Re: [galaxy-user] Problems starting Galaxy Cloudman

2012-03-09 Thread Dannon Baker
Greg, 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

Re: [galaxy-user] question from a new Galaxy user

2012-03-09 Thread Kevin L
If I may add, I believe galaxy will uncompress your files if zipped. Unzipping a 13 GB file, will take a while. Kev ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at

[galaxy-user] Clustal error during Bowtie run (public server)

2012-03-09 Thread Hemarajata, Peera
Dear all, 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

[galaxy-user] Question about aaChange tool.

2012-03-09 Thread Maha Al Kahtani
Hello, 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

Re: [galaxy-user] Problems starting Galaxy Cloudman

2012-03-09 Thread Ross
Since Dannon is likely asleep, maybe this will help until he can respond: http://dev.list.galaxyproject.org/error-on-fastq-file-while-grooming-or-fastqc-report-or-fastqc-converter-td4396664.html ie: try removing the second coverage datatype definition from datatypes_conf.xml and restarting the

Re: [galaxy-user] Clustal error during Bowtie run (public server)

2012-03-09 Thread Jennifer Jackson
Hi Peera, 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 this tool. Sorry for the inconvenience, and thanks for using Galaxy, Best, Jen Galaxy team On 3/9/12 9:29 AM, Hemarajata, Peera wrote:

Re: [galaxy-user] Question about aaChange tool.

2012-03-09 Thread Jennifer Jackson
Hello Maha, 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

Re: [galaxy-user] Job running speed is really slow

2012-03-09 Thread Jennifer Jackson
Hello Jiwen, 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. http://wiki.g2.bx.psu.edu/Big%20Picture/Choices Instructions for getting started are in our wiki: http://getgalaxy.org

Re: [galaxy-user] Tophat

2012-03-09 Thread Jennifer Jackson
Hello Jiwen, The tool NGS: Picard (beta) - SAM/BAM Alignment Summary Metrics gives a nice set of statistics for paired end data. Hopefully this helps, Best, Jen Galaxy team On 3/7/12 12:35 AM, 杨继文 wrote: Dear all, This might be a silly question, but I couldn't figure it out by myself