add new recipe selenzy_wrapper v0.0.4

[kenza12]

Describe your pull request here

Add recipe for selenzy_wrapper 0.0.4: Python wrapper of selenzy tool

https://github.com/brsynth/selenzy-wrapper/

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[BiocondaBot]

Artifacts built on CircleCI are ready for inspection:

Package(s)

Arch	Package	Repodata
noarch	selenzy_wrapper-0.0.4-pyhdfd78af_0.tar.bz2	repodata.json

---

You may also use conda to install these:

• For packages on noarch:

conda install -c https://174299-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

---

Container image(s)

Package	Tag	Install with docker
selenzy_wrapper	0.0.4--pyhdfd78af_0	show curl -L "https://174299-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/selenzy_wrapper%3A0.0.4--pyhdfd78af_0.tar.gz" | gzip -dc | docker load

[telatin]

Hello @kenza12, are you sure you need to restrict biopython to =1.77 only?

[kenza12]

Hello @telatin , I just update the recipe and added a new restriction for biopython >1.70,<=1.77 , I also added some tests but it failed for memory issues. Is there a limit for memory usage in bioconda ? If yes, is it possible to increase it ? Thanks for your work.

[telatin]

Hello @telatin , I just update the recipe and added a new restriction for biopython >1.70,<=1.77 , I also added some tests but it failed for memory issues. Is there a limit for memory usage in bioconda ? If yes, is it possible to increase it ? Thanks for your work.

Not that I'm aware, I usually put the more extensive tests on the repository CI and leave the bare minimum in conda to just check that the program runs / has the correct version. Is that a possibility?

[kenza12]

Hello @telatin , I just update the recipe and added a new restriction for biopython >1.70,<=1.77 , I also added some tests but it failed for memory issues. Is there a limit for memory usage in bioconda ? If yes, is it possible to increase it ? Thanks for your work.

Not that I'm aware, I usually put the more extensive tests on the repository CI and leave the bare minimum in conda to just check that the program runs / has the correct version. Is that a possibility?

Hi @telatin ,

Thanks for your feedback. I don’t think it’s a problem about checking the program version. It doesn’t need so much resources to do that.

And I got this error in the test session :

17:59:59 BIOCONDA INFO (OUT) OSError: [Errno 12] Cannot allocate memory
18:00:13 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmpnu7niyow/build_script.bash:/opt/build_script.bash -v /home/circleci/project/miniconda/conda-bld/:/opt/host-conda-bld -v /home/circleci/project/recipes/selenzy_wrapper:/opt/recipe -e LANG=en_US.UTF-8 -e HOST_USER_ID=1001 quay.io/bioconda/bioconda-utils-build-env-cos7:0.17.8 /bin/bash /opt/build_script.bash

18:00:13 BIOCONDA ERROR BUILD FAILED recipes/selenzy_wrapper
18:00:13 BIOCONDA INFO (COMMAND) conda build purge
18:00:14 BIOCONDA ERROR BUILD SUMMARY: of 1 recipes, 1 failed and 0 were skipped. Details of recipes and environments follow.
18:00:14 BIOCONDA ERROR BUILD SUMMARY: FAILED recipe recipes/selenzy_wrapper

Exited with code exit status 1

I see that bioconda use Linux Medium resources (2 CPU, 7.5 GB RAM), is that set automatically ? I don’t know if it needs to be rerun with larger resources maybe ? I’m a novice in bioconda and all CircleCI tests.

Thanks for your help.

Best wishes.

[kenza12]

Hi @telatin , @bioconda/core ,

Do you have any update about my issue please ?

Thanks for your time.

[BiocondaBot]

Reposting for @kenza12 to enable pings (courtesy of the BiocondaBot):

Hi @telatin , @bioconda/core ,

Do you have any update about my issue please ?

Thanks for your time.

[dpryan79]

Please don't run your full tests.

[dpryan79]

Also, is there no executable installed for this? Typically python packages would be executed like selenzy --help or something like that.

[kenza12]

Hi @dpryan79 ,

Thanks for your reply.

I tried to run only one test but it always returns the same memory error. Finally, we decided not to run tests and to only check the imports and the help command line: python -m selenzy_wrapper --help .
We don't have an executable selenzy --help , we execute the package with this command python -m selenzy_wrapper --help .

Thank your for your work.

[telatin]

Maybe in a future release adding a script to be invoked will make the tool more handy :)

[BiocondaBot]

Artifacts built on CircleCI are ready for inspection:

Package(s)

Arch	Package	Repodata
noarch	selenzy_wrapper-0.0.6-pyhdfd78af_0.tar.bz2	repodata.json

---

You may also use conda to install these:

• For packages on noarch:

conda install -c https://177362-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

---

Container image(s)

Package	Tag	Install with docker
selenzy_wrapper	0.0.6--pyhdfd78af_0	show curl -L "https://177362-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/selenzy_wrapper%3A0.0.6--pyhdfd78af_0.tar.gz" | gzip -dc | docker load

[telatin]

Tests issue bypassed