fastq-dump on Galaxy?

Question: fastq-dump on Galaxy?

3.3 years ago by

France

rioualen • 10 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

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modified 3.3 years ago • written 3.3 years ago by rioualen • 10

3.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link modified 3.3 years ago • written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 24 months ago by Jennifer Hillman Jackson ♦ 25k

3.3 years ago by

rioualen • 10

France

rioualen • 10 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 COMMENT • link written 3.3 years ago by rioualen • 10

Troubleshooting:

Be sure you are running the latest release 15.07
Make sure that both samtools and picard are installed on your server
Check the install status at: Admin > Manage installed tools
Completely uninstall and then reinstall the tool, making sure that the checkbox for 'manage dependencies' is checked
Consider using the alternate tool that is stand-alone (outside of the full package). Search in the Tool Shed by "sra" to locate it
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 REPLY • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

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