Re: [galaxy-user] Need your helps about Galaxy

Hi all, Larry got another problem on our cloud Galaxy ( http://galaxyclass.genenetwork.org/). He cannot execute some commands successfully: /opt/sge/default/spool/execd/ip-10-184-11-27/job_scripts/152: line 13: wigToBigWig: command not found /opt/sge/default/spool/execd/ip-10-152-136-219/job_scrip

[galaxy-user] Galaxy STARTUP ERROR!

Hi! I am trying to launch Galaxy locally but I'm getting the following error: tkx417:galaxy pascarellagiovanni$ sh run.sh Traceback (most recent call last): File "./scripts/paster.py", line 33, in serve.run() File "/Users/pascarellagiovanni/Desktop/galaxy/lib/galaxy/util/pastescript/ser

[galaxy-user] question about samtools in Galaxy

Hi, Can anyone tell me if the ability to randomly sample a sam or bam file (view -s) is available via Galaxy samtools? I can't find it but it might be an option that I am missing. sincerely, Robert Jackman rais...@gmail.com rjack...@bu.edu ___

Re: [galaxy-user] question about samtools in Galaxy

Hi Robert, This function is not wrapped into a tool yet by the dev team. I checked the Tool Shed as well and didn't see it there. But there is another option to get to the same result. The tool "Text Manipulation -> Select random lines from a file" can be used with a SAM file. Don't not use

[galaxy-user] Tophat Error: segment-based junction search failed with err

Hello, I don't know why I still have this problem.. I have run tophat2 with different dataset, sometimes it goes well but sometime I have this error. I run only one job at a time on a virtual machine with 8G memory without using galaxy plateform. I tried --no-coverage-search option but it changes

[galaxy-user] Bioinformatics Training Course in Portugal

Course Announcement NOTE: please apply as soon as possible, the period for applications is exceptionally short due to operational reasons *ARANGS13* Automated and reproducible analysis of NGS data IMPORTANT DATES for ARANGS13 Deadline for applications: October 8th 2013

Re: [galaxy-user] Tophat Error: segment-based junction search failed with err

Hi Delong, If you are mapping against a large reference genome and your datasets are large, 8G of memory may simply not be enough, even with omitting this paramater. Also, if you have set other TopHat parameters to be sensitive, then those can also be contributing to memory usage. Splitting t

Re: [galaxy-user] SNP calling problems (Jennifer Jackson)

Hi Debora, This option was introduced in a version of GATK that is newer than the one on the public Main Galaxy server under the tool group "NGS: GATK Tools (beta)". The version of tools running here is "GATK (1.4)" This is noted here for reference and in the tool output: http://wiki.galaxypr

[galaxy-user] URL problem

Alper, Did you problem get resolved already? Maybe on the galaxy-...@bx.psu.edu mailing list? I am posting it there in case it is still open. Please reply to let us know your current status. Please drop galaxy-u...@bx.psu.edu from the to/cc on reply and future posts to this thread. Thank

Re: [galaxy-user] queue rules for multi-step workflows

Hi Zuzana, Jobs queue individually. But different jobs may queue to different clusters, so if there are no dependencies, you may see jobs execute out of order. Workflows are still a benefit as this places jobs in the queue sooner than waiting for each job to finished (under normal circumstance

Re: [galaxy-user] URL problem

Yes it is solved thanks Sent from my iPhone > On Oct 2, 2013, at 6:14 PM, Jennifer Jackson wrote: > > Alper, > > Did you problem get resolved already? Maybe on the galaxy-...@bx.psu.edu > mailing list? > > I am posting it there in case it is still open. Please reply to let us know > your cu

[galaxy-user] Please save these dates! GCC2014: June 30 - July 2

Hello all, The 2014 Galaxy Community Conference (GCC2014) has been scheduled for June 30 through July 2, at the Homewood Campus of Johns Hopkins University

[galaxy-user] Can TopHat take SNPs into account?

Hi, I have been mapping my RNA-seq data to mouse genome from a different mouse strain using TopHat. I am wondering whether TopHat can take SNPs into account during the alignment? ( using SNPs track as an optional input)? Thanks Thanh ___ The

[galaxy-user] TopHat

Hi all, I am trying to perform TopHat for Illumina from Galaxy's Main Server, and it is in queue for the past 3 to 4 days. Is this normal? Thanks & Regards,Kumar. ___ The Galaxy User list should be