Update samples and cleanup unused #284
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| @@ -48,7 +48,7 @@ The `kubectl` program is only required when bootstrapping a new Galaxy instance, | |||
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| ### Credentials | |||
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| You will need an [API key](https://training.galaxyproject.org/training-material/faqs/galaxy/preferences_admin_api_key.html) for every Galaxy instance you would like to intereact with. You will also need the *kubeconfig* file for each Kubernetes cluster. The `abm` script loads the Galaxy server URLs, API keys, and the location of the *kubeconfig* files from a Yaml configuration file that it expects to find in `$HOME/.abm/profile.yml` or `.abm-profile.yml` in the current directory. You can use the `profile-sample.yml` file as a starting point and it includes the URLs for all Galaxy instances we have used to date (December 22, 2021 as of this writing). | |||
| You will need an [API key](https://training.galaxyproject.org/training-material/faqs/galaxy/preferences_admin_api_key.html) for every Galaxy instance you would like to intereact with. You will also need the *kubeconfig* file for each Kubernetes cluster. The `abm` script loads the Galaxy server URLs, API keys, and the location of the *kubeconfig* files from a Yaml configuration file that it expects to find in `$HOME/.abm/profile.yml` or `.abm-profile.yml` in the current directory. You can use the `samples/profile.yml` file as a starting point and it includes the URLs for all Galaxy instances we have used to date (December 22, 2021 as of this writing). | |||
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the current profile.yml does not seem to contain a list of all Galaxy instances as mentioned in the readme.
| - history_name: 1 | ||
| inputs: | ||
| - name: FASTQ RNA Dataset | ||
| dataset_id: 28fa757e56346a34 |
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should dataset_ids correspond with datasets.yml in the samples folder?
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No. The dataset_id in the benchmark file is the ID (or name) of the dataset in the Galaxy history. So something like ucsc.hg38.knownGene.gtf. That sample should likely be updated or removed. The datasets.yml (and histories.yml andworkflows.yaml) files are used to provide aliases to URLs that are used when importing datasets/histories/workflows into Galaxy.
abm main dataset import rna-1g
abm main workflow import rnaseq-pe
| workflow_conf: | ||
| - benchmarks/example.yml | ||
| - benchmarks/dna-named.yml | ||
| - benchmarks/rna-named.yml |
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benchmark samples need to be updated
| - iu2 | ||
| job_configs: | ||
| - rules/4x8.yml | ||
| - rules/8x16.yml |
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rule files need sample content
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And probably more explanation as the format of the files will depend on what chart was used to install Galaxy. Since GalaxyKubeman installs Galaxy as a dependent chart there is a top level galaxy: key that is not needed if Galaxy is installed from the galaxy-helm chart.
I will also give some thought to rewriting this section. For the cloud costs we only update TPV rules, but any values from the Chart can be specified and updated here.
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Thanks for the issue and PR! |
Partially addresses: #283