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zavolanlab / zarp-cli

A user-friendly command-line interface for the ZARP RNA-seq analysis workflow
https://zavolanlab.github.io/zarp-cli/
Apache License 2.0
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feat: genome resources management #5

Closed mkatsanto closed 1 year ago

mkatsanto commented 3 years ago

Is your feature request related to a problem? Please describe. The issue is how to provide genome availability and compatibility with specific versions and organisms

Describe the solution you'd like Implementation in config/genome_resources.py The user should be able to :

  1. set default genome resources for a given organism and either
  2. choose to always download latest ENSEMBL resources for every sample or
  3. download only missing genome resources not configured in 1. or
  4. never download any resources (app will stop if resources are not available for one or more samples)

Additional context ensembl rest resources: https://rest.ensembl.org/

mkatsanto commented 3 years ago

https://git.scicore.unibas.ch/zavolan_group/pipelines/zarp/-/issues/133

ninsch3000 commented 2 years ago

Note that in the samples table paths to genome and annotation files have to be in the format /path/to/ORGANISM/gene_annotations.gtf (or genome.fa), where ORGANISM has to be exactly the same as the short_name for library source returned by htsinfer. (Or the htsinfer short name has to be replaced in the samples table;)

uniqueg commented 1 year ago

This was addressed with #61