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NBISweden / aMeta

Ancient microbiome snakemake workflow
MIT License
19 stars 14 forks source link

Move github workflow test tweaks to separate installation script #11

Closed percyfal closed 2 years ago

percyfal commented 2 years ago

There are currently three post-installation configuration steps that are required to make github actions work:

  1. building of krakendb database
  2. building of krona taxonomy
  3. reducing malt runtime memory

These steps should be placed in a separate post-(test?)-installation script as these steps are also required for local tests but currently not implemented.

LeandroRitter commented 2 years ago

One has to also manually build bowtie2 index, right? Like this:

bowtie2-build --large-index ref.fa ref.fa --threads 4

percyfal commented 2 years ago

@LeandroRitter I actually added the bowtie build dependency to bowtie align, so that shouldn't be necessary.