If you did what the links posted previously suggested (inc. parallelization of
tools, mutliple server processes),
there is nothing more you can do.
Most of the tools galaxy just calls, so its the tool that you have to change.
Often genomic tools are also IO bound, so a faster storage system
Hi guys,
I have my fresh galaxy install on our cluster and now I'm trying to
figure out which tools are missing and how to install them.
I just came across the toolshed so now I'm really confused.
Question 1:
Can I install EVERY tool I need from the tool shed or are there some
things I need to
Hi Greg,
In case you haven't found it, the tool shed wiki provides a lot of information.
It's available at http://wiki.galaxyproject.org/Tool%20Shed
On Dec 10, 2012, at 10:59 AM, greg wrote:
Hi guys,
I have my fresh galaxy install on our cluster and now I'm trying to
figure out which
Hello,
The tool SAM to BAM generates a dataset from which it is possible to
download two files (instead of one) from the icon save.
As my script generates an output result and another txt output
containing information about linux command, I will wish not to generate
two datasets in history
That worked perfectly! Thanks Nate!
Chris
Galaxy dev:
I'm installing a local galaxy instance (Dec 4, 2012 vintage) and it is
running well under mySQL, but I'm having trouble getting it to work with a
postgres database.
I've done the following to create the db and provide
Fix for SelectToolParameter rerun,workflow when multiple=true
The following change allows multiple select values to be set on rerun and in
workflows. I checked that DrillDownSelectToolParameter and
ColumnListParameter stiil worked.
$ hg diff lib/galaxy/tools/parameters/basic.py
diff -r
Thanks, but I think now I'm even more confused :-(
It seems like a whole lot of the tools that are listed on the left
panel after installing galaxy aren't actually installed.
For example FastQC. Then I do see FastQC in the tool shed, but it
seems like when I go to install it, it will create its
I recently updated the htseq-count tool in the Galaxy toolshed to
version 0.3. This version has some functional changes and thus the tool
version was incremented. I installed this new version of the tool in my
local Galaxy instance.
However, I realized later that I missed updating one part
On Dec 10, 2012, at 1:14 PM, greg wrote:
Thanks, but I think now I'm even more confused :-(
Hmm...sorry. I highly advise you to read the tool shed wiki as it will clear
up a lot of your confusion.
It seems like a whole lot of the tools that are listed on the left
panel after installing
Please see the Megablast section on this page for instructions about getting
and adding target databases to Galaxy:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
Best,
J.
On Dec 10, 2012, at 2:59 PM, greg wrote:
I have a fresh install on our cluster.
I'm trying
On Sat, Jul 21, 2012 at 6:12 AM, Di Pe dip...@gmail.com wrote:
may be some other people would find this a useful enhancement:
https://bitbucket.org/galaxy/galaxy-central/issue/778/add-new-slurm-drmaa-runner-to-galaxy
Hi Di,
I've been testing several grid scheduling software trying to find
So I just want to install one target database so that I can simply
test whether blast is installed and working correctly.
Are there any included with Galaxy, or do I need to download a
database? Could you guys point me to a good file to test with?
Following the directions you sent I got to the
Hi,
Is there a way to export visualizations from Trackster and Sweepster in
.pdf or .jpg format? I have been using these fantastic tools to fine tune
my parameters and would like to show how I did so in figure format
(partially to locally get the word out about these powerful tools).
Screenshots
I made a galaxy tool which is just create a txt file. When I use this tool ,
I wish to let it show the detail of the txt.
In the xml file I use :
output data name=test format=txtoutput/
But it does not work, when I click the eye button in galaxy, a download
dialog appear, but it is just a
Are there any included with Galaxy, or do I need to download a
database?
You need to download them.
Could you guys point me to a good file to test with?
Following the directions you sent I got to the point of downloading a
file. I tried download
Unfortunately, no solutions right now; currently, screenshots are best that can
be done. One trick we often use for publications/posters is zooming, taking
multiple screenshots, and then composing them together; ugly, but pretty
effective for showing details.
We have some ideas about how to
On Dec 10, 2012, at 6:17 PM, Fabiano Lucchese fabiano.lucch...@hds.com wrote:
I appreciate your effort to help me, but it looks like my AWS account
has some serious hidden issues going on. I completely wiped out
CloudMan/Galaxy instances from my EC2 environment as well as their volumes,
Hi,
I have a local galaxy installation.
I've created a data library, selected Upload files from filesystem paths,
pasted a path in the path to upload window, and I've selected to preserve the
directory structure. And the files get imported.
How do I now access these files from my
Guys,
I appreciate your effort to help me, but it looks like my AWS account
has some serious hidden issues going on. I completely wiped out CloudMan/Galaxy
instances from my EC2 environment as well as their volumes, and waited a couple
of hours for the instances to disappear
Did you delete the S3/shapshots buckets? That is where everything is
stored and I think EBS volumes related to everything dynamic are created.
On 12/10/12 6:17 PM, Fabiano Lucchese fabiano.lucch...@hds.com wrote:
Guys,
I appreciate your effort to help me, but it looks like my AWS
I made a galaxy tool which is just create a txt file. When I use this tool ,
I wish to let it show the detail of the txt.
In the xml file I use :
output data name=test format=txtoutput/
But it does not work, when I click the eye button in galaxy, a download
dialog appear, but it is just a
Hello Everyone,
We have found that, in Galaxy, when we add dataset to a library under
Manage data libraries, Galaxy sometimes detects the type of the file and
sometimes does not. What I have noticed is that it detects the type of the
file when we select Copy file into Galaxy under Copy data into
Hi Greg, list
When installing a tool dependency, and the Installation Status shows : Error
In what log would the actual error be specified??
Thanks,
Franco
On 5/12/12 9:10 PM, Greg Von Kuster g...@bx.psu.edu wrote:
If you have not yet updated your Galaxy instance to the revision from the
Never mind, the INSTALLATION .log is in the repository browser...
Sorry,
Franco
On 11/12/12 4:17 PM, Franco Caramia franco.cara...@petermac.org wrote:
Hi Greg, list
When installing a tool dependency, and the Installation Status shows : Error
In what log would the actual error be
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