Add carveme

[lhtxa]

Hi @bgruening !
I saw your previous comments, it just took me a little time to review and fix the issues.
Thank you for the suggestions, here is the updated wrapper.

[bgruening]

Can you please reduce the size of the test data? Then please look at the failing linting tests ...

 .. WARNING: Missing shed metadata field [remote_repository_url] for repository
.. WARNING: Missing shed metadata field [homepage_url] for repository

[bgruening]

https://anaconda.org/bioconda/carveme/files 1.6.1 is the version that you need.

[bgruening]

We now have this error message:

/usr/local/lib/python3.12/site-packages/reframed/core/parser.py:9: SyntaxWarning: invalid escape sequence '\w'
  id_re = '[a-zA-Z]\w*'
/usr/local/lib/python3.12/site-packages/reframed/core/parser.py:10: SyntaxWarning: invalid escape sequence '\d'
  pos_float_re = '\d+(?:\.\d+)?(?:e[+-]?\d+)?'
/usr/local/lib/python3.12/site-packages/reframed/core/parser.py:11: SyntaxWarning: invalid escape sequence '\d'
  float_re = '-?\d+(?:\.\d+)?(?:e[+-]?\d+)?'
/usr/local/lib/python3.12/site-packages/reframed/core/parser.py:13: SyntaxWarning: invalid escape sequence '\s'
  compound = '(?:' + pos_float_re + '\s+)?' + id_re
/usr/local/lib/python3.12/site-packages/reframed/core/parser.py:14: SyntaxWarning: invalid escape sequence '\s'
  expression = compound + '(?:\s*\+\s*' + compound + ')*'
/usr/local/lib/python3.12/site-packages/reframed/core/parser.py:15: SyntaxWarning: invalid escape sequence '\['
  bounds = '\[\s*(?P<lb>' + float_re + ')?\s*,\s*(?P<ub>' + float_re + ')?\s*\]'
/usr/local/lib/python3.12/site-packages/reframed/core/parser.py:15: SyntaxWarning: invalid escape sequence '\s'
  bounds = '\[\s*(?P<lb>' + float_re + ')?\s*,\s*(?P<ub>' + float_re + ')?\s*\]'
/usr/local/lib/python3.12/site-packages/reframed/core/parser.py:15: SyntaxWarning: invalid escape sequence '\s'
  bounds = '\[\s*(?P<lb>' + float_re + ')?\s*,\s*(?P<ub>' + float_re + ')?\s*\]'
/usr/local/lib/python3.12/site-packages/reframed/core/parser.py:17: SyntaxWarning: invalid escape sequence '\s'
  reaction = '^(?P<reaction_id>' + id_re + ')\s*:' + \
/usr/local/lib/python3.12/site-packages/reframed/core/parser.py:18: SyntaxWarning: invalid escape sequence '\s'
  '\s*(?P<substrates>' + expression + ')?' + \
/usr/local/lib/python3.12/site-packages/reframed/core/parser.py:19: SyntaxWarning: invalid escape sequence '\s'
  '\s*(?P<direction>-->|<->)' + \
/usr/local/lib/python3.12/site-packages/reframed/core/parser.py:20: SyntaxWarning: invalid escape sequence '\s'
  '\s*(?P<products>' + expression + ')?' + \
/usr/local/lib/python3.12/site-packages/reframed/core/parser.py:21: SyntaxWarning: invalid escape sequence '\s'
  '\s*(?P<bounds>' + bounds + ')?' + \
/usr/local/lib/python3.12/site-packages/reframed/core/parser.py:22: SyntaxWarning: invalid escape sequence '\s'
  '\s*(?P<objective>' + objective + ')?$'
/usr/local/lib/python3.12/site-packages/reframed/core/parser.py:24: SyntaxWarning: invalid escape sequence '\s'
  self.regex_compound = compile('(?P<coeff>' + pos_float_re + '\s+)?(?P<met_id>' + id_re + ')')
diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 4
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Database input file: /usr/local/lib/python3.12/site-packages/carveme/data/generated/bigg_proteins.faa
Opening the database file... 
Error opening file /usr/local/lib/python3.12/site-packages/carveme/data/generated/bigg_proteins.dmnd: Permission denied
Read-only file system
Error: Error opening temporary file /tmp/tmpu9rg1smj/files/5/1/7/diamond-tmp-tX5Q7D

[bgruening]

You can find the planemo output here: https://github.com/bgruening/galaxytools/actions/runs/9806570824?pr=1446

[lhtxa]

@bgruening, the first time CarveMe runs, it creates a database with Diamond. It seems the error is due to the lack of permissions to write that database in CarveMe's directory because when testing there, it is only allowed to write in the working directory. Do you have any suggestions to work around this?

[bgruening]

In which folder does careme treis to write?

Only the CWD is writeable in a container setting - which we are testing here.

[lhtxa]

It seems it is inside the CarveMe folder itself. In 'carveme/data/generated/'

[bgruening]

That is not allowed. Galaxy is a multi user system and we need to ensure every user can only write to the current job working dir

[bgruening]

Do you need help here?

[lhtxa]

Maybe. The first time CarveMe runs it needs to write in its directory, out of the user's working directory. I understand this is incompatible with the Galaxy user system, so I am thinking of a way to work around it. One possibility is to have a parallel version of CarveMe just to be compatible with Galaxy, another is to keep just one version of the tool and deal with this issue in the next update, but I am waiting for some feedback on this from collaborators. If you have any suggestions, please let me know.

…

________________________________ From: Björn Grüning ***@***.***> Sent: Saturday, July 13, 2024 7:57 PM To: bgruening/galaxytools ***@***.***> Cc: Miguel Alves Magalhaes Teixeira ***@***.***>; Author ***@***.***> Subject: Re: [bgruening/galaxytools] Add carveme (PR #1446) Do you need help here? — Reply to this email directly, view it on GitHub<#1446 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AV7E3QHHDCWFYQSODLEYYB3ZMF2BHAVCNFSM6AAAAABKLKTBX2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRXGA2DMNJVGM>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[bgruening]

Imho a tool installation should be read-only and during runtime no one should be allowed to write into it. This is necessary for reproducibility and to have clean installation environments.

[lhtxa]

I understand that. I will be back on this as soon as possible.

…

________________________________ From: Björn Grüning ***@***.***> Sent: Sunday, July 14, 2024 1:10 PM To: bgruening/galaxytools ***@***.***> Cc: Miguel Alves Magalhaes Teixeira ***@***.***>; Author ***@***.***> Subject: Re: [bgruening/galaxytools] Add carveme (PR #1446) Imho a tool installation should be read-only and during runtime no one should be allowed to write into it. This is necessary for reproducibility and to have clean installation environments. — Reply to this email directly, view it on GitHub<#1446 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AV7E3QC4HFHT6IEML5UMC7DZMJTCZAVCNFSM6AAAAABKLKTBX2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRXGMZDGOJZGM>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[bgruening]

@lhtxa anything we can help here?

[lhtxa]

Hi! We will make some other changes that are taking some more time. Should I keep this branch, or is it better to remove it until we move forward with the changes we need to implement?

…

________________________________ From: Björn Grüning ***@***.***> Sent: Thursday, August 15, 2024 6:09 PM To: bgruening/galaxytools ***@***.***> Cc: Miguel Alves Magalhaes Teixeira ***@***.***>; Mention ***@***.***> Subject: Re: [bgruening/galaxytools] Add carveme (PR #1446) @lhtxa<https://github.com/lhtxa> anything we can help here? — Reply to this email directly, view it on GitHub<#1446 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AV7E3QGOMNNAU3JN3PBVQKDZRTOGJAVCNFSM6AAAAABKLKTBX2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJRG4ZTQMRVGA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[SaimMomin12]

Hi @lhtxa, you can mark this PR as draft. Please feel to let us know if you know any help with the tool integration.