SRA-Toolkit Faster Download and Extract Reads in FASTQ: fasterq-dump: command not found

Hello, I am installed and configured SRA-Toolkit on local galaxy server.

After running script, I have got error:

Downloading accession: SRR27174817…
/home/biodata/galaxy/database/jobs_directory/000/435/ line 62: fasterq-dump: command not found.

Maybe you know what is wrong?

If I install sra-tools via sudo apt it works perfectly

Welcome, @KaunoSeptintasFortas

The “not found” error message means the environment that the job is running in has a configuration problem. The root issue is usually some dependency problem (not installed, or has incorrect permissions).

You can install tools directly in the Galaxy application and check the box to use dependencies resolvers (Admin → Tool Management) or you can batch the work with helper scripts (example → Hands-on: Hands-on: Galaxy Tool Management with Ephemeris / Galaxy Server administration).


Hello, the problem was in dependence version (actually problem was in bad quality of galaxy management). SRA-Toolkit wants dependence version does not existing on galaxy toolshed. I spend this problem changing dependence version in toolkit code.

The more I use galaxy the more I think it is better not to use galaxy…

Hi @KaunoSeptintasFortas

Reproducibility always has some cost/benefit trade offs! But I’m glad that you were able to get this working, and maybe your comments about the how-to will help others :slight_smile:

Actually, it is not history of reproducibility, just one more case to think about proper Galaxy support. It is OK po pay for it and have quality service than have random service with random support :slight_smile:

Now I am fighting with Galaxy Annovar and I am shure I will fail again :frowning:

Hi @KaunoSeptintasFortas

Annovar is no longer available. Why? The original tool author doesn’t want it to be available open source. They may have left the wrapper in the Tool Shed, and that version worked with just one genome (hg19) with earlier Galaxy versions but not likely with current versions. I don’t know the status beyond that and we’ve removed it from the public servers.

If it still interests you, you should contact the tool author directly to see if they will offer a site license for private use and maybe some custom advice for getting more genomes supported, or even hg19 again, plus help with any wrapper updates that may be needed.

As for paying for support, the core team releases everything – all software and all computational infrastructure at public servers – for free with zero monetization. That means others can offer pay-for-service flavors, and they do!

Review here for all of the choices we know about.

And, if the configuration for a stand-alone server seems to include more than you need, we do offer a free Docker version to consider. Same page as the two before but I’ll quote here directly.

And finally, there are many Matrix chats you can visit for one-off administrative questions. These reach the developers directly, both core team and community contributors. We are organized into Working Groups and the resources for all can be found here, including the chats. → Galaxy Working Groups - Galaxy Community Hub