The problem here is that the galaxy update failed to merge a change to run.sh
because of minor customizations it has. We'll have a long term fix out for
this soon, but for now what you can do is ssh in to your instance and update
run.sh yourself prior to restarting galaxy. All you need
If I may add, I believe galaxy will uncompress your files if zipped.
Unzipping a 13 GB file, will take a while.
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
I was trying to use Bowtie on the public server to align my groomed paired
reads to a reference FASTA file. My FASTA contains sequences of 7 contigs (so 7
sequences altogether). After a while this error showed up:
Job output not returned by PBS: the output datasets were deleted while
Recently i have used galaxy to find corresponding amino acids to a list of
SNPs that i have. i used aaChange tool from the tool panel for this
purpose. After obtaining the result i checked the correctness of this
results by searching dbSNP for randomly chosen SNPs. however, some of those
Since Dannon is likely asleep, maybe this will help until he can respond:
ie: try removing the second coverage datatype definition from
datatypes_conf.xml and restarting the
This error was caused by a network problem on our cluster, that has been
resolved. Please let us know if you have any further problems running
Sorry for the inconvenience, and thanks for using Galaxy,
On 3/9/12 9:29 AM, Hemarajata, Peera wrote:
This does sound very strange. Would you please share a link to your
history so that we can examine the data and determine where the problem
originates? Please note which dataset contains this particular problem
if there are several runs from this same tool.
Use Options - Share
Galaxy has been very busy this week. Our recommendation for large
datasets or time constraints is to consider moving to a local or
(better) cloud instance.
Instructions for getting started are in our wiki:
The tool NGS: Picard (beta) - SAM/BAM Alignment Summary Metrics gives
a nice set of statistics for paired end data.
Hopefully this helps,
On 3/7/12 12:35 AM, 杨继文 wrote:
This might be a silly question, but I couldn't figure it out by myself
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