Hi,
I already asked a similar question to the Galaxy mailing list toward this
topic, but it didn't quite solve my problem.
I was seeking help on a way to create a tool which would be able to
retrieve all the details (the information you get when clicking on the
eye icon in a job in the
On Thu, Jun 14, 2012 at 2:08 PM, Jean-Francois Payotte
jean-francois.payo...@dnalandmarks.ca wrote:
My question is then: Is it possible, from a tool, to retrieve the history ID
of the current history?
I think the answer is no - assuming you mean tool as in the script or
binary being executed -
Hi Peter and thank you for your answer,
I think I have misspoken when I said that I would like to retrieve the
history ID from a tool. As you suggest, I was indeed speaking about
retrieving the history ID from the XML file instead.
And I agree with you that showing the history ID on the galaxy
Hi all,
We are using PostreSQL for our production Galaxy server, but for
development I am using SQLite. Typically it is just me is using the
development server, so database contention has not generally
been a problem.
However, while testing job splitting for breaking up tasks for the
cluster, I
On Jun 14, 2012, at 11:37 AM, Peter Cock wrote:
My hunch is that all the child-jobs are created and added to the
queue and some of this is happening in parallel leading to
contention over the SQLite database. Does this sound likely?
Yep, this is exactly what's happening. It isn't just the
Hi Greg
I was using the Galaxy test toolshed to upload the files into a repository. On
my Mac where I develop the tools I have a local instance that I loaded from
zipped file (downloaded April galaxy-galaxy-dist-40f1816d6857.zip) running
python 2.7.
When I download the repository to a local
Hello,
I have a file with fixed-width columns and I would like to use
the second column to populate a select list parameter. My problem
is that the number of whitespaces changes depending on the content of
the first column. Given that split is used in the underlying code,
I wanted to give None
Greetings all,
I've been trying to find a way to query fastq files for particular sequence
elements. Our data was mapped using BWA by our collaborator, and
repetitive elements 'ignored', but we are now interested in determining
whether a couple specific repetitive elements of interest are
Hi everyone,
I tried to create an AMI with my tools integrated on Galaxy, but by default it
mounts the snapshots with the tools from Galaxy. How I can change the snapshots
mounted by default? i.e. before I start a cluster.
Thanks,Jose
On Jun 14, 2012, at 12:48 PM, Peter Cock wrote:
In a separate example with 33 sub-tasks, there were two of these
inversions, while in yet another example with 33 sub-tasks there was
a trio submitted out of order. This non-deterministic behavior is a
little surprising, but in itself not an
On Thu, Jun 14, 2012 at 6:15 PM, Dannon Baker dannonba...@me.com wrote:
On Jun 14, 2012, at 12:48 PM, Peter Cock wrote:
In a separate example with 33 sub-tasks, there were two of these
inversions, while in yet another example with 33 sub-tasks there was
a trio submitted out of order. This
Hi Jane
I recommend mapping the data again yourself
Alternatively, you might wanna play with 'grep' (if you have the Galaxy
Unix tools installed in your Galaxy server), or use the tool 'Select
lines that match an expression'. I would do a Fastq to Tab on your data
first. Or you can try
Hello Birgit,
This issue has been resolved in changeset 7272:b761471d7590, which is currently
available from our Galaxy central repository. Both the Galaxy test and Galaxy
main tool sheds are running this latest changeset revision.
Thanks very much for reporting this problem!
Greg Von Kuster
Jose,
Did you see the 'Share-an-instance' option within CloudMan? It's the green
icon next to the cluster name in the console. It should do exactly what
you're describing.
Cheers,
Enis
On Thu, Jun 14, 2012 at 11:46 AM, Jose Navas josenavasmol...@hotmail.comwrote:
Ok, I will change my XML
Hi all,
I was able to configure Galaxy so that admins can use its Data Library
functionality. My colleague then asked if I could do the same for non-admin
users. I looked at the universe_wsgi.ini file and added a folder for the
users. How will I know that all is ready? I logged-in with a
Can non-admin users also utilize the option using filepaths?
___
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:
16 matches
Mail list logo
