update proteinortho v6.2.3 and some changes to the xml #5184

pmjklemm · 2023-03-10T16:23:59Z

update to 6.2.0

FOR CONTRIBUTOR:

- I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
- License permits unrestricted use (educational + commercial)
- This PR adds a new tool or tool collection
- This PR updates an existing tool or tool collection
- This PR does something else (explain below)

pmjklemm · 2023-03-10T16:24:54Z

Current problems:

Citations do not work (https://usegalaxy.eu/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fproteinortho%2Fproteinortho%2F6.1.2%2Bgalaxy1&version=6.1.2%20galaxy1)
Unsuccessful tests found, inspect the 'All tool test results' artifact for details.
- where do i find these artefacts?
- resolve NameMapper.NotFound: cannot find 'evalue'
- test 1-3 fail with error code 1, no output

bernt-matthias · 2023-03-10T22:07:43Z

The artifacts are here: https://github.com/galaxyproject/tools-iuc/actions/runs/4386446633

You can find them if you go to any of the tests and there go to the summary page.

pmjklemm · 2023-03-11T17:03:00Z

Thank you!
I screened through the JSON output and found NameMapper.NotFound: cannot find 'evalue', I will try to investigate this.

bernt-matthias · 2023-03-11T17:12:22Z

tools/proteinortho/proteinortho.xml

        <section name="more_options" title="Additional Options" expanded="False">
+            <param argument="--evalue" type="float" value="0.001" min="0" label="E-value threshold of the blast algorithm" help="Larger values results in more false positives (connections between proteins)."/>


For consistency I would use $more_options.evalue in the command block (even if $evalue should work as well).

ahh ok, so since these options are nested in the more_options sections, the env var needs this too, I will add this to the xml

Do the test also need this? ~~So e.g. <param name="evalue" value="1"/> needs to be <param name="more_options.evalue" value="1"/> ?~~
I just saw that diamond wraps the nested params in the same section tags, so this is probably the solution for this problem here

bernt-matthias · 2023-03-11T17:13:47Z

I screened through the JSON output

The html output is easier to read (if you click on failed / errored tests below the table the failing tests are shown).

pmjklemm · 2023-03-11T22:08:57Z

OK, i managed to pass all test when removing C2.faa (only for diamond).
C2.faa is designed to make some trouble as the sequences as well as the names are strange but this should be catched by proteinortho and fixed using --ignore-warnings flag.
But the test fails using diamond makedb (using different version) with the error Option is not permitted for this workflow: ignore-warnings.
This error is neither thrown on my computer (linux) nor on a osx system ...

tools/proteinortho/proteinortho.xml

bernt-matthias · 2023-03-12T08:42:16Z

Cool. Looks good to me.

For the problem with the citations I would suggest to check if they also appear if you start a local instance with planemo serve.

I was also wondering if it would be better to include all the requirements in the bioconda recipe? But we don't have to do it now. Advantage would be that they would be included in the container that is built by bioconda.. And we could avoid building yet another container over here.

bernt-matthias · 2023-03-12T08:43:56Z

FYI: the linter warns (for the summary tool) : WARNING: Command template contains TODO text

pmjklemm · 2023-03-12T13:11:56Z

The requirements are optional and not mandatory (only diamond+lapack are required).
So, I do not want to include all of these alternative tools.

I can try to planemo serve but I will take some time to set this up.

Thanks for mentioning the TODO in summary, I will work on resolving this!

bernt-matthias

I checked the citations with planemo serve. They look good. So the problem seems to be at usegalaxy.eu. @bgruening can you check if something is wrong with the citations of proteinortho at the public server?

One last optional suggestion: you could set the column names metadata for the output tables:

tools-iuc/tools/featurecounts/featurecounts.xml

Line 458 in f6ccf9e

    
           <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.element_identifier}"/>

Leave this up to you. Just tell me if I should merge.

pmjklemm · 2023-03-13T10:11:41Z

planemo serve does not produce a localhost:9000 endpoint for me, not sure what is wrong. You just call planemo serve in the root directory of the tools-iuc right?

$ planemo serve
...
[2023-03-13 11:13:08 +0100] [3096343] [INFO] Waiting for application startup.                                                                                                                                                                                         
[2023-03-13 11:13:08 +0100] [3096343] [INFO] Application startup complete.                                                                                                                                                                                            
Exception in thread database_heartbeart_main.1.thread:                                                                                                                                                                                                                
Traceback (most recent call last):                                                                                                                                                                                                                                    
  File "/home/paul/miniconda3/envs/planemo/lib/python3.10/threading.py", line 1016, in _bootstrap_inner                                                                                                                                                               
    self.run()                                                                                                                                                                                                                                                        
  File "/home/paul/miniconda3/envs/planemo/lib/python3.10/threading.py", line 953, in run
...
  File "/home/paul/.planemo/gx_venv_3/lib/python3.10/site-packages/watchdog/observers/inotify_c.py", line 427, in _raise_error                                                                                                                                        
    raise OSError(errno.EMFILE, "inotify instance limit reached")                                                                                                                                                                                                     
OSError: [Errno 24] inotify instance limit reached

Update: I will try the planemo serve tools/proteinortho

I was not aware that you can put variables in the column_names, therefore I just omitted these. I will add those to the metadata, very nice!

bernt-matthias · 2023-03-13T10:14:26Z

planemo serve should be available at localhost:9090/. You should call it planemo serve tools/proteinortho or call it from with in the tool's directory. Otherwise planemo will server all tools in the IUC repos which will need more time.

bernt-matthias · 2023-03-13T10:19:53Z

tools/proteinortho/proteinortho.xml

+              from_work_dir="result.proteinortho.tsv">
+            <actions>
+                <action name="column_names" type="metadata"
+                    default="species,genes,alg.-conn.,${','.join([ f.element_identifier for f in $input_files ])}"/>


Lets see if this works. You should certainly check with planemo serve if this works out as expected. Maybe also include it in the tests https://docs.galaxyproject.org/en/master/dev/schema.html#tool-tests-test-output-metadata

There are even more advanced techniques for setting output metadata. For instance you can deposit a file galaxy.json in the working directory. That describes all sorts of output properties. Unfortunately this is largely undocumented https://planemo.readthedocs.io/en/latest/writing_advanced.html?highlight=galaxy.json#tool-provided-metadata

bernt-matthias · 2023-03-13T19:01:24Z

tools/proteinortho/proteinortho.xml

@@ -4,7 +4,6 @@
        <import>proteinortho_macros.xml</import>
        <xml name="test_outputs">
            <output name="proteinortho">
-                <metadata name="column_names" value="species,genes,alg.-conn.,${','.join([ f.element_identifier for f in $input_files ])}"/> 


I guess you could keep the metadata tag but you would need to replace ${','.join([ f.element_identifier for f in $input_files ])} with a specific list of columns for the respective test. If this list is not constant we can parametrize the macro.

Let me know if you need help with this.

pmjklemm · 2023-03-14T10:00:28Z

I think that is everything from my side!

bernt-matthias · 2023-03-14T17:54:54Z

Hi @pmjklemm I have a few more commits over here https://github.com/bernt-matthias/tools-iuc/tree/tools/proteinortho for some reason I can not push to your branch or open a PR against your fork (probably because you forked from the autoupdate fork).

If you like you can cherry pick them to here.

Mostly stricter tests regarding column and row numbers (please take check test 3 .. row numbers seem to change from call to call .. so I added delta).

Successful linting of the comment attribute of has_n_columns depends on galaxyproject/galaxy#15791 .. I hope that we can merge that in time ..

pmjklemm · 2023-03-14T19:09:42Z

Yes, I tried to push to the autoupdate branch of the last PR of proteinortho and realized that this is not possible.

Your additions look very good, I did take them all! And no hurry, we can wait on #15791 and merge afterwards.

pmjklemm · 2023-03-30T08:14:43Z

I will trigger a new test with v6.2.3 (just squashed in bioconda)

bernt-matthias

Still looks good. But we also still have the problem with the linter.

Btw. you can always trigger CI by closing and reopening a PR.

bernt-matthias · 2023-04-17T08:56:15Z

The linter problem should be fixed once galaxyproject/galaxy#15933 and galaxyproject/galaxy#15873 are merged and new python packages have been released. I'm not sure when this will happen .. people seem busy with the 23.0 release and courses.

Tell me if its pressing. Then we can merge and deploy manually.

pmjklemm · 2023-04-17T10:22:44Z

Tell me if its pressing. Then we can merge and deploy manually.

It is not urgent, I can wait. From time to time I will check if it merges, so that is no problem (:

bernt-matthias · 2023-06-16T20:20:13Z

Finally :) Thanks for all your efforts and patience.

planemo-autoupdate and others added 3 commits December 19, 2022 04:50

Updating tools/proteinortho from version 6.1.5 to 6.1.6

2c48f81

Updating tools/proteinortho from version 6.1.6 to 6.1.7

274f47c

update 6.2.0

c15bae7

pmjklemm changed the title ~~update proteinortho v6.2.0~~ update proteinortho v6.2.0 and some changes to the xml Mar 10, 2023

test

ab3b5f2

bernt-matthias reviewed Mar 11, 2023

View reviewed changes

Paul Klemm added 6 commits March 11, 2023 18:33

update test block with sections

b09844f

added diamond as p option for test1-3

4a50b12

update diamond

5a820db

test wo C.faa

fab286e

another test

e5176d6

w/o C2 diamond test

dbf7ee6

pmjklemm commented Mar 11, 2023

View reviewed changes

tools/proteinortho/proteinortho.xml Show resolved Hide resolved

resolved the TODO

f6547f6

resolved the TODO

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bernt-matthias approved these changes Mar 13, 2023

View reviewed changes

added column_names metadata

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bernt-matthias reviewed Mar 13, 2023

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Paul Klemm added 2 commits March 13, 2023 11:20

additional data tag xml

db4cf99

test metadata

327ec1e

without proteinortho.tsv test metadata

9f75c38

bernt-matthias reviewed Mar 13, 2023

View reviewed changes

Paul Klemm added 4 commits March 14, 2023 09:25

test metadata proteinortho.tsv

c2f99c2

forgot the new parameter -core

7875829

typos and some improvements to the help

6b74efa

order of fasta matters

1ac41c6

thanks bernt-matthias

8648d00

new version 6.2.2

b155c21

pmjklemm changed the title ~~update proteinortho v6.2.0 and some changes to the xml~~ update proteinortho v6.2.2 and some changes to the xml Mar 23, 2023

6.2.3

cbdff6b

pmjklemm changed the title ~~update proteinortho v6.2.2 and some changes to the xml~~ update proteinortho v6.2.3 and some changes to the xml Mar 30, 2023

trigger test

48c7407

pmjklemm requested a review from bernt-matthias April 2, 2023 10:25

bernt-matthias approved these changes Apr 2, 2023

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pmjklemm closed this Apr 11, 2023

pmjklemm reopened this Apr 11, 2023

pmjklemm closed this Apr 13, 2023

pmjklemm reopened this Apr 13, 2023

pmjklemm closed this Apr 17, 2023

pmjklemm reopened this Apr 17, 2023

bernt-matthias closed this May 22, 2023

bernt-matthias reopened this May 22, 2023

bernt-matthias merged commit b4d8b8d into galaxyproject:main Jun 16, 2023

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update proteinortho v6.2.3 and some changes to the xml #5184

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		<section name="more_options" title="Additional Options" expanded="False">
		<param argument="--evalue" type="float" value="0.001" min="0" label="E-value threshold of the blast algorithm" help="Larger values results in more false positives (connections between proteins)."/>

update proteinortho v6.2.3 and some changes to the xml #5184

update proteinortho v6.2.3 and some changes to the xml #5184

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