Re: [galaxy-user] Variable number of inputs in Workflow (or optional inputs)

Hi Jennifer, Thanks for the reply. However, my question was not about building tools. My question was about building a workflow (using the workflow editor with existing tools), as a user of galaxy. Using the workflow editor, when I create a workflow using a tool that allows a variable number

Re: [galaxy-user] Variable number of inputs in Workflow (or optional inputs)

Hi Daniel, My apologies! I misunderstood what your question was about. You are correct, the required inputs are defined when the workflow is created. For tools that accept a variable number of inputs, when that tool is added to a workflow, the run-time parameters, including expected inputs,

[galaxy-user] April GMOD meeting early registration

Hello, This is a reminder that there is only a little over two days left to get in on early registration for the April 2012 GMOD meeting. In addition to getting a $10 discount on the registration fee, you will be entered in a drawing to get a GMOD coffee cup or T-shirt. There are some very good

[galaxy-user] Advice on disabling SGE queue on galaxy-cloudman

Hello All- I'd like to launch a galaxy-cloudman head node which does not accept SGE jobs, but as jobs are submitted go to compute nodes (or cause compute node to be added when auto-scale is on). Primarily, this is b/c I'd like to have the head node be a cheaper instance which can run long term,

[galaxy-user] FastQC in main galaxy server?

Hi, I've tried FastQC in the main galaxy server and it is throwing me an error: 0 bytes An error occurred running this job: /Traceback (most recent call last): File /galaxy/home/g2main/galaxy_main/tools/rgenetics/rgFastQC.py, line 149, in module assert

[galaxy-user] Tophat Mean Inner Distance between Mate Pairs

Hi all, When mapping pair end RNA-seq reads using tophat, we need to type in Mean Inner Distance between Mate Pairs. In galaxy, we can read the following information: This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at

Re: [galaxy-user] Tophat Mean Inner Distance between Mate Pairs

Hi Jiwen, This is a subject that has me very confused too. This thread at seqanswer didn't help much either: http://seqanswers.com/forums/showthread.php?t=8730 But it does have some good comments on the subject. I did try using the two possible options I can think of: fragment length - pair end

[galaxy-user] 'compare two datasets script'?

Hi, I'm wondering if there is a script(s) or set of command lines to download corresponding to the 'Compare two datasets' under 'Join, Subtract and Group' set of tools in Galaxy.I want to run this locally on the command line on many files. I've searched under toolshed but can't seem to find

Re: [galaxy-user] Advice on disabling SGE queue on galaxy-cloudman

Hi John, Theoretically, this is a straightforward task but in reality CloudMan gets in the way of making it stick. Namely, if you are to manually remove the master instance from being an execution host, CloudMan will add it back in the next time a node is added or removed from the cluster, thus

[galaxy-user] Question about plotting circos plot

I wonder if is it possible to visualize mutation data in circular plot termed as circos plot e.g @http://www.eurekalert.org/multimedia/pub/31019.php?from=181881 Any suggestion for an alternative tool will also be appreciated. Thanks Shamsher