Hi Susan, 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 a look.
Thanks for using Galaxy, Dan 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 > > 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) > > http://gcf.pbrc.edu > > ___________________________________________________________ > 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: > > http://lists.bx.psu.edu/
___________________________________________________________ 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: http://lists.bx.psu.edu/
