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:

Iím 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, Iíve run into some difficulty:
 
1)       My input is an interval file which Iíve 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)
 
 
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