Sorry for the delay in response. Are you still experiencing these problems? If
so, would you mind sharing a history and your workflow with me and I will take
Thanks for using Galaxy,
On Sep 20, 2011, at 4:28 PM, Susan Newman wrote:
> I’m working on a SOLiD ChIP-Seq workflow in which I want to use SICER for
> peak detection. In attempting to add SICER to the workflow, I’ve run into
> some difficulty:
> 1) My input is an interval file which I’ve created using Convert SAM.
> In order to connect to the SICER module, I had to use a trick by setting up
> the connection with the Convert SAM set to BED. The SICER algorithm fails to
> run when tested with the bed file. If I then change the connected Convert
> SAM to interval, SICER will run.
> 2) I need to change the default run parameters but they are not saved in
> the workflow. There is always reversion to the default values. I get a
> Server error notice. This workflow also contains Bowtie and MACS. Parameter
> changes for these algorithms are saved correctly.
> 3) I would like to run SICER twice in the workflow with different
> parameters. Is it allowable to load SICER a second time? May I run from the
> same interval conversion file? I tried this and again could not get the
> input file recognized as a valid connection.
> Thanks in advance,
> Susan S. Newman, Laboratory Manager
> Genomics Core Facility, L2012
> Pennington Biomedical Research Center
> 6400 Perkins Road
> Baton Rouge, LA 70808
> 225-763-0255 (o) 225-763-0257 (lab)
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Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: