Question: Error fetching reference genome (from History or URL)
0
gravatar for vebaev
3.0 years ago by
vebaev130
vebaev130 wrote:

HI,

I'm trying to get a reference genome of tomato, I have tried to add it from History (fasta file), and from URL (link to the fasta) in the Reference Genome - fetching, but I got error every time:

"/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/cca219f2b212/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py", line 355, in <module>

(For hg19 genome from USCS there was no problem)

 

fetching regerence genome • 861 views
ADD COMMENTlink modified 3.0 years ago by Jennifer Hillman Jackson25k • written 3.0 years ago by vebaev130
1
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

I just tested this on a Galaxy Cloudman and the job executed fine (I chose to retrieve from the History). Below is what the settings look like in the Galaxy interface. Perhaps this will help you to set up your job correctly?

If there are still issues, first double check that you are running the latest Galaxy code base and version of the Data Manager and re-run. Should problems be persistent, please share more details about your instance with the problem, including a screenshot of the settings and exact error if possible.

Best, Jen, Galaxy team

ADD COMMENTlink written 3.0 years ago by Jennifer Hillman Jackson25k

Hi,  thanks, I used this Data manager from your post and the job from History finished fine, but I cannot see it than in Bowtie index builder datamanager. I see only hg19 that I got from USCS...

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by vebaev130

Hello, I am unable to replicate this using this Bowtie2 Data Manager. Meaning, the new genome I loaded shows up in the list "Source FASTA Sequence". Perhaps try searching for yours? Thanks, Jen

ADD REPLYlink written 3.0 years ago by Jennifer Hillman Jackson25k

I found out it showed up but after galaxy restart....

ADD REPLYlink written 3.0 years ago by vebaev130

Yes, that is needed for most data manipulations, especially when first loading or when on a local. Glad it worked out! Jen

ADD REPLYlink written 3.0 years ago by Jennifer Hillman Jackson25k
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