Hello Tuqa,
Galaxy will not stop by itself. That said, you will want to monitor the
instance and any associated cluster, just as you would any other
important processes.
Please send all follow-up with a cc to the mailing list (reply-all).
The development community is a great resource for
Hi Toqa,
I think you would want to use sh run.sh --daemon, so you don't have
to keep the cli session open. To stop the daemon then you would use
sh run.sh --stop-daemon.
You could read much more about a production server installation at:
This converts line endings to UNIX line endings, so in most cases it wouldn't
break anything to not happen, however, if the uploaded file had DOS line
endings, the uploaded file content would be wrong.
The best way to handle this is probably to change the ownership of the uploaded
temporary
Hi,
I'm trying to develop a workflow using several tools from GATK and
Picard sections among others. I'm able to run all the tools and from
the history I'm creating a workflow, but I'm running into an error. I
have copied the full debugging trace from my local Galaxy, I was able
to import this
I was able to make the error disappear. By trial and error I found the
error appear when I set any tool with Using reference genome as To
be set at runtime. But only for tools which don't display a drop down
menu to select a reference.
I'm confuse by this, I'm guessing these tools will take the
Hi Carlos,
This is a known bug with running workflows and we are working on a fix. Thanks
for reporting this error.
The current work-around is to set the reference genome value in the select
boxes (currently only 'hg_g1k_v37' is available on our public server) directly
within the workflow
Hello,
Thanks very much for contributing locale files for Chinese. I've added your
contribution to the distribution in change set revision 6248:bc399a95e31e,
which should be available in the distribution within the next few weeks. I
downloaded the raw files and committed them instead of
Hi Greg,
Did more digging around today in the Galaxy source and maybe I misjudged
the situation. Although getting a representation of my datasets into
Galaxy appears relatively straightforward, at the end of the day reads of
raw data and passing data to and from external tools, etc all assumes
Hi James,
I haven't gone too far down the implementation path in this area, so I'm
certainly not aware of the issues you may be discovering. The key would be to
implement a layer on top of your database so that Galaxy's data library upload
component can treat the data contained in your
It's not public yet, and it involves a little conundrum - we want it so we can
support large amounts of data efficiently on a variety of aligners, including
our ELAND from CASAVA. However, ELAND does not support unaligned BAM inputs
yet, and apparently it would be a lot of work to make it so
BTW - the pull request for the GZIP-based splitting is actually integrated - I
was referring to the GZIP-based datatype.
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Tel: 858-736-3584
E-mail: jdu...@illumina.com
-Original Message-
On Tue, Nov 8, 2011 at 11:45 PM, Duddy, John jdu...@illumina.com wrote:
It's not public yet, and it involves a little conundrum - we want
it so we can support large amounts of data efficiently on a variety
of aligners, including our ELAND from CASAVA. However, ELAND
does not support unaligned
Ahh - sorry. I finally found the format specification for BGZF in the SAM
format specification, and it seems that it is 100% GZIP-compatible. There is
still the issue of needing an external file index, since all BGZF seems to give
you is the size of the compressed block, not anything
Hi Greg,
So, here are my concerns:
1. From looking through some of the source it *appears* to me that the raw
data input calls are spread across the various libraries as standard file
IO calls. So, if I wanted to use my db underneath I'd need to
replace/catch all of these. I was hoping that
Hi James,
Existing tools mostly take file paths. This has arguably useful side
effects in isolating cluster node execution from the galaxy server
process and persisting the computation input on a file-system -
arguably more stable long term than queries on dynamic database tables
- and maybe not
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