[galaxy-user] add publicly available genomes?

2012-12-19 Thread Camilla Nesbo
Heia, Would it be possible to add the genome of Kosmotoga olearia (NC_012785) and Mesotoga prima (NC_017934) to the genomes availabe in galaxy database? Thanks, Camilla -- Camilla L. Nesbø University of Alberta Biological Sciences 116 street and 85 Avenue Edmonton, Alberta T6G2R3 +1 780 604

[galaxy-user] question on galaxy reference genome window

2012-12-19 Thread Sun, Wenping [USA]
Dear Galaxy members, I am new to galaxy and just installed galaxy on aws cloud. I am testing how it works and have the following question below: 1. I tried to test bowtie2 with the dataset I uploaded, however, the window for reference genome is very narrow and nothing from pull-down

[galaxy-user] How to display data at UCSC main?

2012-12-19 Thread Anna Vilborg
Dear mailing list, I am new to Galaxy and am going through the tutorials, starting with Galaxy 101. Under point 2.5. Recovering exon info and displaying data in genome browsers in the tutorial, there is the option to display data at UCSC. However, I don't have this option, although my history

Re: [galaxy-user] question on galaxy reference genome window

2012-12-19 Thread Dannon Baker
Kathryn, Are you using the galaxy cloud configuration provided by the team, or have you installed your own galaxy on a cloud instance? It sounds like the latter, in which case you'll need to configure reference as detailed here: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. You

[galaxy-user] Error in TopHat

2012-12-19 Thread Sachit Adhikari
This is the error I am getting while running Tophat. What's causing this? I have the default hg19 index files. Error in tophat: [Tue Dec 18 10:08:33 2012] Beginning TopHat run (v1.3.3) --- [Tue Dec 18 10:08:33 2012] Preparing output location

Re: [galaxy-user] Error in TopHat

2012-12-19 Thread Sachit Adhikari
And when I tried running tophat alone like this: tophat -r 20 test_ref reads_1.fq reads_2.fq I get this error: [2012-12-19 06:57:07] Beginning TopHat run (v2.0.7) --- [2012-12-19 06:57:07] Checking for Bowtie Bowtie version: 2.0.2.0 [2012-12-19

Re: [galaxy-user] [External] Re: question on galaxy reference genome window

2012-12-19 Thread Sun, Wenping [USA]
Hi Dannon, Yes, you are correct! I installed galaxy from scratch on the cloud. I will check the site you provided and see how it goes. I also have the preconfigured cloud instance set up recently. However, when I stopped the instances (master and cluster nodes) from aws, I couldn't get the

Re: [galaxy-user] [External] Re: question on galaxy reference genome window

2012-12-19 Thread Dannon Baker
On Dec 19, 2012, at 11:09 AM, Sun, Wenping [USA] sun_wenp...@bah.com wrote: I also have the preconfigured cloud instance set up recently. However, when I stopped the instances (master and cluster nodes) from aws, I couldn't get the galaxy web running again (the instance running however the

Re: [galaxy-user] add publicly available genomes?

2012-12-19 Thread Jennifer Jackson
Hi Camilla, For small genomes like these, the quickest option is to use the 'custom reference genome' function with tools. Details about how to use are in our wiki: http://wiki.galaxyproject.org/Support#Custom_reference_genome Hopefully this helps! Best, Jen Galaxy team On 12/18/12 12:40

[galaxy-user] upload workflow on cloudman

2012-12-19 Thread Sun, Wenping [USA]
Dear galaxy users, I tried to follow the instruction to see how the workflow worked by using the one on the support site Galaxy-Workflow-mt_analysis_0.01_strand-specific_(fastq_double).ga However, it takes very very long time and remains the following state for several hours. Is this normal?