SRA file and run fastq-dump error on local Galaxy

[rubens]

Continuing the discussion from Repeat Explorer:

@rubens

If I could disturb you a little more, I upload an SRA file and run fastq-dump. I received an error message

home/pasa/galaxy/database/jobs_directory/000/10/tool_script.sh: 
linha 9: /Users/xuebing/tools/sratoolkit.2.1.9-mac32/fastq-dump: 
Arquivo ou diretório não encontrado (file or directory not found)

Thanks!

[jennaj]

Hello,

Check that you are using the latest version of these tools and update them if not:

https://toolshed.g2.bx.psu.edu/view/iuc/sra_tools/1790dcf3c32d

There was an earlier problem with extracting fastq data from SRA archives (now fixed). A newer issue with extracting bam data is undergoing a fix. So, upgrade now, then watch for the next update (should be soon).

Related issues/tickets for these tools: https://github.com/search?q=org%3Agalaxyproject+ncbi+tools&type=Issues

FAQ that explains how I found the known issues.

@jennaj

If you think you found a software bug, review the issue FAQ and linked known issues to find out if it has already been reported and to learn how to report a new problem:

• Reporting Usage Issues or Software bugs

[rubens]

HI!

It is strange, but I install another package, that also have this tool, run from there and works. Maybe it is really the version. I’m getting the same issue with rnammer now.

Thanks!

Cheers,
Rubens.

[jennaj]

Install the latest NCBI data retrieval tools published by the IUC – these were just updated again to fix a few bugs and are now installed/working at Galaxy Main & Galaxy EU.

Extracting data using 3rd party API’s can be a bit of a moving target as they make changes and the Galaxy tools that utilize it need to be adjusting in response to restore functionality.

The author of the other package may need to do some updates, too, if the function is failing. Authors can be contacted through the ToolShed (when logged in), or you can open an issue at their development repository (should be linked in the ToolShed as well, and if not, use the tools with some caution!).

[rubens]

Thank you very much! I’m using only tools from toolshed, except for the Repeat Explorer, because I’m very noobie in such analysis.

Cheers!