I'm trying to run Picard MarkDups through Galaxy. Picard is using the
standard 4g for the java max heap size. I need to increase this. Is it
possible to offer this as an option to the user? If not, where do I change
this? I see the entry in picard_wrapper.py. Do I change it here or in the
XML
in picard_wrapper.py. Do I change it here or in
the
XML file for MarkDups?
Ryan
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? If not, where do I
change
this? I see the entry in picard_wrapper.py. Do I change it here or in
the
XML file for MarkDups?
Ryan
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I'm trying to download a fastq sanger file from my Galaxy (Main) account
and getting the error message below as of 2:15pm, Wed, 1/11/12. I have a
concatenated fastq file and I get this message when clicking the download
(floppy disk) icon. Any help would be appreciated. Thanks,
Jeremy
Duplicate
sometimes the scheduler can't keep up with all the work in it's 15sec
cycle, so it doesn't respond to some messages. here's a fix i've been
trying that seems to work.
in lib/galaxy/jobs/runners/drmaa.py:
def check_watched_items( self ):
Called by the monitor thread to look
Any ideas as to how to fix this? We are interested in using Galaxy to host
all our NGS data. If indexing on the head node is going to happen, then
this is going to be an extremely slow process.
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