search

open2c / distiller-nf

A modular Hi-C mapping pipeline
MIT License
87 stars 24 forks source link

fastq-dump fails with "This sra toolkit installation has not been configured." when docker is disabled #157

Open agalitsyna opened 4 years ago

agalitsyna commented 4 years ago

Hi! I'm stuck with a problem that happens with my distiller-nf runs sometimes.

I usually install distiller-nf from github and create conda environment from environment.yml. Then I run distiller-nf to download from SRA with fastq-dump. Sometimes, when I try it on a new cluster, I get:

This sra toolkit installation has not been configured.
Before continuing, please run: vdb-config --interactive

However, fastq-dump outside of distiller works perfectly, and vdb-config does not help.

It looks like some problem with the path to ncbi config (located at /home/user/.ncbi/user-settings.mkfg by default), which cannot be loaded appropriately in distiller after the change of home dir with:

HOME=`readlink -e ./`

Simple addition of cp -r /home/user/.ncbi/ . to fastqDumpCmd works like a charm.

I wouldn't say I like this dirty fix, and I wonder what might be the problem's source. What do I miss here? Have someone solved it more elegantly?

Thanks!

Phlya commented 3 years ago

Why is that problematic line even required? I got this issue and commenting it out solves the problem with no apparent adverse effects...