Fix q2-fondue Conda environment

lina-kim commented 7 months ago

With the download pipeline option, Nextflow fails when trying to run with the given Conda environment for q2-fondue.

The issue is that the sra-toolkit package requires configuration that is only possible interactively (vdb-config --interactive):

Command output:
  Retrieving data from SRA using q2-fondue...
  2024-02-05 07:31:26,578 [MainThread] [INFO] [q2_fondue.sequences]: Downloading sequences for 5 accession IDs...
  2024-02-05 07:31:26,902 [MainThread] [INFO] [q2_fondue.sequences]: Retrying to download the following failed accession IDs in 1.0 min: ['SRR10948297', 'SRR11115880', 'SRR11115881', 'SRR9270274', 'SRR9270275']
  2024-02-05 07:32:27,157 [MainThread] [INFO] [q2_fondue.sequences]: Retrying to download the following failed accession IDs in 1.5 min: ['SRR10948297', 'SRR11115880', 'SRR11115881', 'SRR9270274', 'SRR9270275']
  2024-02-05 07:33:57,441 [MainThread] [INFO] [q2_fondue.sequences]: Download finished. 5 out of 5 runs failed to fetch. Below are the error messages of the first 5 failed runs:
  ID=SRR10948297, Error=This sra toolkit installation has not been configured.
  Before continuing, please run: vdb-config --interactive
  For more information, see https://www.ncbi.nlm.nih.gov/sra/docs/sra-cloud/

For a possible automated solution, consider what was done for the fondue Docker image or a GitHub suggestion for using default, non-interactive configurations.

lina-kim commented 5 months ago

@ChristosMatzoros remind me why we decided to keep this open? I can't remember what we wanted to do before finalizing its close.

ChristosMatzoros commented 5 months ago

Hey @lina-kim,

We left it open to allow us some time to validate its effectiveness during the last focus group session. We can close this issue.

lina-kim commented 5 months ago

Perfect, thanks!

bokulich-lab / nf-ducken

Fix q2-fondue Conda environment #98