galaxy-iuc/iuc

Chat with the Intergalactic Utility Commission of Galaxy tool developers

pvanheus

@pvanheus

@bernt-matthias:matrix.org ok new Galaxy deploy and everything works fine... which means I can rewrite how I did the DM :)

M Bernt

@bernt-matthias:matrix.org

[m]

... with the next release you might have another opportunity to rewrite galaxyproject/galaxy#12941 ;)

pvanheus

@pvanheus

yep :) but at least I can write-out the $__app__ thing for now

wm75 (Wolfgang Maier)

@wm75:matrix.org

[m]

Since this came up twice within two days in our team: what's the current recommended way of using bio.tools and edam info in tool wrappers? Specify "bio.tools" as an xref, use <edam> or both?

Björn Grüning

@bgruening

only bio.tools

if there is no bio.tools, use edam directly

1 reply

both are not needed

wm75 (Wolfgang Maier)

@wm75:matrix.org

[m]

so a missing bio.tools record is the only valid reason to use edam?

So edam would be mostly for script-like things that we provide only via Galaxy? In other cases, I suppose it would be better to try to get them added to bio.tools?

Björn Grüning

@bgruening

so a missing bio.tools record is the only valid reason to use edam?

Yes, and even that we try to make simple that you can add you own bio.tools entries ... however, this will take more time

So edam would be mostly for script-like things that we provide only via Galaxy? In other cases, I suppose it would be better to try to get them added to bio.tools?

yes

With the system that John develops we get the recent and up-to-date EDAM tags from bio.tools

no need to annotate

Nicola Soranzo

@nsoranzo:matrix.org

[m]

Galaxy can derive the EDAM tags from bio.tools, so adding tools to bio.tools with EDAM annotations would be nice, but not a requirement.

Yep

wm75 (Wolfgang Maier)

@wm75:matrix.org

[m]

Thanks Nicola Soranzo bgruening !
https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html?highlight=edam#tool-cross-references could use rephrasing then?

Nicola Soranzo

@nsoranzo:matrix.org

[m]

That's a pretty new feature, so the section hasn't been updated, but a PR is welcome ;)

wm75 (Wolfgang Maier)

@wm75:matrix.org

[m]

ok, I'll see if I find some time for it next week

bgruening

@bgruening:matrix.org

[m]

Oh yes, we haven't updated this yet. Also we need to take into consideration that EDAM/bio.tools is bioinformatics driven. Its not excluding others, but its only "popular" in bioinformatics/bioimaging. So other communities are not well supported at the moment.

(they use EDAM terms (if they exists) directly, e.g. climate)

Nicola Soranzo

@nsoranzo:matrix.org

[m]

We need to move to all.tools :)

bgruening

@bgruening:matrix.org

[m]

;-)

pvanheus

@pvanheus

I personally find EDAM rather challenging to navigate (what to put exactly where) so I'm happy that bio.tools is an option :)

Lucille Delisle

@lldelisle

Hi,
I wanted to use the tool idr_download on my small galaxy instance with the omero instance of my institution but it seems that the omero version that idr_download uses is not compatible with the omero installed on my institution. I can connect to the omero instance of my institution using the last omero-py version but this version is not available on the channels used by galaxy (it is on the ome channel). Do you have any solution to "update" the tool in tools-iuc?
Thanks

Björn Grüning

@bgruening

You need 5.10?

@lldelisle you can upload the bioconda package if you like

and the bot will simply bump the tools in a few day, or we bump the IUC tool manually

bioconda/bioconda-recipes#28210

Lucille Delisle

@lldelisle

Thanks @bgruening I will check the PR.

bgruening

@bgruening:matrix.org

[m]

I will try to take care during on of my meetings

Lucille Delisle

@lldelisle

Thanks @bgruening:matrix.org but there is no emergency. Once it is updated in bioconda I will write a PR for the IUC tool because I wanted to add an option.

bgruening

@bgruening:matrix.org

[m]

galaxyproject/tools-iuc#4208

please vote IUC members

Matej Troják

@xtrojak:matrix.org

[m]

Hi,

I would like to ask about a specific input type. My tool takes as an input a list of elements from a fixed set of options. The point is that it is a list, i.e. the order is essential. Also, it would be cool if the user could change the order easily by moving the elements.

I have tried a solution using a param tag with type="select", but it only allows to select a subset with no information about the order. I have also considered the usage of the repeat tag in combination with a select, which, although laborious, would preserve the order. However, changing the order of selected values would be a pain.

Does anyone have an idea about a solution? Thank you!

M Bernt

@bernt-matthias

Could someone review galaxyproject/tools-devteam#561.. Ready since 10 month :(

bgruening

@bgruening:matrix.org

[m]

Go for it!

Simon Bray

@simonbray:matrix.org

[m]

Hi,
I would like to ask about a specific input type. My tool takes as an input a list of elements from a fixed set of options. The point is that it is a list, i.e. the order is essential. Also, it would be cool if the user could change the order easily by moving the elements.
I have tried a solution using a param tag with type="select", but it only allows to select a subset with no information about the order. I have also considered the usage of the repeat tag in combination with a select, which, although laborious, would preserve the order. However, changing the order of selected values would be a pain.
Does anyone have an idea about a solution? Thank you!

Matej Troják unfortunately the multiple option doesn't preserve order, as you have observed. I have had similar problems in the past, my solution was to use a dataset collection as input

Matej Troják

@xtrojak:matrix.org

[m]

Thank you Simon Bray for your answer! I will consider that option.

Nate Coraor

@natefoo:matrix.org

[m]

Please excuse my continual ignorance... I thought IUC tools had containers automatically built? This update to trinotate appears to have no corresponding container: https://github.com/galaxyproject/tools-iuc/pull/4189/files

galaxy.tool_util.deps.container_resolvers.mulled DEBUG 2021-12-07 15:14:53,787 [pN:main_w4_handler1,p:8809,tN:SlurmRunner.work_thread-0] Image name for tool toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.2.2+galaxy0: mulled-v2-5b53309c4f8449fec3814df567dbf53f97b59e8e:e28bbdedb596096aed9625f6662b8568960f36ca

nate@pdp-11% docker pull quay.io/biocontainers/mulled-v2-5b53309c4f8449fec3814df567dbf53f97b59e8e:e28bbdedb596096aed9625f6662b8568960f36ca
Error response from daemon: manifest for quay.io/biocontainers/mulled-v2-5b53309c4f8449fec3814df567dbf53f97b59e8e:e28bbdedb596096aed9625f6662b8568960f36ca not found: manifest unknown: manifest unknown