Dynamically adding tools to Galaxy
by Sumedha Ganjoo
Hello,
I am a student at the University Of Georgia. We had developed a tool for
Galaxy 1.3 that enables accessing
various web services as tools from Galaxy.
We are currently working on a similar tool for the current version of
Galaxy. This requires adding a tool dynamically
without having to restart Galaxy. I was wondering if someone has already
implemented that feature? We do have most
of the code for this in place. Is there a way, once complete, this code can
be added to the main Galaxy source code?
Also I would really appreciate if someone could tell me where can I find the
older versions ( v 1.3 ) of Galaxy?
Thanks in advance.
Regards,
Sumedha
Sumedha Ganjoo
Graduate Assistant
Computer Science Department
University Of Georgia
11 years, 2 months
Re: [galaxy-dev] [galaxy-user] MACS input format
by Steve Taylor
On 30/04/2010 15:37, Daniel Blankenberg wrote:
> Hi Steve,
>
> The latest version in the repository and on the test server accepts bed, sam, bam, eland and elandmulti for single-end and elandmulti only for paired-end. The version currently on the main public server accepts bed, sam, and bam for single-end with paired-end not functioning. The newest version of MACs will be available on the main public server the next time it is updated.
>
>
Strange. On our local Galaxy instance I got
ERROR:root:Format "SAM" cannot be recognized!
and the bowtie (SAM) format was generated from within Galaxy.
Any ideas why?
Steve
11 years, 5 months
Asking for Galaxy main public instance support, thanks!
by WangJun
Hello Dr Greg Von Kuster,
We are developing a Rice Genome Browser: Rice-Map. I am writing to ask if you can add our resource to your main public instance so that users can get data from Rice-Map and do analysis in your platform conveniently.
Steps for adding Rice-Map:
1. Add tool definition file "cbi_rmap_browser.xml" under tools/data_source directory (attached).
2. Add this tool into file "tool_conf.xml" in the "Get Data" section:
<tool file="data_source/cbi_rmap_browser.xml" />
Thank you in advance!
Best wishes,
Kathleen
Center for Bioinformatics
Peking University
11 years, 5 months
Galaxy issue
by Modi, Amit
Hi,
We are trying to configure Galaxy to work with our tool.
So far I have been able to configure it well and link it with the cluster to do process all the jobs as per the documentation .
Now what we want is the before the actual processing starts the validations for the input files are done on the
Local. And the job processing is done on the cluster.
Is there anyway we can configure this.
We are using sge on the cluster.
Thanks a lot.
Regards,
Amit Modi
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11 years, 5 months
tiny usability issue - cloning vs. importing shared history
by Assaf Gordon
Hi,
I've noticed a small usability annoyance with shared histories.
Scenario:
A user shared a history with me.
The new history appears in the "Histories shared with you by others" page.
I click on the history name, get a popup menu with three options: View, Clone, Unshare.
If I choose "clone", the history is cloned and appears in my "saved history".
If I choose "view" (and look at the library) then click on the green import button, I get a red error message:
"The owner of this history has disabled imports via this link.
You can return to the previous page."
I understand that "cloning" is technically different from "import via link",
but conceptually, the end result is the same - I should get the shared history into my histories.
So it's quite confusing when I get this error message.
Since I'm slightly familiar with Galaxy, I realized that the correct thing to do is go back to the list of shared-histories, then "clone" instead of import.
An inexperienced user might think that something is wrong with the sharing.
Somewhat related:
After importing a history via link, the "start using this history" link does not work if the current history a non-empty.
To reproduce:
1. go to http://main.g2.bx.psu.edu/
2. click "options" -> "create new".
3. current history is empty.
4. go to http://main.g2.bx.psu.edu/history/list_published
5. select any one of the histories (e.g. "SM_1186088")
6. Click on the green plus button to import the history.
7. The following message is displayed:
History "imported: SM_1186088" has been imported.
You can start using this history or return to the previous page.
8. click on "start using this history", you'll be back on the main galaxy web site, with this new history selected.
So far, so good.
Now, repeat steps 1-8, but instead of creating a new, empty history (step 2,3), select a non-empty history or upload some dummy data set.
After clicking "start using this history" (step 8) you'll be at the *old* history, not the newly imported one.
-gordon
11 years, 5 months
grouping and sorting error at a bare local installation
by Jordi Rambla
Hi,
I'm quite new to Galaxy and Python, but I have near 25 years of experience
at computing (development, databases, web development, systems.)
I've performed a local installation in order to learn Galaxy and it's
"internals".
In order to test the installation, I'm reproducing the Galaxy screencast
tutorials locally.
When reproducing the screencast named : "Finding Exons with the highest
number of nucleotide polymorphisms", at step 4 (grouping and counting).
I'm receiving the following error: "An error occurred running this job:
Sorting input dataset resulted in error: 512: sort: multi-character tab
`$\t'".
Just to doublecheck, I've tried to just sort the dataset on column 4 (Name),
and I'm receiving a quite similar error ("An error occurred running this
job: sort: multi-character tab `$\t'").
I've tried to locate the error source at the configuration/ source code
files. but found nothing promising on filters/sorter.py nor
stats/grouping.py.
Thus, I'm asking for a tip on where to look at.
Thanks in advance.
Jordi Rambla
Universitat de Barcelona
11 years, 5 months
data visualization in galaxy trackster
by Vipin TS
Hi Galaxy team,
I am trying to visualize data in galaxy using trackster. I made necessary
requirement based on the documentation in
http://bitbucket.org/galaxy/galaxy-central/wiki/Visualization.
My data set in wiggle variableStep format. below here is few lines from my
wiggle file
track type=wiggle_0 name="test run"
variableStep chrom=III
1841 1
1842 1
1843 1
1844 1
1845 1
1846 1
1847 1
1848 1
1849 1
1850 1
1851 1
1852 1
1853 1
It is about 3.2MB in size and I tried to create a new track browser in my
local galaxy instance. Unfortunately it just shows the message "Loading
data ..." for the last five hours.
Any ideas are sincerely appreciated.
many thanks, Vipin T S
11 years, 5 months
Error for one user when using edit properties
by SHAUN WEBB
Hi, we are having problems with a single user account. When using the
'edit attributes' button on a dataset an error is returned (traceback
below). This is happening with each dataset/history. However, if the
dataset is shared then properties can be edited by a different user or
while logged out. It appears to be solely linked to this users account.
Thanks in advance for any help.
Shaun Webb
When trying to 'Edit Attributes'
URL: http://bifx3.bio.ed.ac.uk:8080/root/edit?id=2558
File
'/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/exceptions/errormiddleware.py', line 143 in
__call__
app_iter = self.application(environ, start_response)
File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/debug/prints.py',
line 98 in __call__
environ, self.app)
File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/wsgilib.py', line
539 in intercept_output
app_iter = application(environ, replacement_start_response)
File '/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/opt/galaxy_dist/eggs/Paste-1.6-py2.5.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File '/opt/galaxy_dist/lib/galaxy/web/framework/base.py', line 125 in
__call__
body = method( trans, **kwargs )
File '/opt/galaxy_dist/lib/galaxy/web/controllers/root.py', line 364 in
edit
all_roles = trans.app.security_agent.get_legitimate_roles( trans,
data.dataset, 'root' )
File '/opt/galaxy_dist/lib/galaxy/security/__init__.py', line 174 in
get_legitimate_roles
return sort_by_attr( [ role for role in roles ], 'name' )
File '/opt/galaxy_dist/lib/galaxy/security/__init__.py', line 142 in
sort_by_attr
intermed = map( None, map( getattr, seq, ( attr, ) * len( seq ) ),
xrange( len( seq ) ), seq )
AttributeError: 'NoneType' object has no attribute 'name'
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11 years, 5 months
Job Control in Galaxy
by Steve Taylor
Hi,
We have configured our Galaxy system to use Sun Grid Engine in shared mode. We noticed that on submission of a job that running qstat does not show the jobs status. It looks the a wrapper shell script defining the environment and the command(s) is being submitted and then as far as SGE is concerned the job is done (however, the job is still running on the application server).
I don't understand when using this system how you can manage submitted jobs. Isn't the point of using a queuing system like SGE that you can manage the load on the servers using the SGE configuration tool (qconf) to control the queues? Or am I misunderstanding something?
Thanks for any advice,
Steve
11 years, 5 months
Re: [galaxy-dev] NGS peak calling: MACS
by Vipin TS
Hi Kanwei,
I am sorry, I am using a BED formatted wiggle file. Here is first few lines
from my file
track type=wiggle_0 name=polyA_left
chrIII 329 405 1
chrIII 1841 1868 1
chrIII 1868 1917 3
chrIII 1917 1944 2
chrIII 8486 8496 1
chrIII 8496 8498 12
chrIII 8498 8504 13
chrIII 8504 8509 14
chrIII 8509 8512 15
chrIII 8512 8551 18
chrIII 8551 8562 20
chrIII 8562 8572 19
chrIII 8572 8574 8
chrIII 8574 8579 7
chrIII 8579 8580 8
chrIII 8580 8585 7
chrIII 8585 8588 6
chrIII 8588 8627 3
chrIII 8627 8655 1
each line with four required fields, they are 1| chromosome/contig ID of the
reference sequence, 2| feature start position 3| feature end position and 4|
feature coverage score.
thnaks, Vipin T S
On 27 April 2010 19:17, Kanwei Li <kanwei(a)gmail.com> wrote:
> Hi Vipin,
>
> What is a bed wiggle file? We support both, but not at the same time :P
>
> Kanwei
>
11 years, 5 months
