Hi Kanwei, and thanks for your reply.
I might have missed something really big but I'm kinda confused.
I just double checked galaxy-dist and galaxy-central on bitbucket and I
would like to know if I understood the code properly. Please correct me
if I'm wrong.
Let's look at the is_checked()
Thanks Nate,
putting the upload_store_access directive into the nginx.conf indeed
did the trick.
Joern
On 08/24/2011 07:45 PM, Nate Coraor wrote:
You can also use the 'upload_store_access' option to the nginx upload
module to make the files readable:
Dear Community,
our lab has developed a NGS analysis pipeline for viral sequence
analysis (both genomic resequencing and RNA-Seq, including some novel pathogen
detection and viral quasi-species reconstruction approaches) that fulfills
various analytical needs of our clinical
Hi Kanwei,
I tried that and it didn't seem to work. It seems like Galaxy parses the
output name BEFORE execution... although that doesn't make sense. In any
case, I couldn't get it to work. Also, in the example below the % should
really be # right? Anything anyone can think of that I might be
Hi all,
Is there a relatively easy way to create your own input/output formats?
Some of the formats from programs that I am trying to install on our local
Galaxy do not exist as an option. Any ideas?
- Nik.
___
Please keep all replies on
On 08/25/2011 12:12 PM, Nikhil Joshi wrote:
Hi all,
Is there a relatively easy way to create your own input/output formats?
Some of the formats from programs that I am trying to install on our local
Galaxy do not exist as an option. Any ideas?
Hi
have you looked at the following wiki
Edward Kirton wrote:
also, delete and purge a quota seems to have no effect.
Hi Ed,
They work for me. Note that delete/purge do not actually delete the db
row itself.
Delete marks the quota as deleted, and it no longer counts against any
associated users. Purge removes all of the user/group
you can use label=${input.name}
Shaun
Quoting Nikhil Joshi najo...@ucdavis.edu on Thu, 25 Aug 2011 03:10:21 -0700:
Hi Kanwei,
I tried that and it didn't seem to work. It seems like Galaxy parses the
output name BEFORE execution... although that doesn't make sense. In any
case, I
Hi
The option to filter a BED file by the score in the visualization tool
is brilliant! There is just one draw back: you can only filter by
integers. Hence a score of 1.1 is the same as of score of 1.3.
How difficult would it be to change the code in order to allow floats
for the filter?
Hi Curtis,
Changeset details:
http://bitbucket.org/galaxy/galaxy-central/changeset/07de40a5a0b9
We are planning on releasing a distribution within a week, so
alternatively you could wait and pull from there, if you normally work
from the galaxy-dist repository.
And for everyone tracking
The option to filter a BED file by the score in the visualization tool is
brilliant! There is just one draw back: you can only filter by integers.
Hence a score of 1.1 is the same as of score of 1.3.
How difficult would it be to change the code in order to allow floats for the
filter?
I just remembered what I did for the tophat wrapper. All I did was change the
default behavior of the use coverage search option. I believe no is the
default behavior and you have it as yes.
From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Sent: Thursday, August 11, 2011 7:22 AM
To:
I am running a local instance of Galaxy and I've been trying to sort out
some issue with dataset cleanup. For the most part, things are working
OK running the shell scripts in the recommended order:
delete_userless_histories.sh
purge_histories.sh
purge_libraries.sh
Hi Curtis,
This is a good question.
I'll post back to the list to (hopefully) gather some feedback.
Thanks!
Jen
On 8/25/11 8:44 AM, Robert Curtis Hendrickson wrote:
Wonderful. We're on galaxy-dist, but we can pull that patch.
Are most local installs on Dist or Central?
Thanks!
Curtis
Has anyone gotten galaxy installed on a mac 10.5 with EPD (enthought) python
2.6 (EPD version 6.1-1)? I get this error which I suspect is related to the
fact that I have EPD python, not the generic python that was preinstalled?
Any ideas?
Thanks!
Some eggs are out of date, attempting to
Hi,
We have a local instance of galaxy at our institution. I've been
trying to use several existing wrappers for tools on galaxy right now,
for example, bwa_wrapper, cufflinks_wrapper to run bwa, cufflinks
through galaxy. I keep seeing the following error:
An error occurred running
It's actually a boolean checkbox. so I basically want the label to
change based upon whether or not the checkbox is checked. Is there any way
to do that? Again, I've tried using the Cheetah syntax to do the #if #end
inside the output tags but that didn't work.
- Nik.
On Thu, Aug 25,
I'd like to have a datatype with a dict as metadata. This dict() would store
file offsets to enable seeking around to process different sections of the file.
How do I add a dictionary data metadata element?
John Duddy
Sr. Staff Software Engineer
Illumina, Inc.
9885 Towne Centre Drive
San
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