KRONA: link to "updateAccessions.sh" needs to be placed in PATH during install

[jvollme]

Issue #1527 already dealt with placing a link to "updateTaxonomy.sh" in PATH during installation (renaming it as "ktUpdateTaxonomy" to avoid name-conflicts.

However, the same needs to be done for "updateAccessions.sh", which is needed to get reliable Taxonomy information from e.g. BLAST results (perhaps renaming the link as "ktUpdateAccessions"?)

[yesimon]

Sounds good. Feel free to submit a PR and I'll merge it.

[jvollme]

Hi, thanks. Will try to do so, but may need a little help...

I created a fork, made the changes locally in a new branch and started running the recommended tests using the "Circle CI client method" and the "bootstrapping method" described in the bioconda guidelines.

I do not know exactly what behavior to expect from these tests (sorry not a trained Informatician here), but i expect they should all pass without errors before i should push my changes and submit a pull-request, right?

However at the second step running bioconda-utils lint recipes config.yml --git-range master gives me the following error:

18:21:59 BIOCONDA INFO Recipes to consider according to git: 
recipes/krona/2.5
 recipes/krona/2.5
 recipes/krona/2.6
 recipes/krona/2.6
 recipes/krona
 recipes/krona
18:21:59 BIOCONDA INFO Recipes to lint:
recipes/krona
 recipes/krona/2.5
 recipes/krona/2.6
Setting build platform. This is only useful when pretending to be on another platform, such as for rendering necessary dependencies on a non-native platform. I trust that you know what you're doing.
Multiple meta.yaml files found. The meta.yaml file in the base directory will be used.
Adding in variants from internal_defaults
Adding in variants from /tmp/miniconda/miniconda/conda_build_config.yaml
Adding in variants from /tmp/miniconda/miniconda/lib/python3.6/site-packages/bioconda_utils/bioconda_utils-conda_build_config.yaml
18:22:01 BIOCONDA ERROR 

The following recipes failed linting. See https://bioconda.github.io/linting.html for details:

                                              failed_tests
recipe                                                    
recipes/krona                          [should_not_use_fn]
recipes/krona/2.5  [uses_perl_threaded, should_not_use_fn]
recipes/krona/2.6  [uses_perl_threaded, should_not_use_fn]

How can I fix this error, and how should i proceed?

[yesimon]

The recipe should be migrated to conda3 with the removal of the fn section in the source section of meta.yaml. Perhaps your fork is out of date? A git pull should resolve that.

[jvollme]

Well the fork is new (created and pulled just now), but I forgot that I am using conda2 (silly really, but i am used to pyhton 2.7 and having that as the default python seemed good at the time). So in order to create, modify and test recipes i should be using conda3?

[yesimon]

Yes, bioconda recently migrated to conda 3 build. You can still use python2.7 in your personal conda environment. conda 3 is only used for building packages.

[jvollme]

OK, thanks. I'll switch to conda3 and retry (not today though). BTW on a related note: is there any chance i can just export/import my existing environments from conda2 to conda3 (so i can just keep on working on my projects seamlessly)?

[yesimon]

You don't need to do anything to maintain working on your projects. conda-build 3 is used for building packages. Anaconda and miniconda are package managers which maintain your packages in your projects - they don't need conda-build at all if you're just using packages.