[galaxy-dev] Secure Passwords
Hi, is there any current functionality or plans to enforce secure passwords when registering a new account? By secure I mean tests on length, use of capitals and alphanumeric characters etc. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] casOT wrapper
Hi, I was just wondering if anyone has put any work in to developing wrappers for casOT: http://eendb.zfgenetics.org/casot/index.php Couldn't see anything in the toolshed. If not I'll have a go myself. Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tool shed tool error
Hi, I have created a tool and added it to a local tool shed. It installs ok but when I run the tool I get the following error: Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator. I get the same error with other tools in my tool shed both on our test galaxy site (updated to latest release and using new job_conf.xml file) and our production site (Feb 8th dist). I then loaded the tool to the main glaxy test tool shed and installed from there, I still get the same error. I am now assuming that the problem is with the tool. The error is rather vague, can anyone point me to what could possibly cause this error? Thanks Shaun Webb University of Edinburgh -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Manage Local data
Hi I am trying to load the mm10 genome and indexes using the manage local data admin feature. The genome downloads ok and so do the liftOver chain files, however the main controller and indexing jobs fail. They just display error, is there any way I can find out more about what is happening here and what is failing? Thanks Shaun Webb University of Edinburgh -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] customtrack visualisation
Hi Jen, I should have said this is in my own install. It works fine at the main server. I only noticed this as I was running a tutorial I created last year. So I can only say that something has changed in the last year.. I was wondering where in the configuration files or scripts galaxy is told to provide this link for this type of dataset, perhaps there is something I need to reconfigure. Thanks Shaun Quoting Jennifer Jackson j...@bx.psu.edu on Wed, 20 Mar 2013 07:08:13 -0700: Hi Shaun. Is this still an issue for you this morning, on the public Main Galaxy server at https://main.g2.bx.psu.edu/? I am unable to reproduce with a test dataset: - bed custom track - datatype = customtrack - database = hg18 display at UCSC main is functional, and it is the only external display (this is expected). If you want to share a history with me, please send a link and note the dataset with the problem. Thanks, Jen Galaxy team On 3/19/13 2:44 AM, Shaun Webb wrote: Hi, I have lost my view in UCSC link on my customtrack datatypes, I'm not sure when this happened. External display links are still working ok for other datatypes. I have set the genome database to hg18. Any idea what I will need to edit to get this back? Thanks Shaun webb -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] customtrack visualisation
Hi, I have lost my view in UCSC link on my customtrack datatypes, I'm not sure when this happened. External display links are still working ok for other datatypes. I have set the genome database to hg18. Any idea what I will need to edit to get this back? Thanks Shaun webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Blast+ tools
Thanks for your reply Peter The other tools work fine. I noticed that the makeblastdb process was still running on the server even after Galaxy said the job was complete, but still no files appeared in this directory. I have killed that process for now and will play around with it and see if I can figure it out. I'll let you kno if I find something. Shaun Quoting Peter Cock p.j.a.c...@googlemail.com on Wed, 5 Dec 2012 15:44:47 +: On Wed, Dec 5, 2012 at 2:37 PM, Shaun Webb swe...@staffmail.ed.ac.uk wrote: I have just installed the Blast+ tools from the Galaxy tool shed and tried to make a Blast DB from a fasta file in history. The tool runs ok and indicates that a blastdb has been created in: /storage/home/galaxy/production/galaxy-dist/database/files/085/dataset_85192_files/blastdb There should be a collection of files named blastdb.* in the folder /storage/home/galaxy/production/galaxy-dist/database/files/085/dataset_85192_files/ However there is no directory dataset_85192_files. I have blast installed and I'm able to run makeblastdb on the command line. Do I have to make any other modifications before I can use Blast tools? I'm unsure what could be wrong. Do the other BLAST+ tools seem to work (e.g. blastp)? Are all the BLAST tools configured the same way in terms of universe_wsgi.ini and their job runners - or do you have some running on the cluster and some on the head node? My guess is something about the mounted storage, but then I would have expected problems with other tools as well. Peter -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Workflow loading problem
Hi, I have imported a workflow to my local Galaxy with unrecognised tools. When I try to edit this workflow it will not load. I now realise I have the same problem with some existing workflows where a tool has been removed from Galaxy, I would like to replace these workflow steps without creating a new workflow. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Another trackster issue?
I am looking at bigwig files in trackster. When I zoom in the point where 20kb is displayed on screen I get large blocks of the track separated by empty gaps. When I zoom in to these gaps there is definitely track signal there. Is this a bug or is this intended to limit the amount of data to load? Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy and Toolshed issues
Hi Greg. I had the tool shed and Galaxy opened in two tabs so this may have been the issue. I am using a mysql database. I will check tis again when I next update Galaxy and let you know if there is a problem. Thanks for your help Shaun Quoting Greg Von Kuster g...@bx.psu.edu on Wed, 1 Aug 2012 11:24:44 -0400: Hi Shaun, Thanks very much for the details - they have helped me discover a weakness which I've fixed. if the browser page is opened to the Manage repository page in the tool shed when the repository is cloned for the first time, the repository name could be changed after the clone. This has been fixed in change set 7441:513a95abb738. However, your step 4 (return to toolshed, find repository) implies that this is not what you were doing. Can you update to the tip from Galaxy central and see if my latest fix still allows you to change the repository name after it has been cloned in your environment? If so, I'll need to figure out what you are doing differently that is still allowing for this. Also, what database are you using? I found some issues with sqlite that I've fixed that would not eve have allowed for the repository to be cloned in the first place. Thanks again! Greg On Aug 1, 2012, at 7:03 AM, SHAUN WEBB wrote: Quoting Greg Von Kuster g...@bx.psu.edu on Wed, 1 Aug 2012 06:23:11 -0400: I cannot reproduce this behavior, so can you let me know the steps you use to do so? I need the page on which you are able to change the name of the tool shed repository in the tool shed after it has been cloned. 1. Create new repository in local toolshed and fill in name, synopsis, description and category 2. Upload a .pl script file then upload a .xml wrapper file 3. Go to my local Galaxy and install repository via admin panel 4. Return to toolshed, find repository and name etc are still editable Screen shot attached. I noticed that times downloaded is still 0 after installing the repository. I have cloned the repository using hg on command line and this is still not updated. I'm guessing this is the problem. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Changing Install Directory
Hi all, I would like to change the name of the directory where my Galaxy instance is installed. What is the best way to go about this without breaking any paths/links. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy and Toolshed issues
Hi Greg, thanks for the response Quoting Greg Von Kuster g...@bx.psu.edu on Tue, 31 Jul 2012 11:50:36 -0400: Hi Shaun, On Jul 31, 2012, at 9:37 AM, SHAUN WEBB wrote: Hi, I have been trying out the latest version of Galaxy and a newly installed local toolshed and I have a few questions/suggestions/bug reports: 1. Tool Versioning: a) As I understand from the wiki, when I create a new version of a tool in a tool shed I must then install the latest version in my Galaxy instance. This is not correct - you can choose to install any valid version of the tool(s). Can you let me know what content of the wiki resulted in this confusion? I'll be sure to make it more clear. This then shows up as two separate tools in my tool menu. Presumably it is best to change the xml description tag to reflect the version number and make tool versions distinguishable in the Galaxy tool menu? b) Would it make more sense to have a single entry for each tool in the tool menu and a drop down to choose which version to run in the tool gui? Similar to when I try to rerun a tool that is no longer installed I get a drop down option to use a derivative of that tool if it exists. Your above recommendation in (b) is exactly what will occur as soon as I get a chance to implement it. Perhaps my wording was unclear here. What I meant was if a new version of a tool is created in a tool shed I have to install that version to be able to use it, rather than using 'get updates'. This then results in multiple listings of the tool. But it sounds like you plan on improving this process anyway. c) The toolshed interface allows me to change the name of my tool. If I do this, then go to my Galaxy admin ui and try to get updates for my tool then it fails. Does it make sense to change a tools name after it is created? Is it possible to track previous tool names to avoid this happening? This should not occur. Where are you able to change the name of your tool? You are not even allowed to change the name of the repository if it has been cloned (you can change the name of the repository as long as it has not been cloned). Can you send me a screen shot of hte page that allows you to change the name of your tool in the tool shed? I'll provide a fix as soon as I see where the issue lies. OK, I guess I changed the name of my repository not tool. I then installed the tool via my local Galaxy instance. I can still change the name of the repository in my toolshed and when I try to get updates via Galaxy admin panel I get the following server error: AttributeError: 'NoneType' object has no attribute 'repo_path' Running toolshed tools: I have no problems installing tools from toolsheds via Galaxy admin interface, however I can't get these tools to run. They stay Grey forever and look like this in the manage jobs table: 65 x...@.xx.ac.uk 0 minutes ago toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_coveragebed_counts/0.1.0 new None None None Do I have to set a tool runner or some other option for shed_tools? No special configuration settings are required in your local Galaxy instance to to run tools installed from a tool shed. If they stay in the queued state, there must be an issue in your local Galaxy instance that causes installed tools as well as tools included in the distribution to remain queued. It has nothing to do with the fact they were installed. No. All other tools run fine. Tools installed from either my toolshed or the Galaxy toolshed remain queued. If this is not a known issue then I will try to dig a little deeper to find the problem. Any pointers would be useful if you can think of why there should be a difference. Thanks for your help! Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Problem with proxy
Hi, I have set up a test version of Galaxy running on the same hostname as our production server. I have set up the test version to include web scaling and to run behind a proxy served on a sub-directory. The production version has neither of these features. When I enable the following code in universe.wsgi.ini I am unable to login. There is no error, also I cannot access a history if I try to upload datasets as an anonymous user, again there is no error but datasets do not appear in the history: [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy_test [app:main] filter-with = proxy-prefix cookie_path = /galaxy_test The cookie_path code appears to be causing the issue. Is the problem having 2 instances on the same hostname and only one behind a proxy? If I comment out the code everything seems to work okay (apart from the problem I had previously http://gmod.827538.n3.nabble.com/Error-loading-data-tt4013269.html). Thanks in advance for any help Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Error loading data
Hi, I have just upgrade my test version of Galaxy to the latest dist release and I am getting an error trying to load data either as an upload, a pasted entry or from UCSC. I have only altered conf files, any pointers to what could be causing this would be appreciated. The error is below: Traceback (most recent call last): File /storage/home/galaxy/test/pre-dev/galaxy-dist/tools/data_source/upload.py, line 403, in module __main__() File /storage/home/galaxy/test/pre-dev/galaxy-dist/tools/data_source/upload.py, line 378, in __main__ registry.load_datatypes( root_dir=sys.argv[1], config=sys.argv[2] ) AttributeError: 'Registry' object has no attribute 'load_datatypes' Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Delete multiple datasets
Hi, is there any plan to add capability to delete multiple datasets at once, similar to the copy datasets interface in the history options menu. If I am running workflows and want to delete all the created datasets (during testing or if I've used the wrong parameters etc) it is quite tedious to delete each individual dataset. It would be useful to see and delete any hidden datasets in a similar fashion. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Deleted datasets
Hi, looking at Galaxy reports I have 505 datasets which have been deleted 60 days ago but have not been purged. My purging scripts seem to be working correctly in cron. Why do these datasets not get deleted? Is it likely that these are in shared or accessible histories and only deleted by the owner? Any tips would be good, trying to free up some space on our server. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Feature requests - viewing data and annotations
Restricting datasets to show only the first megabyte is a great idea when dealing with large data files but sometimes I want to see the end of a file to check it is complete or to check the progress of a running job. At the moment I use the helper script to find the file on the server and then use tail. Would it be possible to add a button in the dataset view (next to show all and save) that allows you to see the end of the file? Also, I have noticed a few discussions regarding tracking datasets through a history and sensible naming of history items. In my experience the best way to keep track of a history, especially one you haven't visited for a while, is to keep good notes. The tags and annotations for individual history items is good but I don't think the space provided for a history annotation is practical either in size or format. Ideally I would like to have a large area to add notes while still being able to view datasets. Perhaps turning on annotation could split the main pane in to 2 areas with adjustable size with an annotation area on the bottom? Maybe there would be a way to link Galaxy pages directly to histories? I'm not sure what the best way to implement this would be but I'd like to see an improvement. Thanks to all the Galaxy team Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Coverage for paired end data
Hi all. I am analysing paired end chip-seq samples. With single end reads I have seen people extend reads by an inferred insert size and then create coverage files in wig format. I was wondering if there are any tools available for paired end data that will create a coverage file by looking at properly mapped paired ends in a bam file and extending coverage across the distance between them. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] googlebot
Thanks. Do I need to have Galaxy running via apache for this to take effect? Quoting Redmond, James jredm...@wustl.edu on Mon, 12 Dec 2011 18:30:02 +: That's the correct configuration, and it should disallow all bots from all files in that tree. Robot exclusion files are just a request, though, and not compulsory; if that particular user-agent becomes a real issue, then it may be better to find a way to block it through your HTTP server. Jim Redmond Department of Developmental Biology Washington University in St. Louis jredm...@wustl.edu -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of SHAUN WEBB Sent: Monday, December 12, 2011 8:40 AM To: galaxy dev Subject: [galaxy-dev] googlebot Hi, my paster.log is full of errors relating to a googlebot trying to access a library file. I noticed a robots.txt file in the static folder configured as such. User-agent: * Disallow: / I thought this would stop all bots accessing all files. Should this be configured differently? Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/ -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] googlebot
Hi, my paster.log is full of errors relating to a googlebot trying to access a library file. I noticed a robots.txt file in the static folder configured as such. User-agent: * Disallow: / I thought this would stop all bots accessing all files. Should this be configured differently? Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Server Error after Update
Hi, I updated my test server today and everything seemed fine. I added
a new library item via a URL. After that my history panel displays
Internal Server Error and I am getting the error below in paster.log:
Any ideas how this has occurred and if there is a fix?
Shaun
Exception happened during processing of request from ('2.218.9.31', 63227)
Traceback (most recent call last):
File
/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 1053, in
process_request_in_thread
self.finish_request(request, client_address)
File /usr/lib/python2.6/SocketServer.py, line 320, in finish_request
self.RequestHandlerClass(request, client_address, self)
File /usr/lib/python2.6/SocketServer.py, line 615, in __init__
self.handle()
File
/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 432, in
handle
BaseHTTPRequestHandler.handle(self)
File /usr/lib/python2.6/BaseHTTPServer.py, line 329, in handle
self.handle_one_request()
File
/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 427, in
handle_one_request
self.wsgi_execute()
File
/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 290, in
wsgi_execute
self.wsgi_write_chunk(chunk)
File
/storage/home/galaxy/test/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py, line 125, in
wsgi_write_chunk
Content returned before start_response called)
RuntimeError: Content returned before start_response called
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Re: [galaxy-dev] HOW TO RETRIEVE DATA FROM HISTORY??!!
Hi Nate. Could you provide more info on how to run this script. I have a history and dataset name and I want to find the file stored on the server. Thanks Shaun Thanks Assaf, This has come up enough times that I've just committed a script that will return the filename if provided a numeric or encoded HDA. I've posted it to the list before as galaxythinger.py, it's in the source as galaxy-dist/scripts/helper.py as of 5919:0f878ea61e98. It will also decode and encode IDs. More functionality for common sysadmin tasks would be welcomed. --nate hope this helps, -gordon ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/ -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Tab sniffer
Hi. I am using the upload tool to enter some test data in the text box and checking the convert spaces to tabs box. However Galaxy is setting the file as txt rather than tabular, this seems to be a new bug. Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Version String
Hi. I am using the tag: version_stringpath to tool --version/version_string In my xml file. I would expect the tool version to be printed in the information window for each dataset but the version field is blank. I am running the latest Galaxy dist, is there anything else I need to do? I have tried using version_command also. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Setting the output label based on input parameters?
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 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 doing
wrong?
- Nik.
On Wed, Aug 24, 2011 at 5:34 PM, Kanwei Li kan...@gmail.com wrote:
Hi Nikhil,
The tool templates are Cheetah templates, so you can do things like:
outputs
%if param == True:
data format=txt name=blah label=Label1 /
%else
data format=txt name=blah label=Label2 /
%endif
/outputs
Thanks,
K
On Wed, Aug 24, 2011 at 8:24 PM, Nikhil Joshi najo...@ucdavis.edu wrote:
Hi all,
Is there a way to set the label of the output based on the input
parameters? Perhaps by using the action tag? Basically, I want the
output label to be different if the user sets a particular parameter to be
true.
- Nik.
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[galaxy-dev] Sam2interval.py bug
Hi, I've noticed a bug in sam2interval.py. There are a few indentation errors in the final lines of code. I think there should be an indent after: if not ref_name == '*': And this whole if statement should be included in the for loop above. Also, would you be able to add read_name to the truncated output (when not printing all fields). This makes downstream analysis a lot easier, e.g. looking at reads that map multiple times. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Tool XML parameter options from locally stored files
Hi.
I'm still searching for a solution to this problem.
Currently we have to implement a tool to read the GTF file selected
via a from_data_table parameter and output a list of feature types.
Secondly we have a second tool that reads this file using a
from_dataset parameter so the user can select a specific datatype.
Not really ideal, I would prefer to do this in one tool if possible.
If I could reference the file chosen in the first select then this
should work.
For instance in the output data tags I can put label=${gtf.value}
and it returns the name of the selected file from the datatable.
If I do the same in inputs section: options from_file=${gtf.value}
galaxy tries to find the file [galaxy_dir]/tool-data/${gtf.value}.
So the solution would ideally look like this:
param name=gtf type=select label=GTF File --gtf
options from_data_table=pycrac_gtf/ !--link to .loc file with
gtf file per species --
/param
param name=feature type=select label=Select feature
options from_file=${gtf.value}
column name=name index=2/
column name=value index=2/
filter type=unique_value name=unique column=1/
/options
/param
Hope that makes sense.
Thanks
Shaun
Quoting SHAUN WEBB swe...@staffmail.ed.ac.uk on Fri, 15 Jul 2011
10:17:44 +0100:
Hi Greg,
thanks for the suggestion. This line doesn't seem to work:
options from_file=some_value
Galaxy looks for a file at galaxy_dir/tool-data/some_value rather
than the value given in the .loc file
I would also like to be able to use the galaxy data tables rather
then referring directly to a .loc file.
Any ideas?
Shaun
Quoting Greg Von Kuster g...@bx.psu.edu on Wed, 13 Jul 2011 10:28:30 -0400:
Hi Shaun,
This should be possible. It's been quite a long time since I
worked on tools, so maybe others can provide better assistance if I
am incorrect here. You'll need to have a conditional something
like the following ( not tested whatsoever ):
conditional name=selected_file_select_list
param name=selected_gtf_file type=select label=Gtf
file by species
options from_file=some_file
column name=name index=2/
column name=some_value index=1/
/options
/param
when value=some_value
param name=values_from_selected_gtf_file
type=select label=Values from selected gtf file /
options from_file=some_value
column name=name index=2/
column name=some_value index=1/
/options
/when
/conditional
On Jul 13, 2011, at 9:45 AM, SHAUN WEBB wrote:
Hi Greg, I'm not sure if this answers my question. Using
options_from_file is fine if I want to refer to the same file each
time.
In this case I want the first select to choose which gtf file to
look at (by species) and the second select to pull options (gtf
annotation types) from this file.
So I would somehow have to reference the file using the first
parameter rather than giving a hard-coded path.
Is that possible?
Shaun
Quoting Greg Von Kuster g...@bx.psu.edu on Wed, 13 Jul 2011
09:23:19 -0400:
Hello Shaun,
Use the 'from_file' option. The referenced file should be in the
~/tool-data directory in the Galaxy root. There are several
example tools in the distribution that use this option. Here is
the example code from the annotation profiler tool:
param name=table_names type=drill_down display=checkbox
hierarchy=recurse multiple=true label=Choose Tables to Use
help=Selecting no tables will result in using all tables.
from_file=annotation_profiler_options.xml/
and here is an example from the microbial import tool:
param name=kingdom type=select label=Select the Desired
Kingdom
options from_file=microbial_data.loc startswith=ORG
column name=name index=3/
column name=value index=3/
filter type=unique_value name=unique column=3/
/options
/param
On Jul 13, 2011, at 6:17 AM, SHAUN WEBB wrote:
Hi,
I am trying to write a tool xml file and want to do the following:
I have a number of GTF files stored locally and referenced in a
data table. I give the user a drop down list of those available
using the following code:
param name=gtf type=select label=GTF File
options from_data_table=gtf_files/
/param
I then want them to choose an annotation type based on those
present in the selected gtf file above. It seems simple enough
to do this if the gtf file is in your history already:
param name=feature type=select multiple=true
label=Extract features
options from_dataset=gtf
column name=name index=2/
column name=value index=2/
filter type=unique_value name=unique column=2/
/options
/param
But is there a way to query locally stored files via
datatables/.loc files to pull out options when the file is
dynamically chosen
[galaxy-dev] Error preparing job
Hi all, I'm getting the following error running a custom tool. I'm not really sure where the problem is coming from, it doesn't happen every time I run the tool. Can anyone point me in the right direction? Thanks Shaun Traceback (most recent call last): File /storage/home/galaxy/test/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 58, in run_job job_wrapper.prepare() File /storage/home/galaxy/test/galaxy-dist/lib/galaxy/jobs/__init__.py, line 372, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /storage/home/galaxy/test/galaxy-dist/lib/galaxy/tools/__init__.py, line 1585, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /storage/home/galaxy/test/galaxy-dist/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /storage/home/galaxy/test/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File cheetah_DynamicallyCompiledCheetahTemplate_1311417753_92_55587.py, line 88, in respond NotFound: cannot find 'checktype' -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Error preparing job - PLEASE IGNORE PREVIOUS
Ignore previous email, I found the error, it was not a Galaxy problem Thanks Shaun Quoting SHAUN WEBB swe...@staffmail.ed.ac.uk on Mon, 25 Jul 2011 11:21:43 +0100: Hi all, I'm getting the following error running a custom tool. I'm not really sure where the problem is coming from, it doesn't happen every time I run the tool. Can anyone point me in the right direction? Thanks Shaun Traceback (most recent call last): File /storage/home/galaxy/test/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 58, in run_job job_wrapper.prepare() File /storage/home/galaxy/test/galaxy-dist/lib/galaxy/jobs/__init__.py, line 372, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /storage/home/galaxy/test/galaxy-dist/lib/galaxy/tools/__init__.py, line 1585, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /storage/home/galaxy/test/galaxy-dist/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /storage/home/galaxy/test/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File cheetah_DynamicallyCompiledCheetahTemplate_1311417753_92_55587.py, line 88, in respond NotFound: cannot find 'checktype' -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] checkers
Hi, I recently update to the latest dist release and I'm getting this error whenever I try to upload files Traceback (most recent call last): File /storage/home/galaxy/test/galaxy-dist/tools/data_source/upload.py, line 11, in from galaxy.datatypes.checkers import * ImportError: No module named checkers Should this module be provide with Galaxy or do I have to download it from somewhere? Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] checkers
Yeah it's there. I'm guessing something isn't configured right then. Any ideas? Thanks Shaun Quoting Kanwei Li kan...@gmail.com on Mon, 18 Jul 2011 11:36:11 -0400: Hi Shaun, It is included in galaxy... do you see the checkers.py file in lib/galaxy/datatypes/checkers.py ? -K On Mon, Jul 18, 2011 at 11:31 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk wrote: Hi, I recently update to the latest dist release and I'm getting this error whenever I try to upload files Traceback (most recent call last): File /storage/home/galaxy/test/galaxy-dist/tools/data_source/upload.py, line 11, in from galaxy.datatypes.checkers import * ImportError: No module named checkers Should this module be provide with Galaxy or do I have to download it from somewhere? Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/ -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Tool XML parameter options from locally stored files
Hi Greg, thanks for the suggestion. This line doesn't seem to work: options from_file=some_value Galaxy looks for a file at galaxy_dir/tool-data/some_value rather than the value given in the .loc file I would also like to be able to use the galaxy data tables rather then referring directly to a .loc file. Any ideas? Shaun Quoting Greg Von Kuster g...@bx.psu.edu on Wed, 13 Jul 2011 10:28:30 -0400: Hi Shaun, This should be possible. It's been quite a long time since I worked on tools, so maybe others can provide better assistance if I am incorrect here. You'll need to have a conditional something like the following ( not tested whatsoever ): conditional name=selected_file_select_list param name=selected_gtf_file type=select label=Gtf file by species options from_file=some_file column name=name index=2/ column name=some_value index=1/ /options /param when value=some_value param name=values_from_selected_gtf_file type=select label=Values from selected gtf file / options from_file=some_value column name=name index=2/ column name=some_value index=1/ /options /when /conditional On Jul 13, 2011, at 9:45 AM, SHAUN WEBB wrote: Hi Greg, I'm not sure if this answers my question. Using options_from_file is fine if I want to refer to the same file each time. In this case I want the first select to choose which gtf file to look at (by species) and the second select to pull options (gtf annotation types) from this file. So I would somehow have to reference the file using the first parameter rather than giving a hard-coded path. Is that possible? Shaun Quoting Greg Von Kuster g...@bx.psu.edu on Wed, 13 Jul 2011 09:23:19 -0400: Hello Shaun, Use the 'from_file' option. The referenced file should be in the ~/tool-data directory in the Galaxy root. There are several example tools in the distribution that use this option. Here is the example code from the annotation profiler tool: param name=table_names type=drill_down display=checkbox hierarchy=recurse multiple=true label=Choose Tables to Use help=Selecting no tables will result in using all tables. from_file=annotation_profiler_options.xml/ and here is an example from the microbial import tool: param name=kingdom type=select label=Select the Desired Kingdom options from_file=microbial_data.loc startswith=ORG column name=name index=3/ column name=value index=3/ filter type=unique_value name=unique column=3/ /options /param On Jul 13, 2011, at 6:17 AM, SHAUN WEBB wrote: Hi, I am trying to write a tool xml file and want to do the following: I have a number of GTF files stored locally and referenced in a data table. I give the user a drop down list of those available using the following code: param name=gtf type=select label=GTF File options from_data_table=gtf_files/ /param I then want them to choose an annotation type based on those present in the selected gtf file above. It seems simple enough to do this if the gtf file is in your history already: param name=feature type=select multiple=true label=Extract features options from_dataset=gtf column name=name index=2/ column name=value index=2/ filter type=unique_value name=unique column=2/ /options /param But is there a way to query locally stored files via datatables/.loc files to pull out options when the file is dynamically chosen by a different parameter? This code is also wrapped in a conditional, I'm not sure if that will affect anything. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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
Re: [galaxy-dev] Tool Shed Problem
Thanks Greg, could you delete the repository I created please? I guess that step isn't necessary as most people won't create repositories until they are ready to go. It would stop curious users like me creating empty repositories by just clicking buttons.. Is there more documentation on what is required to publish a new tool in the tool shed? Shaun Quoting Greg Von Kuster g...@bx.psu.edu on Tue, 12 Jul 2011 10:24:28 -0400: Hello Shaun, On Jul 12, 2011, at 6:07 AM, SHAUN WEBB wrote: Hi Galaxy team, I created a new repository on the tool shed called test, I wanted to see what steps were required to publish a tool before I go ahead and release the production version. I then tried to change the name of the repository and got a server error. This problem was due to a bug which I've fixed, so the tool shed is functional with your renamed repository. Thanks for finding the bug... When I search for test, try to navigate to 2nd page of the repository list or view my own repositories the server error occurs. Apologies if I broke it... You didn't , sorry for the bug! On a side note, I did not see an option to delete a created repository. Yes, currently only a tool shed admin ( me ) can delete a repository. I've considered allowing owners to delete repositories, but that may open up problems with users that want to be able to download tools from that repository because they have downloaded them in the past. Obviously this issue affects the reproducibility factor. We'll have to figure out how to handle this optimally... Also, my test repository went live straight away. Would it make sense to be able to create a repository and load files then have a publish button for when you choose to release. I'm not sure I understand the issue here. Why do you feel that it is important to have this extra step? Is it just that repositories should not be displayed until they contain files? if so, I can probably make that change, and it won't require clicking a Publish button. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Tool Shed Problem
I am, but I would like to be able to change the category. It will be an RNA-seq tool. Shaun Quoting Greg Von Kuster g...@bx.psu.edu on Tue, 12 Jul 2011 12:38:08 -0400: On Jul 12, 2011, at 11:54 AM, SHAUN WEBB wrote: Thanks Greg, could you delete the repository I created please? Are you eventually going to use your repository? If you are planning to never upload a tool, I'll delete it. Otherwise, I'll leave it active so you can eventually use it. I guess that step isn't necessary as most people won't create repositories until they are ready to go. It would stop curious users like me creating empty repositories by just clicking buttons.. Is there more documentation on what is required to publish a new tool in the tool shed? Nothing yet, but as time permits, there will be. It's basically just common sense. If you have developed a tool that you feel is useful, upload it. Additional things like including working functional tests with small input / output datasets makes it even more useful. A very important feature that I recently added is baseline functionality for repository metadata. An attempt is made to generate repository metadata with each new change set. If the attempt is not successful, metadata is not generated for that change set. This metadata will eventually be an important ingredient in allowing the tool to be automatically installed from the tool shed into a Galaxy instance with just a few mouse clicks. Shaun Quoting Greg Von Kuster g...@bx.psu.edu on Tue, 12 Jul 2011 10:24:28 -0400: Hello Shaun, On Jul 12, 2011, at 6:07 AM, SHAUN WEBB wrote: Hi Galaxy team, I created a new repository on the tool shed called test, I wanted to see what steps were required to publish a tool before I go ahead and release the production version. I then tried to change the name of the repository and got a server error. This problem was due to a bug which I've fixed, so the tool shed is functional with your renamed repository. Thanks for finding the bug... When I search for test, try to navigate to 2nd page of the repository list or view my own repositories the server error occurs. Apologies if I broke it... You didn't , sorry for the bug! On a side note, I did not see an option to delete a created repository. Yes, currently only a tool shed admin ( me ) can delete a repository. I've considered allowing owners to delete repositories, but that may open up problems with users that want to be able to download tools from that repository because they have downloaded them in the past. Obviously this issue affects the reproducibility factor. We'll have to figure out how to handle this optimally... Also, my test repository went live straight away. Would it make sense to be able to create a repository and load files then have a publish button for when you choose to release. I'm not sure I understand the issue here. Why do you feel that it is important to have this extra step? Is it just that repositories should not be displayed until they contain files? if so, I can probably make that change, and it won't require clicking a Publish button. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] options from file
Hi, I have created a tool that will fetch sequences for selected IDs from a tabular file containing multiple IDs and additional info. I want the tool config to scan the first column of the tab file for IDs and provide the user with a selection box where they can select a single ID or multiple IDs and get output for all selected. The following method does this: param name=tabfile type=data format=tabular label=ID File/ param name=selection type=select multiple=true accept_default=true label=ID options from_dataset=tabfile column name=name index=0/ column name=value index=0/ /options /param The issue is, if the top file in my history is a SAM file containing ~30,000 IDs in the first column the tool initially attempts to load these all in to the selection box and effectively crashes my local instance. I only want to use this on tab files that ill have ~100 IDs at most. I have got around this by creating a new datatype indexfile as a class of Tabular in tabular.py: class IndexFile( Tabular ): file_ext = 'indexfile' def sniff( self, filename ): return False And changing the input file to: param name=tabfile type=data format=tabular label=ID File/ This means I must first set the tabular file to type indexfile, then it will be the only dataset shown under tabfile. Selecting options from a file is really useful, I was wondering if there is a better workaround for this or if a similar indexfile datatype could be included in Galaxy. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Uploading Zip Files
Hi, I have a tool that takes a zipped archive as input, finds all the sequence files (~90 of them), separates them by barcode, does a little extra processing and outputs a single fasta file. I would like this to run on Galaxy in a workflow with a few other tools. I know there have been discussions about uploading zip files to Galaxy before and that currently Galaxy automatically unzips a file and uploads the first file in the archive. Are there any plans to change this behaviour and be able to upload a zipped file without decompressing. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] MySQL 2 Postgres
We are experiencing issues with workflows where jobs are running before the previous step is completed (especially with large workflows). I am wondering if the problem is MySQL. Does anyone know of a reliable script for converting a MySQL dump to PostgreSQL? Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Data Library Upload Issues
Thanks Greg. 1. Non-admin users with add permissions on a library are offered the option to upload from file systems path. Should this be restricted to admin users only? Yes, this should be restricted to admin users only as access to the file system for all users could result in undesired security problems or other issues. Has this also been fixed in the latest change-set or do I have to manually set an option to make this exclusive to admin users? I want to give users the ability to add data to their libraries but I'm not willing to do that until this option is removed. Shaun Quoting Greg Von Kuster g...@bx.psu.edu: Hello Shaun, Thanks for your message. On Feb 11, 2011, at 6:54 AM, SHAUN WEBB wrote: Hi, I have notice a few problems which may or may not have been fixed in the latest distribution (I am yet to update) but wanted to make you aware. 1. Non-admin users with add permissions on a library are offered the option to upload from file systems path. Should this be restricted to admin users only? Yes, this should be restricted to admin users only as access to the file system for all users could result in undesired security problems or other issues. 2. If a user chooses the option upload a directory of files but does not have a folder with their username in the library upload directory they get a server error. Would be nicer to get a help message that says they are not set up for this method and to contact the Galaxy admin. This issue was corrected in change set 4999. 3. If files are being uploaded to a library and I click on the manage jobs tab in the admin section I get a server error. This persists until the server is restarted. I am not able to reproduce this behavior in the latest change set, which is 5053. This change set should be available in the distribution within a few weeks, or if you want to run the latest code you could pull directly from our development repo at: https://your account@bitbucket.org/galaxy/galaxy-central Keep in mind that the development repo is less stable than the distribution. Thanks for your help! Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev Greg Von Kuster Galaxy Development Team g...@bx.psu.edu -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Setting Metadata
I seem to remember there being talk of a parameter you can set in the universe file that allows you to limit the size of files for which metadata is set when galaxy uploads a file. Was this put in to production? Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
