Question: fastq-dump on Galaxy?
0
gravatar for rioualen
3.3 years ago by
rioualen10
France
rioualen10 wrote:

Hello,

I'm just getting my hands on Galaxy. I imported local .sra files as my starting data, but I can't find the fastq-dump conversion tool under the left menu "Convert formats". Is there something I am not doing right? This should be a very simple operation I guess...

Thanks

fastq fastq-dump sra • 1.9k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by rioualen10
2
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

SRA toolkit tools can be found in the Tool Shed for use in a local or cloud Galaxy

When loading local SRA data to http://usegalaxy.org, convert the files locally using the tools from SRA first, then upload just the FASTQ datasets.

Best, Jen, Galaxy team

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Jennifer Hillman Jackson25k

Update: New tools are at http://usegalaxy.org to extract SRA data from NCBI. These are also in the Tool shed for local/cloud Galaxies.

NCBI SRA Tools Extract reads in SAM or BAM format from NCBI SRA. Extract reads in FASTQ/A format from NCBI SRA. Generate pileup format from NCBI sra.

ADD REPLYlink written 24 months ago by Jennifer Hillman Jackson25k
0
gravatar for rioualen
3.3 years ago by
rioualen10
France
rioualen10 wrote:

Thanks! I was indeed thinking of this explanation.

So I went for the local installation, and added fastq-dump tool from the Tool Shed following this tutorial: https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial

However I get the following error when converting my files:

/home/rioualen/Desktop/workspace/galaxy/database/job_working_directory/000/16/galaxy_16.sh: 21: /home/rioualen/Desktop/workspace/galaxy/database/job_working_directory/000/16/galaxy_16.sh: /Users/xuebing/tools/sratoolkit.2.1.9-mac32/fastq-dump: not found

Apparently Galaxy can't find the tool because of a path problem. Any tip on how top manage this issue?

Thank you again

ADD COMMENTlink written 3.3 years ago by rioualen10

Troubleshooting:

  1. Be sure you are running the latest release 15.07
  2. Make sure that both samtools and picard are installed on your server
  3. Check the install status at: Admin > Manage installed tools
  4. Completely uninstall and then reinstall the tool, making sure that the checkbox for 'manage dependencies' is checked
  5. Consider using the alternate tool that is stand-alone (outside of the full package). Search in the Tool Shed by "sra" to locate it
  6. If all else fails, then contact the tool author (through the tool shed, an option when logged in). It could be that recent Galaxy updates are causing a problem with the tool. The original author needs to make changes when issues are present. 

Since this has gone on a while and I am sure that you wish to get your analysis going, it might be simplest to just follow the instructions at SRA, download the tool package directly, and then run the tool line-command. After that, load the fastq data into Galaxy and start work from there. 

Best, Jen

ADD REPLYlink written 3.3 years ago by Jennifer Hillman Jackson25k
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