Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Error fetching reference genome (from History or URL)
0
gravatar for vebaev
3.3 years ago by
vebaev • 130
vebaev • 130 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 • 1.0k views
ADD COMMENT • link •
modified 3.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.3 years ago by vebaev • 130
1
gravatar for Jennifer Hillman Jackson
3.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link modified 3.3 years ago • written 3.3 years ago by vebaev • 130

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

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

ADD REPLY • link written 3.3 years ago by vebaev • 130

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

ADD REPLY • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour