Re: [galaxy-dev] Data Library - upload files from filesystem paths

2011-02-01 Thread Greg Von Kuster
be a bug, but if so, I'll need some help tracking it down. Can you confirm from what view you are adding hte sub-folders, and what the permissions are on the parent folder and library? Thanks! Greg Von Kuster Any help would be appreciated, Thanks, Nicki - Nicki Gray

Re: [galaxy-dev] Data Library Upload Issues

2011-02-15 Thread Greg Von Kuster
. Shaun Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

Re: [galaxy-dev] undelete data library

2011-02-21 Thread Greg Von Kuster
: davide.citt...@ifom-ieo-campus.it */ ___ 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

Re: [galaxy-dev] undelete data library

2011-02-21 Thread Greg Von Kuster
What version of Galaxy are you running. I believe this issue was corrected a while back, so can you update to the latest version? On Feb 21, 2011, at 10:41 AM, Davide Cittaro wrote: Hi Greg On Feb 21, 2011, at 4:36 PM, Greg Von Kuster wrote: Hi Davide, Yes, in the Library actions popup

Re: [galaxy-dev] undelete data library

2011-02-21 Thread Greg Von Kuster
Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

Re: [galaxy-dev] Fwd: Galaxy process

2011-03-10 Thread Greg Von Kuster
no idea what is could be... Thanks Shaun Quoting Greg Von Kuster g...@bx.psu.edu: Hi Shaun, Security checks are performed on every active ( undeleted ) dataset within a data library as it's contents are rendered upon opening. For the current user, every dataset is checked

Re: [galaxy-dev] Fwd: Galaxy process

2011-03-10 Thread Greg Von Kuster
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

Re: [galaxy-dev] Creating Roles and groups

2011-03-10 Thread Greg Von Kuster
better reflected the intent. Let me know if you disagree. Thanks for your message! Greg Von Kuster On Mar 10, 2011, at 11:15 AM, Peter Cock wrote: Hi all, I've had a little play with our local Galaxy to try and get a feel for libraries, groups and roles. I see when you create a new role

Re: [galaxy-dev] NoneType dereference on the jobs view

2011-03-11 Thread Greg Von Kuster
Hello Ry4an, Thanks for the patch - it's been applied in change set 5214:0b9bba943c8f. Greg Von Kuster On Mar 10, 2011, at 6:15 PM, Ry4an Brase wrote: Intermittently, and always during periods of high load we'll get a 500 Server error from the Admin 'Manage Jobs' list. In the logs

Re: [galaxy-dev] inputs sanitization...

2011-03-11 Thread Greg Von Kuster
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your

Re: [galaxy-dev] Upload files from filesystem paths - backwards checkboxes

2011-03-11 Thread Greg Von Kuster
Hello Peter, Thanks for the patch - I've applied a corrected version of it in change set 5215:74c4dd43485a. Let me know if you'd rather have me flip the Copy data into Galaxy? feature. I'd be happy to, but I don't want to reinvent the wheel if you're close. Thanks! Greg Von Kuster

Re: [galaxy-dev] Upload files from filesystem paths - backwards checkboxes

2011-03-11 Thread Greg Von Kuster
Hi Peter, This has been resolved in change set 5217:70d7d0bfaad6, where I've changed the check box into a select list per your suggestion. Thanks! Greg Von Kuster On Mar 10, 2011, at 12:24 PM, Peter Cock wrote: Hi all, Via the Galaxy admin interface, I'm currently importing some BAM

Re: [galaxy-dev] Database cleanup and user management

2011-03-14 Thread Greg Von Kuster
, please use the interface at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions

Re: [galaxy-dev] Database cleanup and user management

2011-03-14 Thread Greg Von Kuster
: Is there a way to completely delete a user and their data at the same time? We would like to keep published pages and shared data though. Thank you for your time. -- Sebastian Greg Von Kuster Galaxy Development Team g...@bx.psu.edu

Re: [galaxy-dev] Database cleanup and user management

2011-03-14 Thread Greg Von Kuster
, please use the interface at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions

Re: [galaxy-dev] Database cleanup and user management

2011-03-14 Thread Greg Von Kuster
I've created the following ticket for this which you can follow if you want. https://bitbucket.org/galaxy/galaxy-central/issue/492/add-the-ability-to-display-purged-history Thanks for all of your input, greg Von Kuster On Mar 14, 2011, at 2:30 PM, Sebastian J. Schultheiss wrote: Dear all

Re: [galaxy-dev] Error importing BAM file into Library

2011-03-15 Thread Greg Von Kuster
not pass the current simple, rigid test in the Bam class's method. Thanks for your message, Greg Von Kuster On Mar 10, 2011, at 1:18 PM, Peter Cock wrote: Hi all, I think I have fallen over the same problem Glen Beane reported in Nov 2010, http://lists.bx.psu.edu/pipermail/galaxy-dev/2010

Re: [galaxy-dev] functional and acceptance tests

2011-03-21 Thread Greg Von Kuster
. 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 ___ Please keep all replies on the list by using reply all

Re: [galaxy-dev] Sequencer Configuration

2011-03-29 Thread Greg Von Kuster
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 ___ Please keep all replies on the list by using reply

Re: [galaxy-dev] Ratings on Tool Shed broken?

2011-04-11 Thread Greg Von Kuster
Hello Peter, Thanks for reporting this - it has been corrected within the tool shed. Greg Von Kuster On Apr 5, 2011, at 11:50 AM, Peter Cock wrote: Hi all, I had wondered why none of the tools on the Galaxy Tool Shed had a rating, and had assumed it was just that so far no-one had

Re: [galaxy-dev] Error when adding datasets

2011-04-14 Thread Greg Von Kuster
in the window in which you started Galaxy. Thanks On Apr 14, 2011, at 10:46 AM, Louise-Amélie Schmitt wrote: Hello Greg Thank you for answering. Please find the answers after each question. Le jeudi 14 avril 2011 à 10:19 -0400, Greg Von Kuster a écrit : Hello Louise, I do not think

Re: [galaxy-dev] Error when adding datasets

2011-04-14 Thread Greg Von Kuster
-0400, Greg Von Kuster a écrit : I assume when you dropped the old database and recreated the new, empty database, you made sure the database connection string in universe_wsgi.ini was correctly set. if so, when you started up Galaxy, it would have created all of the required tables in the new

Re: [galaxy-dev] Error when adding datasets

2011-04-14 Thread Greg Von Kuster
to our using LDAP? Thanks L-A On Thu, 14 Apr 2011 12:06:55 -0400, Greg Von Kuster g...@bx.psu.edu wrote: On Apr 14, 2011, at 11:49 AM, Louise-Amélie Schmitt wrote: Here is the result I got from the debug statements: galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286

Re: [galaxy-dev] Error in user registration

2011-04-15 Thread Greg Von Kuster
___ 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

Re: [galaxy-dev] uploading a large number of files to a library

2011-04-15 Thread Greg Von Kuster
will load two to three times quicker. See our news brief at https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_04_08 for details. Perhaps you've discovered a different problem, but upgrading will at least eliminate some known issues. Greg Von Kuster On Apr 15, 2011

Re: [galaxy-dev] Galaxy Tool Shed:- Uploading tool packages fails with Server Error message

2011-04-18 Thread Greg Von Kuster
, and for taking the time to contribute your tools to the Galaxy community. Greg Von Kuster On Apr 18, 2011, at 3:58 PM, Vipin TS wrote: On Apr 18, 2011, at 11:28 AM, Vipin TS wrote: Dear Galaxy team, I would like to upload a set of converter programs available for Generic Feature Format (GFF

Re: [galaxy-dev] Data libraries management: error on moving a dataset

2011-04-28 Thread Greg Von Kuster
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your

Re: [galaxy-dev] Data libraries management: error on moving a dataset

2011-04-29 Thread Greg Von Kuster
Here is the problem, you must have something configured incorrectly in your apache server that is not properly handling the request. serving Galaxy through Apache On Apr 29, 2011, at 9:10 AM, Greg Von Kuster wrote: Hi Joachim, Your hg environment looks good, so there must be something

Re: [galaxy-dev] tool parameter attribute for option display value (not passed value)?

2011-05-02 Thread Greg Von Kuster
Hello Leandro, Try $input1.value_label Greg Von Kuster On Apr 28, 2011, at 10:17 AM, Leandro Hermida wrote: Hi, For a tool select input parameter: param name=input1 type=select option value=hs33Homo sapiens/option option value=mm19Mus musculus/option option value

Re: [galaxy-dev] Upload fails, webapp and job runner running on different machines

2011-05-10 Thread Greg Von Kuster
Hello Louise, Sorry about the delay, but significant time has passed since you sent the message below, so I wanted to check with you to confirm this is still an issue for you. Can you let me know? Thanks, Greg Von Kuster On Mar 23, 2011, at 12:09 PM, Louise-Amélie Schmitt wrote: Hi

Re: [galaxy-dev] Community server bug and request

2011-05-11 Thread Greg Von Kuster
Assaf, thanks for pointing this out. I'll be presenting at the Galaxy Community Conference a talk that pertains to this issue. Greg Von Kuster On Apr 1, 2011, at 5:59 PM, Assaf Gordon wrote: Tiny bug: When viewing a file inside a tarball, the content-type is forced to text/plain. Works

Re: [galaxy-dev] User list and disk space?

2011-05-16 Thread Greg Von Kuster
-A ___ 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

Re: [galaxy-dev] User list and disk space?

2011-05-17 Thread Greg Von Kuster
that should eliminate datasets falling into this category - not tested at all though... On May 17, 2011, at 8:42 AM, Louise-Amelie Schmitt wrote: But I still have a question: It comprises the datasets stored in libraries right? Is there a way to ignore them? Greg Von Kuster wrote: Hello Louise

Re: [galaxy-dev] User list and disk space?

2011-05-17 Thread Greg Von Kuster
list with the sum of the file size of every dataset in each user's histories that don't belong to any ibrary. Is there a way to do that? On Mon, May 16, 2011 at 7:18 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Louise, I've pasted a diff below for the file ~/lib/galaxy/web/controller

Re: [galaxy-dev] galaxy download

2011-05-24 Thread Greg Von Kuster
://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@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

Re: [galaxy-dev] Error getting to http://galaxy/user/create on local instance

2011-05-24 Thread Greg Von Kuster
/ Greg Von Kuster Galaxy Development Team g...@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

Re: [galaxy-dev] Error getting to http://galaxy/user/create on local instance

2011-05-24 Thread Greg Von Kuster
it occur with different browsers, or is it related to a certain browser brand? What version of Galaxy are your running? Thanks Dave, Greg Von Kuster On May 24, 2011, at 6:06 PM, Dave Walton wrote: Greg, We've tried just reloading the browser and that didn't do anything. As for deleting

Re: [galaxy-dev] Error getting to http://galaxy/user/create on local instance

2011-05-26 Thread Greg Von Kuster
whatever version of galaxy-dist was available about a week and a half ago, which is when Glen did the upgrade. Thanks, Dave On 5/24/11 11:29 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Dave, If you do not have a template_cache_path config setting in universe_wsgi.ini, then your cached

Re: [galaxy-dev] Error getting to http://galaxy/user/create on local instance

2011-05-26 Thread Greg Von Kuster
that will help. We are running whatever version of galaxy-dist was available about a week and a half ago, which is when Glen did the upgrade. Thanks, Dave On 5/24/11 11:29 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Dave, If you do not have a template_cache_path config setting

Re: [galaxy-dev] Import Library Datasets into Histories - automatically imports into current AND new history - Bug?

2011-05-31 Thread Greg Von Kuster
Lisa, Thanks very much for reporting this bug. It has been fixed in our development repo in change set 5608, which should be available in the distribution within the next few weeks. Greg Von Kuster On May 31, 2011, at 8:39 AM, Liisa Koski wrote: Hello, I noticed a change in the newest

Re: [galaxy-dev] The new hg based Galaxy Tool Shed

2011-06-01 Thread Greg Von Kuster
Greg Von Kuster Galaxy Development Team g...@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

Re: [galaxy-dev] The new hg based Galaxy Tool Shed

2011-06-01 Thread Greg Von Kuster
Von Kuster Galaxy Development Team g...@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

Re: [galaxy-dev] Defining new file formats in Galaxy (for new tool wrappers)

2011-06-02 Thread Greg Von Kuster
at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@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

Re: [galaxy-dev] CSV import of Sample information Error

2011-06-07 Thread Greg Von Kuster
___ 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

Re: [galaxy-dev] CSV import of Sample information Error

2011-06-08 Thread Greg Von Kuster
/wiki/Home. Greg Von Kuster On Jun 7, 2011, at 6:21 PM, Joe Cruz wrote: For my sample forms I have fields for Sample type, concentration, run type, and read length. I greatly appreciate your help Greg. If you have any other questions let me know. Thanks, Joe On Tue, Jun 7, 2011

Re: [galaxy-dev] Defining new file formats in Galaxy (for new tool wrappers)

2011-06-09 Thread Greg Von Kuster
Hello Peter, On Jun 6, 2011, at 6:41 AM, Peter Cock wrote: On Thu, Jun 2, 2011 at 6:39 PM, Greg Von Kuster g...@bx.psu.edu wrote: We will certainly include support for new data formats into the Galaxy core. In case you haven't seen it, details for adding new formats is available in our

Re: [galaxy-dev] Defining new file formats in Galaxy (for new tool wrappers)

2011-06-09 Thread Greg Von Kuster
to keep up on some of this documentation, so hopefully we'll have something soon. Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your

Re: [galaxy-dev] Recommended method to pull from ToolShed ?

2011-06-09 Thread Greg Von Kuster
___ 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

Re: [galaxy-dev] CSV import of Sample information Error

2011-06-09 Thread Greg Von Kuster
to fill out all the fields repetitively. joe On Thu, Jun 9, 2011 at 3:20 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Joe, Sorry you've bumped into problems - we know we're lacking on documentation for the sample tracking stuff currently. I believe this new issue is due to a field

Re: [galaxy-dev] CSV import of Sample information Error

2011-06-10 Thread Greg Von Kuster
, joe On Thu, Jun 9, 2011 at 8:50 PM, Greg Von Kuster g...@bx.psu.edu wrote: Joe, Try editing your Sample Form Definition, changing the Field name value from the default of 1_field_name to be your desired agctac. Then, your csv file with the line Sample1,Library1,Lib1Folder1,History

Re: [galaxy-dev] Updating tools on new hg based Galaxy Tool Shed

2011-06-16 Thread Greg Von Kuster
Hi Peter, On Jun 16, 2011, at 10:10 AM, Peter Cock wrote: On Thu, Jun 16, 2011 at 2:45 PM, Greg Von Kuster g...@bx.psu.edu wrote: Peter, I've added comments to each of these issues in bitbucket, and have pated them inline below as well. On Jun 16, 2011, at 5:03 AM, Peter Cock wrote: Hi

Re: [galaxy-dev] CSV import of Sample information Error

2011-06-16 Thread Greg Von Kuster
it, create two samples (Sample1 and Sample10) and assign the rest of the values to the corresponding fields for each sample. Thanks, joe On Thu, Jun 9, 2011 at 8:50 PM, Greg Von Kuster g...@bx.psu.edu wrote: Joe, Try editing your Sample Form Definition, changing the Field name value

Re: [galaxy-dev] [galaxy-bugs] tool updates for local installation

2011-06-20 Thread Greg Von Kuster
the tools get updated? --- Ravi Sanka ICS - Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 --- From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Friday, June 17, 2011 3:24 PM

Re: [galaxy-dev] user_library_import_dir configuration

2011-06-23 Thread Greg Von Kuster
if you bump into additional questions. Greg Von Kuster On Jun 22, 2011, at 5:41 PM, Shantanu Pavgi wrote: Hi, I have setup 'user_library_import_dir' to allow non-admin users to import data libraries. The configured directory contains subdirectories with galaxy-login (email) name. I

Re: [galaxy-dev] user_library_import_dir configuration

2011-06-23 Thread Greg Von Kuster
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your

Re: [galaxy-dev] database migration issue 64 -65 - postgresql

2011-06-28 Thread Greg Von Kuster
AS f SET f.fields='%s' WHERE id=%i %( fields_json, form_definition_id ) Greg Von Kuster On Jun 28, 2011, at 6:58 AM, michael burrell (TSL) wrote: Good Afternoon, Firstly am a massive fan of galaxy, really like the things that it can do, but I am a bit stuck updating our instance here

Re: [galaxy-dev] database migration issue 64 -65 - postgresql

2011-06-30 Thread Greg Von Kuster
SET fields='%s' WHERE id=%i %( to_json_string( fields_list ), form_definition_id ) db_session.execute( cmd ) On Jun 30, 2011, at 12:04 PM, Greg Von Kuster wrote: Hell all, Michael discovered a bug in the lib/galaxy/model/migrate/versions/0065_add_name_to_form_fields_and_values.py

Re: [galaxy-dev] New galaxy tool shed

2011-06-30 Thread Greg Von Kuster
, a new feature which I am currently implementing. It should be available fairly soon. Cheers, Marcel On 06/28/2011 10:05 PM, Greg Von Kuster wrote: Hello Marcel, Thanks for your message - see my inline comments below. On Jun 28, 2011, at 5:55 AM, Marcel Schumann wrote: Hi Greg

Re: [galaxy-dev] Cleanup scripts - question or bug ?

2011-07-06 Thread Greg Von Kuster
Hello Assaf, Thanks very much for your patch - I've applied it in change set 5770:a5e0a5d3c0a1. Greg Von Kuster On Jul 1, 2011, at 5:35 PM, Assaf Gordon wrote: Hi, I'm trying to use the built-in cleanup scripts (instead of my own), came across a possible bug: 1. When running

Re: [galaxy-dev] New galaxy tool shed

2011-07-07 Thread Greg Von Kuster
looks much better this way and the new metadata features will certainly be very helpful as well ... Cheers, Marcel On 06/30/2011 07:55 PM, Greg Von Kuster wrote: This issue has been fixed - thanks for pointing it out. Yes, attributes like tool_id, version, etc, fall

Re: [galaxy-dev] Error when changing default permissions for new histories

2011-07-08 Thread Greg Von Kuster
Hello Sarah, This is a bug which I've fixed in change set 5776:a787213d08e1, which is currently available from our development repository and should be available in the distribution within the next few weeks. Thanks for finding this. Greg Von Kuster On Jul 8, 2011, at 3:53 AM, Sarah Diehl

Re: [galaxy-dev] Tool Shed Problem

2011-07-12 Thread Greg Von Kuster
. ___ 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

Re: [galaxy-dev] Tool Shed Problem

2011-07-12 Thread Greg Von Kuster
Shaun, I forgot to mention, if you want to just fool around with tool shed features, check out the test version of the tool shed at http://testtoolshed.g2.bx.psu.edu/ On Jul 12, 2011, at 10:24 AM, Greg Von Kuster wrote: Hello Shaun, On Jul 12, 2011, at 6:07 AM, SHAUN WEBB wrote: Hi

Re: [galaxy-dev] Tool Shed Problem

2011-07-12 Thread Greg Von Kuster
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

Re: [galaxy-dev] Tool Shed Problem

2011-07-12 Thread Greg Von Kuster
You can now manage your repository's category associations in the tool shed. On Jul 12, 2011, at 12:54 PM, SHAUN WEBB wrote: I am, but I would like to be able to change the category. It will be an RNA-seq tool. Shaun Greg Von Kuster Galaxy Development Team g...@bx.psu.edu

Re: [galaxy-dev] Tool XML parameter options from locally stored files

2011-07-13 Thread Greg Von Kuster
. ___ 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

Re: [galaxy-dev] Tool XML parameter options from locally stored files

2011-07-13 Thread Greg Von Kuster
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

Re: [galaxy-dev] more cleanup scripts messages

2011-07-14 Thread Greg Von Kuster
Hello Assaf, Thanks for this patch as well. I've added it in change set 5792:a3fc507f2b42. Greg Von Kuster On Jul 13, 2011, at 1:53 PM, Assaf Gordon wrote: Hi Greg (again), This patch adds messages for the purge histories step: 1. A message is printed when processing a new history (so

Re: [galaxy-dev] fyi: can't upload to toolshed

2011-07-15 Thread Greg Von Kuster
Hello Ed, Looking at the logs, I see that you uploaded to your Roche454 tool suite repo. Is that correct? I don't see any exceptions in the logs, so not sure what happened. Are you still having this issue? Thanks, Greg Von Kuster On Jul 14, 2011, at 9:32 PM, Edward Kirton wrote: Server

Re: [galaxy-dev] fyi: can't upload to toolshed

2011-07-19 Thread Greg Von Kuster
on a Mac. I've added exception handling in the latest version of the tool shed that uses a different approach to committing the changes whenever the intermittent exception is thrown. Thanks for finding this issue, and please let me know if you bump into any problems in the future. Greg Von Kuster

Re: [galaxy-dev] EpiGRAPH

2011-07-21 Thread Greg Von Kuster
Hello Christoph, This is the result of a bug that I've corrected in change set 5819:0f15591f2acd, which should be available in our main Galaxy instance, as well as the distribution, within the next few weeks. Thanks for pointing this out, and very sorry for the inconvenience. Greg Von Kuster

Re: [galaxy-dev] Detailed SGE timing information about galaxy jobs

2011-07-21 Thread Greg Von Kuster
Hello Assaf, I've added this to the ~/contrib directory in change set 5820:c609c2574c66. Thanks very much for contributing this. Greg Von Kuster On Jul 19, 2011, at 2:45 PM, Assaf Gordon wrote: Hi all, I got around to writing the report I always needed: how much time each job actually

Re: [galaxy-dev] Upload of images - jpg/png - binary file contains inappropriate content

2011-07-22 Thread Greg Von Kuster
Hello Jelle, There are a few things you need to do to add support for a new data type. The steps are described here: http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes Greg Von Kuster On Jul 22, 2011, at 8:49 AM, Jelle Scholtalbers wrote: Hi all, I would like to be able

Re: [galaxy-dev] Where to find the toolconfig parser code?

2011-07-22 Thread Greg Von Kuster
Samuel, Look at the parse(0 method in the Tool class in ~/lib/galaxy/tools/__init__.py for most of it. You should be able to find everything you need from there. Greg Von Kuster On Jul 22, 2011, at 9:41 AM, Samuel Lampa wrote: Quick question to you devs, I need to find the code where

Re: [galaxy-dev] error reading tool from path (epigraph.xml, epigraph_test.xml, access_libraries.xml)

2011-07-22 Thread Greg Von Kuster
at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@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

Re: [galaxy-dev] Metadata in Galaxy Tool Shed

2011-07-22 Thread Greg Von Kuster
working to resolve this problem. Your choice for organizing the files looks good. Thanks for sharing your tool on the tool shed, and let us know if you come across any other issues. Greg Von Kuster On Jul 22, 2011, at 11:37 AM, Lance Parsons wrote: I recently created a new repository

Re: [galaxy-dev] Upload of images - jpg/png - binary file contains inappropriate content

2011-07-22 Thread Greg Von Kuster
, 2011 3:26 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Jelle, There are a few things you need to do to add support for a new data type. The steps are described here: http://wiki.g2.bx.psu.edu/Admin/Datatypes/Adding%20Datatypes Greg Von Kuster On Jul 22, 2011, at 8:49 AM

Re: [galaxy-dev] Upload of images - jpg/png - binary file contains inappropriate content

2011-07-27 Thread Greg Von Kuster
at it, feel free! Thanks very much for your contributions! Greg Von Kuster On Jul 25, 2011, at 11:23 AM, Jelle Scholtalbers wrote: Hi Greg, this was indeed causing the problem. I added some code which now allows to sniff image files. It is practically untested (it does work for me on bmp

Re: [galaxy-dev] Upload of images - jpg/png - binary file contains inappropriate content

2011-07-27 Thread Greg Von Kuster
Hi Peter, On Jul 27, 2011, at 9:34 AM, Peter Cock wrote: On Wed, Jul 27, 2011 at 2:28 PM, Greg Von Kuster g...@bx.psu.edu wrote: Helo Jelle, I've taken a look at your patches and the code looks good. However, I'm wondering why you find it necessary to upload image files to Galaxy. Do tools

Re: [galaxy-dev] manage library permission interface glitch

2011-07-27 Thread Greg Von Kuster
. 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 ___ Please keep all replies on the list by using reply all in your

Re: [galaxy-dev] Upload of images - jpg/png - binary file contains inappropriate content

2011-07-27 Thread Greg Von Kuster
. Thanks very much for your contribution! Greg Von Kuster On Jul 25, 2011, at 11:23 AM, Jelle Scholtalbers wrote: Hi Greg, this was indeed causing the problem. I added some code which now allows to sniff image files. It is practically untested (it does work for me on bmp, jpg, png, tiff

Re: [galaxy-dev] manage library permission interface glitch

2011-07-29 Thread Greg Von Kuster
it sooner. Greg Von Kuster On Jul 27, 2011, at 2:08 PM, Glen Beane wrote: I should preface this by saying we are running a galaxy-dist that is a couple months old now (we are planning on updating soon), but here is an annoying issue we are seeing managing data library permissions: The Roles

Re: [galaxy-dev] Creating and adding new repositories for the new tool shed

2011-08-03 Thread Greg Von Kuster
tool config, the syntax of which is defined on our wiki at http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax Thanks very much for you interest in the tool shed, Greg Von Kuster On Aug 2, 2011, at 10:36 PM, Nikhil Joshi wrote: Hi all, I have been using Galaxy for a few years now

Re: [galaxy-dev] Problem with Tool Shed mock ups?

2011-08-04 Thread Greg Von Kuster
file a bug? Looking at Konrad's XML file, perhaps the tool doesn't like the space in the first help line? (star)(star)Interproscan(space)(star)(star) I've not installed the XML file locally to see how it is rendered within Galaxy. Peter Greg Von Kuster Galaxy Development Team g

Re: [galaxy-dev] Adding Link to Sequencing Requests Page

2011-08-15 Thread Greg Von Kuster
in the RequestsGrid class in ~/lib/galaxy/web/controllers/requests_common.py. Good luck, and thanks for using Galaxy, Greg Von Kuster Sequencing Requests Create new request Advanced Search NameDescription Samples TypeLast Updated ↑ State No Items For 0 selected items: Submitted

Re: [galaxy-dev] problems with Access Libraries stored locally tool

2011-08-16 Thread Greg Von Kuster
, please use the interface at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@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

Re: [galaxy-dev] tool which using web service

2011-08-24 Thread Greg Von Kuster
Hello Sashi, Look at our tool wikis at http://wiki.g2.bx.psu.edu/Admin/Tools You probably want to base your tool config file on ~/tools/data-source/ucsc_tablebrowser.xml. Greg Von kuster On Aug 24, 2011, at 9:12 AM, shashi shekhar wrote: hi, I have application , i want to integrate

Re: [galaxy-dev] tool which using web service

2011-08-24 Thread Greg Von Kuster
Shashi, You may find this wiki useful as well - sorry I missed it in my initial response. http://wiki.g2.bx.psu.edu/Admin/Internals/Data%20Sources On Aug 24, 2011, at 12:15 PM, Greg Von Kuster wrote: Hello Shashi, On Aug 24, 2011, at 11:55 AM, shashi shekhar wrote: i have an application

Re: [galaxy-dev] contribute tools to galaxy?

2011-08-31 Thread Greg Von Kuster
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 ___ Please

Re: [galaxy-dev] HOW TO RETRIEVE DATA FROM HISTORY??!!

2011-09-02 Thread Greg Von Kuster
Hello Steve, Thanks for making this available. If you could email me the script, I'll include it in the ~/contrib directory in the Galaxy distribution. Greg Von Kuster On Sep 2, 2011, at 3:20 AM, Steve Taylor wrote: Hi, We have written a tool that we call gls (galaxy ls). Running

Re: [galaxy-dev] Tool Shed problems with browse repository files?

2011-09-07 Thread Greg Von Kuster
at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@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

Re: [galaxy-dev] Server Error

2011-09-09 Thread Greg Von Kuster
Hello Alex, This issue was the result of a configuration error that should now be corrected. Please let us know if you encounter further issues. thanks for reporting this, Greg Von Kuster On Sep 9, 2011, at 12:41 PM, Alex R Bigelow wrote: Hi, I am a new developer interested in writing

Re: [galaxy-dev] Contribution of tools to galaxy main server

2011-09-14 Thread Greg Von Kuster
, and local Galaxy instances will install them from the Galaxy tool shed. This same process will be used for populating our main Galaxy instance here at Penn State with tools. So for now, please upload your tool to the tool shed. Thanks again, Greg Von Kuster On Sep 9, 2011, at 4:08 PM, Dongjun

Re: [galaxy-dev] Galaxy installation with mysql database

2011-09-14 Thread Greg Von Kuster
create all of the tables for you. Greg Von Kuster On Sep 14, 2011, at 7:35 PM, Alex R Bigelow wrote: Hi, I am trying to install a local instance of Galaxy with an infobright mysql server; I created a database called galaxy (the user is also galaxy, and it has all the privileges it should need

Re: [galaxy-dev] Galaxy installation with mysql database

2011-09-15 Thread Greg Von Kuster
Alex, I've created the following ticket for this issue as it looks to be a bug with Galaxy / mysql. You can follow the ticket to be aware of progress. https://bitbucket.org/galaxy/galaxy-central/issue/660/galaxy-installation-with-mysql-database Thanks for reporting this, Greg Von Kuster

Re: [galaxy-dev] Quick question regarding dist and central

2011-09-19 Thread Greg Von Kuster
. ___ 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

Re: [galaxy-dev] [galaxy-user] Problem with new tool shed

2011-10-04 Thread Greg Von Kuster
name like shed_tool_conf.xml, you should not have a problem installing from a tool shed. I'll have a fix for the bug you've discovered shortly, but making this change will fix the behavior until then. Let me know if you bump into any additional problems. Thanks for finding this! Greg Von Kuster

Re: [galaxy-dev] Tool shed and datatypes

2011-10-05 Thread Greg Von Kuster
://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@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

Re: [galaxy-dev] [galaxy-user] Problem with new tool shed

2011-10-06 Thread Greg Von Kuster
$base_name = $output.id -base_name $base_name ; $script2 $output_dir $base_name /command On 04/10/11 22:55, Greg Von Kuster wrote: Hello Florent, Sorry for the confusion on this - we are preparing a new Galaxy distribution, and the tool shed wiki has been

Re: [galaxy-dev] Tool shed and datatypes

2011-10-06 Thread Greg Von Kuster
Tel: 858-736-3584 E-mail: jdu...@illumina.com From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Wednesday, October 05, 2011 6:25 PM To: Duddy, John Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tool shed and datatypes Hello John, The Galaxy tool shed currently

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