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Fix TIDDIT #18971

Merged
merged 9 commits into from
Nov 29, 2019
Merged

Fix TIDDIT #18971

merged 9 commits into from
Nov 29, 2019

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dpryan79
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Bioconda requires reviews prior to merging pull-requests (PRs). To facilitate this, once your PR is passing tests and ready to be merged, please add the please review & merge label so other members of the bioconda community can have a look at your PR and either make suggestions or merge it. Note that if you are not already a member of the bioconda project (meaning that you can't add this label), please ping @bioconda/core so that your PR can be reviewed and merged (please note if you'd like to be added to the bioconda project). Please see #15332 for more details.

  • I have read the guidelines for bioconda recipes.
  • This PR adds a new recipe.
  • AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
  • This PR updates an existing recipe.
  • This PR does something else (explain below).

@dpryan79 dpryan79 mentioned this pull request Nov 28, 2019
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I think we're overwriting the TIDDIT script.

@dpryan79 dpryan79 changed the title Fix TIDDIT Fix TIDDIT (do not merge) Nov 28, 2019
@dpryan79 dpryan79 added the WIP label Nov 28, 2019
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@bioconda-bot please fetch artifacts

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Package(s) built on CircleCI are ready for inspection:

Arch Package Repodata
linux-64 tiddit-2.8.1-py27hb3f55d8_2.tar.bz2 repodata.json
linux-64 tiddit-2.8.1-py36hb3f55d8_2.tar.bz2 repodata.json
linux-64 tiddit-2.8.1-py37hb3f55d8_2.tar.bz2 repodata.json

You may also use conda to install these:

  • For packages on linux-64:
conda install -c https://84518-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

conda install -c https://84518-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

conda install -c https://84518-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag Install with docker
tiddit 2.8.1--py27hb3f55d8_2
showcurl "https://84518-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/tiddit%3A2.8.1--py27hb3f55d8_2.tar.gz" | gzip -dc | docker load
tiddit 2.8.1--py36hb3f55d8_2
showcurl "https://84518-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/tiddit%3A2.8.1--py36hb3f55d8_2.tar.gz" | gzip -dc | docker load
tiddit 2.8.1--py37hb3f55d8_2
showcurl "https://84518-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/tiddit%3A2.8.1--py37hb3f55d8_2.tar.gz" | gzip -dc | docker load

@maxulysse
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Thanks a lot for looking into it

@dpryan79 dpryan79 changed the title Fix TIDDIT (do not merge) Fix TIDDIT Nov 28, 2019
@dpryan79 dpryan79 removed the WIP label Nov 28, 2019
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@bioconda-bot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Nov 28, 2019
mbargull
mbargull reviewed Nov 29, 2019
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recipes/tiddit/build.sh
echo $PREFIX

mkdir build
cd build
cmake ..
make
cp ../bin/TIDDIT $PREFIX/bin
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Should a tiddit symlink for the be created?

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I don't think so, they don't seem to use it in their documentation that I noticed. I think I added that last time by accident.

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Okay, then change the test to use TIDDIT?

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Crap, I forgot to reenable the tests. Nevermind on this one.

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Actually that won't hurt anything and I guess they mention it in the conda section.

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Yes, no, what? Now I'm confused, hehe.

Well, in their docs they mention tiddit in the context of Bioconda: https://github.com/SciLifeLab/TIDDIT/blame/TIDDIT-2.8.1/README.md#L36

So, probably run tiddit --help in the tests to make sure that works?

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It's a symlink to the python script :)

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Yeah, I saw that. I just meant testing tiddit to avoid regressions if that symlink might be accidentally removed in the future.

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@bioconda-bot please fetch artifacts

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Package(s) built on CircleCI are ready for inspection:

Arch Package Repodata
linux-64 tiddit-2.8.1-py27hb3f55d8_2.tar.bz2 repodata.json
linux-64 tiddit-2.8.1-py36hb3f55d8_2.tar.bz2 repodata.json
linux-64 tiddit-2.8.1-py37hb3f55d8_2.tar.bz2 repodata.json

You may also use conda to install these:

  • For packages on linux-64:
conda install -c https://84599-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

conda install -c https://84599-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

conda install -c https://84599-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag Install with docker
tiddit 2.8.1--py27hb3f55d8_2
showcurl "https://84599-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/tiddit%3A2.8.1--py27hb3f55d8_2.tar.gz" | gzip -dc | docker load
tiddit 2.8.1--py36hb3f55d8_2
showcurl "https://84599-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/tiddit%3A2.8.1--py36hb3f55d8_2.tar.gz" | gzip -dc | docker load
tiddit 2.8.1--py37hb3f55d8_2
showcurl "https://84599-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/tiddit%3A2.8.1--py37hb3f55d8_2.tar.gz" | gzip -dc | docker load

@dpryan79 @mbargull
Update recipes/tiddit/meta.yaml
0d689db 
Co-Authored-By: Marcel Bargull <mbargull@users.noreply.github.com>
@dpryan79
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@bioconda-bot please merge

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I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.

@BiocondaBot BiocondaBot merged commit d001dfc into master Nov 29, 2019
@BiocondaBot BiocondaBot deleted the fix_tiddit branch November 29, 2019 14:53
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@dpryan79 @BiocondaBot @maxulysse @mbargull