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Removing export that pollutes conda env PATH #16009

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merged 3 commits into from
Jun 19, 2019

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eggzilla
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@eggzilla eggzilla commented Jun 19, 2019

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  • 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).

@eggzilla eggzilla requested a review from dpryan79 June 19, 2019 11:50
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biocondabot bot commented Jun 19, 2019

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

Arch Package Repodata
linux-64 blast-2.9.0-pl526h979a64d_3.tar.bz2 repodata.json
osx-64 blast-2.9.0-pl526hae12ce6_3.tar.bz2 repodata.json

You may also use conda to install these:

  • For packages in linux-64:
    conda install -c https://62100-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>
    
  • For packages in osx-64:
    conda install -c https://62108-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>
    

Docker image(s) built:

Package Tag Install with docker
blast 2.9.0--pl526h979a64d_3
showcurl "https://62100-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/blast%3A2.9.0--pl526h979a64d_3.tar.gz" | gzip -dc | docker load

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Hi, i commented out following export in get_species_taxids.sh
export PATH=/bin:/usr/bin:/am/ncbiapdata/bin:$HOME/edirect:$PATH
After executing the command my environment has the system perl in the PATH with higher precedence than the one in the conda env. The script also works without this export.

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Can you bump the build number?

@eggzilla
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I already did, it now strangely fails due to linting problems in other recipes.
Thanks for the quick response :-)

@dpryan79
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@christiam Can you have a look at this? I think it's fine but it'd be best if you had a look as well :)

@dpryan79
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I don't understand the linter some times, at least we can ignore that.

@cjandrasits cjandrasits mentioned this pull request Jun 19, 2019
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@christiam Can you have a look at this? I think it's fine but it'd be best if you had a look as well :)

Changes look fine to me, thanks!

@dpryan79 dpryan79 merged commit cf3c4d2 into bioconda:master Jun 19, 2019
kpalin pushed a commit to kpalin/bioconda-recipes that referenced this pull request Aug 7, 2019
* Removing export that pollutes conda env PATH

* Incremented build nr
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3 participants