afd. Is this tool used with the thanhlv-owned amrfinderplus tool https://toolshed.g2.bx.psu.edu/view/thanhlv/amrfinderplus/a9e5d593228e?
M Bernt
@bernt-matthias:matrix.org
[m]
Greg Von Kuster: question is if it uses the same data table.
Greg Von Kuster
@gvonkuster:matrix.org
[m]
The iuc-owned data manager uses amrfinderplus_database and the thanhlv tool uses amrfinder_databases, so they are not using the same data table. I guess the question I'm asking is how is the iuc-owned data manager being used in Galaxy instances if there is no tool that uses the associated data table? Does the iuc want an amrfinderplus tool in the iuc repo, or is there already a tool in anther 3rd party repo?
M Bernt
@bernt-matthias:matrix.org
[m]
tools/bakta/bakta.xml uses it as grep amrfinderplus_database tools -r --include "*xml" revealed
Maybe @pimarin nows something?
wm75 (Wolfgang Maier)
@wm75:matrix.org
[m]
The idea is that bakta can reuse the amrfinderplus_database instead of downloading it again as part of its own data management. This was actually partly my idea, then implemented by @pimarin.
gloomtoto
@gloomtoto:matrix.org
[m]
Hi everyone, as mentioned by wm75 (Wolfgang Maier), bakta tool need to build a database by integrating amrfinderplus database, but the thanhlv datamanager was just an update of the last version of amrfinderplus so we can’t fix the specific version of amrfinderplus, that’s why I decided to submit another datamanager available with bakta and also with a choice of the amrfinderplus en version to download
I think it could be work with other tools but I didn’t test it
Greg Von Kuster
@gvonkuster:matrix.org
[m]
Thanks for the info on this. I'm planning to wrap the amrfinderplus tool for Galaxy, so I'll be using the data manager for it.