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phnmnl / container-galaxy-k8s-runtime

PhenoMeNal runtime for Galaxy running inside a container orchestrator
Apache License 2.0
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fixed configs #221

Closed ArturasG closed 6 years ago

ArturasG commented 6 years ago

Adding tameNMR.

The XMLs work and I am able to run the tools in the test environment. There are a couple of packages missing making a couple tools to not run properly but I'll modify the Dockerfile for the tool container asap (tonight). Other than that I think it should all be good.

korseby commented 6 years ago

Hi Arturas,

sorry I have missed your pull request here.

PR looks fine to me.

Instead of "latest" you probably should use the version of the container: dev_v1.0_cv0.5.9.

Best wishes, *Kristian

djcomlab commented 6 years ago

If this is going to be part of the D-release, please get Jenkins to build your container on master to generate a tag without dev_.

korseby commented 6 years ago

Hi, I merged develop into master and triggered a new jenkins build. I replaced "latest" with the version in the stable release: v1.0_cv0.5.10

ilveroluca commented 6 years ago

The last two commits:

  1. fix a typo in the ttest wrapper
  2. insert a prefix tamenmr- to all new tools ids in this PR.

I still generate the following warnings as Galaxy starts up. It would be nice to fix them as they seem to be indicating problems with the wrappers.

galaxy.tools WARNING 2018-07-02 16:10:34,616 Tool tamenmr-normalise_data: a when tag has not been defined for 'method_choice (method) --> totInt', assuming empty inputs.
galaxy.tools WARNING 2018-07-02 16:10:34,616 Tool tamenmr-normalise_data: a when tag has not been defined for 'method_choice (method) --> PQN', assuming empty inputs.
galaxy.tools WARNING 2018-07-02 16:10:34,619 Tool tamenmr-normalise: a when tag has not been defined for 'method_choice (method) --> totInt', assuming empty inputs.
galaxy.tools WARNING 2018-07-02 16:10:34,619 Tool tamenmr-normalise: a when tag has not been defined for 'method_choice (method) --> PQN', assuming empty inputs.
galaxy.tools WARNING 2018-07-02 16:10:34,621 Tool tamenmr-pca: a when tag has not been defined for 'group_choice (group) --> N', assuming empty inputs.
galaxy.tools WARNING 2018-07-02 16:10:34,630 Tool tamenmr-plotnmr: a when tag has not been defined for 'groups_choice (factCond) --> N', assuming empty inputs.
galaxy.tools WARNING 2018-07-02 16:10:34,631 Tool tamenmr-plotnmr: a when tag has not been defined for 'aggr_choice (aggr) --> N', assuming empty inputs.
galaxy.tools WARNING 2018-07-02 16:10:34,631 Tool tamenmr-plotnmr: a when tag has not been defined for 'plotBins_choice (plotBins) --> N', assuming empty inputs.
galaxy.tools WARNING 2018-07-02 16:10:34,643 Tool tamenmr-prepPattern: a when tag has been defined for 'method_choice (method) --> intelligent', but does not appear to be selectable.