[galaxy-dev] My last day as a core Galaxy Development Team member

2014-08-17 Thread Greg Von Kuster
feel that Galaxy is far from reaching its peak and that its future remains very bright. I look forward to seeing how far it will go. Warm regards to each of you, Greg Von Kuster ___ Please keep all replies on the list by using reply all

Re: [galaxy-dev] Main Galaxy Tool Shed is running the next-stable branch

2014-08-06 Thread Greg Von Kuster
Hi Eric, Sorry for the inconvenience. The tool shed server was out of space. I've corrected the problem and have successfully installed repositories into my local Galaxy instance. Please try again and let us know if you encounter problems. Greg Von Kuster On Aug 6, 2014, at 10:59 AM

Re: [galaxy-dev] Issues with dependencies for toolshed packages

2014-08-06 Thread Greg Von Kuster
Hi Iry, Sorry for the inconvenience. The tool shed server was out of space - I've corrected the problem and have successfully installed repositories. Please try again and let us know if you encounter problems. Thanks! Greg Von Kuster On Aug 6, 2014, at 12:20 PM, Iry Witham iry.wit

Re: [galaxy-dev] Uploads with embedded citations causing red error on Tool Shed

2014-07-30 Thread Greg Von Kuster
Both Galaxy Tool Sheds have been updated with this fix. Greg On Jul 30, 2014, at 7:14 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Thanks John - is there any point/benefit to re-uploading my tool once the fix is live on the Tool Shed? i.e. Was it a harmless warning? Peter On Wed

Re: [galaxy-dev] Uploads with embedded citations causing red error on Tool Shed

2014-07-30 Thread Greg Von Kuster
Yes, it looks like metadata just needs to be regenerated on the affected repositories. Let me know if doing so uncovers something else. Greg On Jul 30, 2014, at 7:20 AM, John Chilton jmchil...@gmail.com wrote: ... that might be a Greg question. The tool shed isn't going to use the citation

[galaxy-dev] Main Galaxy Tool Shed is running the next-stable branch

2014-07-29 Thread Greg Von Kuster
to the stable branch when it is created for the upcoming Galaxy release. Thanks very much, 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

Re: [galaxy-dev] [galaxy-iuc] writing datatypes

2014-07-22 Thread Greg Von Kuster
Hi Björn, On Jul 22, 2014, at 6:01 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Greg, thanks for the clarification. Please see my comments below. On Jul 20, 2014, at 3:22 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Sun, Jul 20, 2014 at 6:23 PM, Björn Grüning bjo

Re: [galaxy-dev] [galaxy-iuc] writing datatypes

2014-07-22 Thread Greg Von Kuster
guid identifier for tools. I haven't thought too much about whether this would pose backward compatibility issues or not. Discussion is welcomed on this. Greg Von Kuster On Jul 22, 2014, at 7:19 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Björn, On Jul 22, 2014, at 6:01 PM, Björn

Re: [galaxy-dev] writing datatypes

2014-07-21 Thread Greg Von Kuster
will correctly install the 4 repositories. Let me know if I'm missing something here. Thanks! Greg Excellent example! How to handle versions of datatypes? Extra repositories for stockholm 1.0 and 1.1? If so ... the associated python file (sniffing, splitting ...) should be also versioned

Re: [galaxy-dev] writing datatypes

2014-07-21 Thread Greg Von Kuster
unsniffable binary datatypes are treated as sniffiable if there was ever an installed version that was some sniff-able datatype. -John On Jul 17, 2014 12:35 PM, Greg Von Kuster g...@bx.psu.edu wrote: This would be easy to implement, but could adversely affect reproducibility. If a repository

Re: [galaxy-dev] writing datatypes

2014-07-17 Thread Greg Von Kuster
would no longer be available. Greg On Jul 17, 2014, at 1:30 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Jul 17, 2014 at 6:10 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: ... but the problem will stay the same ... one [datatype definition] repository can have multiple

Re: [galaxy-dev] Toolshed : tool_dependency xml, action problem

2014-07-17 Thread Greg Von Kuster
I wasn't aware of a scenario where the value of dir could be None, so thanks for pointing this out. It should be fixed in 14088:23f0c41b1cd7 Greg Von Kuster On Jul 17, 2014, at 8:15 AM, Nicolas Lapalu nicolas.lap...@versailles.inra.fr wrote: Hi Greg, not in the current, in version 2014

Re: [galaxy-dev] writing datatypes

2014-07-17 Thread Greg Von Kuster
Here's a Trello card for this: https://trello.com/c/s8tfbW4x On Jul 17, 2014, at 1:38 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Good point Greg. Let's refine this slightly then, a new special ToolShed repository type for a *single* datatype definition. That avoids this problem

Re: [galaxy-dev] writing datatypes

2014-07-16 Thread Greg Von Kuster
Assuming this comment: Finally, we will talk to the devteam to rewrite EMBOSS to depend on our separate data type repositories. refers to the emboss_5 repository owned by devteam, then what is being proposed should work (although I may not be fully understanding what is being proposed). If

Re: [galaxy-dev] Toolshed : tool_dependency xml, action problem

2014-07-15 Thread Greg Von Kuster
Are the problems described in this thread occurring with the latest Galaxy release? The references to the code lines do not seem to reflect the latest Galaxy release. Thanks, Greg Von Kuster On Jul 7, 2014, at 10:34 AM, Nicolas Lapalu nicolas.lap...@versailles.inra.fr wrote: Hi There's

Re: [galaxy-dev] Toolshed roadmap

2014-07-15 Thread Greg Von Kuster
Howdy Greg, Since there isn't really a public/published roadmap and you're the toolshed guy, I'm emailing to see if I can find out what's in the toolshed's future. The tool shed Trello board at https://trello.com/b/vHqpKpZF/galaxy-tool-shed is the roadmap for the Tool Shed. Just like the Galaxy

Re: [galaxy-dev] Toolshed roadmap

2014-07-15 Thread Greg Von Kuster
-for-completion-by-october-2014). In the meantime, you may find my blog posts to be helpful ( see http://gregvonkuster.org ) Greg Von Kuster On Jul 15, 2014, at 4:00 PM, Eric Rasche rasche.e...@yandex.ru wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Greg, Sorry about

Re: [galaxy-dev] Control on versioning in toolshed tools

2014-06-24 Thread Greg Von Kuster
the repository containing the tool into the test and main Galaxy Tool Sheds for additional validation and sharing. Greg Von Kuster On Jun 24, 2014, at 8:15 AM, Eric Kuyt eric.ku...@wur.nl wrote: Hi All, I am playing around with putting a tool in testtoolshed. Now when changes to dependency

Re: [galaxy-dev] Import of Capsules failing on local toolshed instance

2014-06-18 Thread Greg Von Kuster
Thanks for the corrections Will, and I'm glad this worked for you. Greg Von Kuster On Jun 18, 2014, at 12:22 PM, Will Holtz who...@lygos.com wrote: Hi Greg, I used the toolshed bootstrapping script and was able to get capsules from testtoolshed to import. Here are a couple of notes

Re: [galaxy-dev] Import of Capsules failing on local toolshed instance

2014-06-17 Thread Greg Von Kuster
in this area in the June 2, 2014 release. Here is some information for more easily setting up a local development Tool Shed that use new features introduced in the release. Hopefully this will help. Greg Von Kuster Bootstrapping a New Development Tool Shed The June 2, 2014 release introduces

Re: [galaxy-dev] Toolshed upload error message

2014-06-11 Thread Greg Von Kuster
Hi Vipin, Can you elaborate on the error you are seeing? Thanks, Greg Von Kuster On Jun 10, 2014, at 8:07 PM, Vipin TS vipin...@gmail.com wrote: Hi Greg, When I trying to upload a next release version o my https://toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf converter program

Re: [galaxy-dev] Toolshed update list?

2014-06-10 Thread Greg Von Kuster
the repository somehow and determine whethere an update has been made to the repository since it was marked. Is this what you are looking for? Thanks, Greg Von Kuster On Jun 10, 2014, at 12:39 PM, Eric Rasche rasche.e...@yandex.ru wrote: Is there any way to access a list of repository updates

Re: [galaxy-dev] gatk2 wrapper issue

2014-06-04 Thread Greg Von Kuster
pull hg update stable If you are tracking the galaxy-dist repository, you can get the fix later today. Thanks for reporting this, and sorry for the inconvenience. Greg Von Kuster On Jun 4, 2014, at 6:25 AM, Geert Vandeweyer geert.vandewey...@uantwerpen.be wrote: Hi, I installed the GATK2

Re: [galaxy-dev] devteam packages

2014-06-04 Thread Greg Von Kuster
-by-devteam Thanks, Greg Von Kuster On Jun 4, 2014, at 9:59 AM, Jan Kanis jan.c...@jankanis.nl wrote: Hi all, Where are the toolshed packages owned by devteam maintained? The galaxy sources don't seem to include those tool shed packages and I was unable to find a related repository on github

Re: [galaxy-dev] Unable to access admin after install EMBOSS 5 from galaxy test repo

2014-06-02 Thread Greg Von Kuster
. There is a Trello card here to enhance the Galaxy API to support uninstalling a repository, but the featue is not yet implemented: https://trello.com/c/4VktpvTd/207-enhance-the-galaxy-api-for-the-tool-shed-to-allow-uninstalling-a-repository Sorry for the inconvenience! Greg Von Kuster

Re: [galaxy-dev] New tool on TestToolShed still not tested

2014-05-27 Thread Greg Von Kuster
the following Trello card for this issue: https://trello.com/c/YElEsCWl/208-install-and-test-framework-stage-2-does-not-run Greg Von Kuster On May 26, 2014, at 6:46 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi guys, I updated this new tool on Wednesday last week, but it still has

Re: [galaxy-dev] Main ToolShed wrong report: Repository does not have a test-data directory.

2014-05-27 Thread Greg Von Kuster
/c/9mLrFhTJ/209-install-and-test-framework-does-not-locate-test-data-directory-for-repositories-on-main-tool-shed Greg Von Kuster On May 26, 2014, at 6:54 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi guys, I just noticed two of my tools on the main ToolShed were listed under Latest

Re: [galaxy-dev] Installation failure on Test Tool Shed

2014-05-27 Thread Greg Von Kuster
Hi Peter, I've created the following Trello card for this - we'll take a look and get this resolved as soon as possible. https://trello.com/c/G5hZEajv/210-tool-dependency-installation-may-not-be-properly-handling-broken-package-urls Thanks for reporting this! Greg Von Kuster On May 21, 2014

Re: [galaxy-dev] Old Tool Shed URL http://community.g2.bx.psu.edu/ dead

2014-05-27 Thread Greg Von Kuster
Hi peter, It seems that we have stopped redirecting the old Tool Shed URL http://community.g2.bx.psu.edu/ to the new Tool Shed URL http://toolshed.g2.bx.psu.edu/ . I'm not sure when this happened. Sorry for the inconvenience. Greg Von Kuster On May 21, 2014, at 9:37 AM, Peter Cock p.j.a.c

Re: [galaxy-dev] ToolShed: Uploaded archives can only include regular directories and files

2014-05-27 Thread Greg Von Kuster
Hello Peter, This issue should be resolved in 13630:33b1ff4b9985, which is now running on the test Tool Shed. Thanks for reporting this! Greg Von Kuster On May 19, 2014, at 1:41 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Greg, Dave, I just tried to upload an updated tar-ball

Re: [galaxy-dev] Old Tool Shed URL http://community.g2.bx.psu.edu/ dead

2014-05-27 Thread Greg Von Kuster
Peter, sorry, this one is out of my hands. I'm hoping Nate can answer this when he gets a chance. Greg Von Kuster On May 27, 2014, at 11:16 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, May 27, 2014 at 3:39 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi peter, It seems that we

Re: [galaxy-dev] RFC: Citations for tools

2014-05-27 Thread Greg Von Kuster
Peter, this may be the Trello card you were thinking of. https://trello.com/c/kY7RCnd0/95-tool-shed-citation-for-tools-dois Greg Von Kuster On May 27, 2014, at 1:09 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Eric, I was sure there was a Trello card for this, but I can't find

Re: [galaxy-dev] Repository installation on multiple servers

2014-05-23 Thread Greg Von Kuster
be clarified with the upcoming release notes. Greg Von Kuster On May 23, 2014, at 8:56 AM, Langhorst, Brad langho...@neb.com wrote: I had the same concern, and heard that this is being worked on. Meanwhile I’m using a rolling restart method from pjbriggs https://github.com/pjbriggs/galaxy-admin

Re: [galaxy-dev] uninstalling tools via web api

2014-05-23 Thread Greg Von Kuster
, but it is at the repository level, just like installing is. You'll need to use the Manage installed tool shed repositories option from the Admin perspective. The list of installed repositories each provide a pop-up menu to that includes options to uninstall. Greg Von Kuster On May 23, 2014, at 1:34 PM

Re: [galaxy-dev] new_tool_panel_section_label web api

2014-05-23 Thread Greg Von Kuster
, Greg Von Kuster On May 23, 2014, at 1:33 PM, Evan Bollig boll0...@umn.edu wrote: I am using the new_tool_panel_section_label option when installing tools from the toolshed (via scripts/api/install_tool_shed_repository.py. It works, but I'm curious if its producing the wrong result. See

Re: [galaxy-dev] uninstalling tools via web api

2014-05-23 Thread Greg Von Kuster
Hi Evan, Sorry I somehow missed that in your original message - here is a Trello card for enhancing the Galaxy API for the Tool Shed. I'll get to this as soon as I can. https://trello.com/c/4VktpvTd/207-enhance-the-galaxy-api-for-the-tool-shed-to-allow-uninstalling-a-repository Greg Von

Re: [galaxy-dev] TestToolShed NameError: global name 'suc' is not defined

2014-05-22 Thread Greg Von Kuster
Hi Peter, I've been doing some refactoring in the central branch which caused this issuee. It's been fixed in 13582:581e7c8e353e, which is now running on the test tool shed, ao this bad behavior should be resolved. Thanks so much for reporting this. Greg Von Kuster On May 22, 2014, at 8:39

Re: [galaxy-dev] error: flexbar dependency is not installed by the toolshed

2014-05-20 Thread Greg Von Kuster
. Greg Von Kuster On May 19, 2014, at 10:07 PM, ruiwang.sz ruiwang...@gmail.com wrote: Hi Guys, I tried to install flexbar from toolshed, but upon running, error said it could not find it. I checked and found idtoolshed.g2.bx.psu.edu/repos/jtilman/flexbar/flexbar/2.4/id

[galaxy-dev] The main Tool Shed is now tracking the next-stable branch in preparation for the upcoming Galaxy release

2014-05-19 Thread Greg Von Kuster
additions made to the next-stable branch between now and the upcoming Galaxy release. Please let us know if you encounter any issues. Thanks very much, Greg Von Kuster ___ Please keep all replies on the list by using reply all in your mail

Re: [galaxy-dev] New tool listed under Latest revision: failing tool tests yet not tested

2014-05-16 Thread Greg Von Kuster
in 13496:26b9fe985ee7, which is now running on the test tool shed. Thanks for reporting this problem, and please let us know if you discover any other problems related to this. Greg Von Kustet On May 16, 2014, at 7:22 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Dave et al, Yesterday I

Re: [galaxy-dev] Packaging pycurl on toolshed

2014-04-29 Thread Greg Von Kuster
python2.6 python2.6-dev pkg-config subversion python-dev python-pip Greg Von Kuster On Apr 29, 2014, at 4:34 PM, Saket Choudhary sake...@gmail.com wrote: Hi Bjoern, There is no script installed, I generally just do this on my local system $ python setup.py build --with-ssl $ python setup.py

Re: [galaxy-dev] problem with bioc_qvalue, Version: 1.34.0

2014-04-22 Thread Greg Von Kuster
Hi Tony, It may be easiest to just uninstall / reinstall the repository from the Manage installed tool shed repositories option in the admin menu. Greg Von Kuster On Apr 22, 2014, at 4:21 PM, Tony Kusalik kusa...@cs.usask.ca wrote: Thanks for the response. I have made some progress, but I

Re: [galaxy-dev] Using Galaxy ToolShed API for uploading a tar-ball

2014-04-10 Thread Greg Von Kuster
Hi Peter, This is not yet available, but we'll certainly implement it. I've created this Trello card for it. https://trello.com/c/fykf8IPO/197-enhance-api-to-enable-tar-archive-uploads Thanks! Greg Von Kuster On Apr 10, 2014, at 7:50 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all

Re: [galaxy-dev] Package/Module RPY

2014-04-08 Thread Greg Von Kuster
Hello Curt, I believe that version 1.0.3 of the rpy package should be installing successfully from the main tool shed if you have a repository that contains a tool that defines a dependency to the rpy repository owned by devteam at http://toolshed.g2.bx.psu.edu/view/devteam/package_rpy_1_0_3

Re: [galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool

2014-04-04 Thread Greg Von Kuster
! Greg Von Kuster On Apr 3, 2014, at 10:24 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi, thanks for fixing it Greg. Would it also be possible to get a more concrete error message in such cases where the repository_dependencies.xml file is somehow broken? Thanks, Bjoern Am

[galaxy-dev] The main Galaxy Tool Shed is now running the next-stable branch

2014-04-04 Thread Greg Von Kuster
wnen the main Tool Shed is updated to the stable branch when it is tagged for the next Galaxy release. As usual, the test Galaxy Tool Shed continues to track the default branch. Thanks! Greg Von Kuster ___ Please keep all replies

Re: [galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool

2014-04-03 Thread Greg Von Kuster
Yes, if that is the behavior, that is definitely a bug. I'll take a look and get back to you on this. Thanks! On Apr 3, 2014, at 7:35 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi JanakiRam, I will take Greg into CC. He is the main Tool Shed developer, maybe we spotted a bug

Re: [galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool

2014-04-03 Thread Greg Von Kuster
/commits/773578e65580e3488fadc144739d82f86d9b30f3 Greg Von Kuster On Apr 3, 2014, at 7:53 AM, Greg Von Kuster g...@bx.psu.edu wrote: Yes, if that is the behavior, that is definitely a bug. I'll take a look and get back to you on this. Thanks! On Apr 3, 2014, at 7:35 AM, Björn Grüning

Re: [galaxy-dev] Reg: Issue while adding simple repository dependencies for custom tool

2014-04-03 Thread Greg Von Kuster
:greg date:Thu Apr 03 10:19:46 2014 -0400 summary: Upon import, handle problematic prior_installation_required attribute incorrectly added (and set to False) to the repository tag when a repository was exported. Greg Von Kuster On Apr 3, 2014, at 9:53 AM, Janaki Rama Rao Gollapudi

Re: [galaxy-dev] How to write test cases for custom tool

2014-03-27 Thread Greg Von Kuster
As Janaki replied below, see: http://wiki.galaxyproject.org/Admin/RunningTests?action=showredirect=Admin%2FRunning+Tests On Mar 27, 2014, at 7:15 AM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, I have added tests to tool dependency xml, but how should I

Re: [galaxy-dev] How to write test cases for custom tool

2014-03-27 Thread Greg Von Kuster
. export GALAXY_TOOL_DEPENDENCY_DIR=tool_dependencies; sh run_functional_tests.sh -installed Greg Von Kuster On Mar 27, 2014, at 8:58 AM, Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com wrote: Hi, Thanks for reply. I composed a details email for better clarity

Re: [galaxy-dev] Galaxy startup takes very long. Normal?

2014-03-26 Thread Greg Von Kuster
with no problems. In the future I'll introduce additional benefits for this feature, and I'll look at ways to improve the startup speed. Greg Von Kuster On Mar 26, 2014, at 3:43 AM, Geert Vandeweyer geert.vandewey...@uantwerpen.be wrote: hi Greg, I don't have that setting in my universe

Re: [galaxy-dev] Galaxy startup takes very long. Normal?

2014-03-26 Thread Greg Von Kuster
(which it looks like you are doing), then you should be able to pull it from there. Greg Von Kuster On Mar 26, 2014, at 8:04 AM, Geert Vandeweyer geert.vandewey...@uantwerpen.be wrote: Hi Greg, The setting was not in my universe_sample file. I added it, set log_info to DEBUG and restarted

Re: [galaxy-dev] prims workflows

2014-03-25 Thread Greg Von Kuster
currently abvailable in the Galaxy instance. Hopefully at some point soon something like this will be introduced. Greg Von Kuster On Mar 25, 2014, at 6:47 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi Bjoern, I think you may have misunderstood me. What I mean is : instead of me having

Re: [galaxy-dev] tophat2 install

2014-03-25 Thread Greg Von Kuster
If you installe dit from the main Tool Shed, then this repository has the recipe for installing the package. http://toolshed.g2.bx.psu.edu/view/devteam/package_tophat2_2_0_9 Greg Von Kuster On Mar 25, 2014, at 9:25 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca wrote: Hi

Re: [galaxy-dev] Galaxy startup takes very long. Normal?

2014-03-25 Thread Greg Von Kuster
repository. #manage_dependency_relationships = True Greg Von Kuster On Mar 25, 2014, at 11:08 AM, Geert Vandeweyer geert.vandewey...@uantwerpen.be wrote: Dear all, I'm wondering if the following behaviour is normal. Since I reinstalled the latest galaxy distribution, every restart hangs/loads

Re: [galaxy-dev] tool_dependencies.xml Environmental Variable Question

2014-03-24 Thread Greg Von Kuster
Hello Michael, Environment variables properly defined in a tool's associated tool_dependencies.xml file contained in an installed Tool Shed repository should be available to the tool's environment at runtime. Do you have an example where you are not seeing this? Greg Von Kuster On Mar 21

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Greg Von Kuster
Hi Sheldon, I recommend not manually changing any database entries. You should be able to install the repository and all of its dependencies using the Repair Repository feature. See https://wiki.galaxyproject.org/RepairingInstalledRepositories Greg Von Kuster On Mar 20, 2014, at 8:59 AM

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Greg Von Kuster
You should be able to click on the missing tool dependency and see its installation log. It should show you whatever error is occuring that is not allowing successful installation. Greg Von Kuster On Mar 20, 2014, at 9:46 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca wrote: Hi

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Greg Von Kuster
...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon Sent: Thursday, March 20, 2014 10:52 AM To: 'Greg Von Kuster' Cc: 'galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] tophat2 install Hi, Yes the error is: Error installing tool dependency package

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Greg Von Kuster
-spc.gc.ca wrote: Hi, dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473 contains only: env.sh If that isn’t the right place to look let me know. -Sheldon From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Thursday, March 20, 2014 2:04 PM To: Briand

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Greg Von Kuster
://toolshed.g2.bx.psu.edu; / From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Thursday, March 20, 2014 2:23 PM To: Briand, Sheldon Cc: 'galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] tophat2 install What version of Galaxy are you running? You want to look in the tophat2

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Greg Von Kuster
. Cheers, Bjoern Am 20.03.2014 18:46, schrieb Briand, Sheldon: pulling from https://bitbucket.org/galaxy/galaxy-dist searching for changes no changes found From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Thursday, March 20, 2014 2:36 PM To: Briand, Sheldon Cc: 'galaxy-dev

Re: [galaxy-dev] Installing homer into galaxy

2014-03-20 Thread Greg Von Kuster
Hi Pete, Here is the recipe for installing homer from this repository: http://toolshed.g2.bx.psu.edu/view/kevyin/homer ?xml version=1.0? tool_dependency package name=homer version=4.1 install version=4.1 actions action

Re: [galaxy-dev] Installing homer into galaxy

2014-03-20 Thread Greg Von Kuster
on the server? I found this in the tool shed tree. On 3/20/14, 3:03 PM, Greg Von Kuster wrote: Hi Pete, Here is the recipe for installing homer from this repository: http://toolshed.g2.bx.psu.edu/view/kevyin/homer ?xml version=1.0? tool_dependency package name=homer version

Re: [galaxy-dev] http://toolshed.g2.bx.psu.edu/ is down?

2014-03-17 Thread Greg Von Kuster
Sheds are available. Greg Von Kuster On Mar 17, 2014, at 1:17 PM, changyu changyu_...@mail.dfci.harvard.edu wrote: Is http://toolshed.g2.bx.psu.edu/ down? ___ Please keep all replies on the list by using reply all in your mail client

Re: [galaxy-dev] http://toolshed.g2.bx.psu.edu/ is down?

2014-03-17 Thread Greg Von Kuster
Both the test and main Galaxy Tool Sheds should now be available. Please let us know if you encounter issues. Thanks, Greg Von Kuster On Mar 17, 2014, at 1:31 PM, Greg Von Kuster g...@bx.psu.edu wrote: Yes, both the test and main Galaxy Tool Sheds are temporarily unavailable due

Re: [galaxy-dev] tool_dependency_dir (Installed, missing tool dependencies)

2014-03-11 Thread Greg Von Kuster
dependencies installed into a single location. Greg Von Kuster On Mar 6, 2014, at 5:41 PM, Wang, Xiaofei xfw...@ku.edu wrote: Dear there, I am trying to install some tools from toolshed on my local galaxy instance, like bwa_wrappers, package_picard_1_56_0, package_samtools_0_1_18

Re: [galaxy-dev] tool trouble

2014-03-07 Thread Greg Von Kuster
-Original Message- From: Briand, Sheldon Sent: Monday, March 03, 2014 2:16 PM To: 'Greg Von Kuster' Subject: RE: [galaxy-dev] tool trouble Hi, Not sure if you were still scratching your head about this one. I am going to be moving my galaxy install to a new larger file system

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-03-06 Thread Greg Von Kuster
Hello Peter, On Feb 20, 2014, at 10:20 AM, Greg Von Kuster g...@bx.psu.edu wrote: On Thu, Feb 20, 2014 at 9:59 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster g...@bx.psu.edu wrote: Your installation recipe for mira attempts to download

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-03-06 Thread Greg Von Kuster
Hi Peter, On Mar 6, 2014, at 1:07 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Mar 6, 2014 at 5:24 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Mar 6, 2014 at 4:53 PM, Greg Von Kuster g...@bx.psu.edu wrote: On Feb 20, 2014, at 10:20 AM, Greg Von Kuster g...@bx.psu.edu

Re: [galaxy-dev] Test ToolShed misfiling missing tool tests

2014-03-03 Thread Greg Von Kuster
Hi peter, Thanks for reposrting this. I've created the follwoing Trello card for this issue, and we'll get it taken care of asap. https://trello.com/c/rArkn49z/173-incorrect-tool-test-results-for-tools-missing-tool-test-components Gfreg Von Kuster On Mar 3, 2014, at 8:38 AM, Peter Cock

Re: [galaxy-dev] Exporting Importing Tool Shed repository is just great!

2014-03-03 Thread Greg Von Kuster
discovered issues! Greg Von Kuster On Mar 3, 2014, at 12:02 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Tool Shed Team! I know I'm always finding bugs and keeping you busy, but this mail is different! The Tool Shed exporting and importing feature is just great, its save so much

Re: [galaxy-dev] Exporting Importing Tool Shed repository is just great!

2014-03-03 Thread Greg Von Kuster
On Mon, Mar 3, 2014 at 5:58 PM, Greg Von Kuster g...@bx.psu.edu wrote: Many thanks, Björn for your very kind words. The Tool Shed would not be what it is without your hard work as well. We hoped the export/import capsule feature would be beneficial, so it's great to hear confirmation

Re: [galaxy-dev] tool trouble

2014-02-28 Thread Greg Von Kuster
database suing sql commands. If you have done this, it could be the cause of the behavor you are describing. The Galaxy UI or API should be used. Greg Von Kuster My shed tool path: toolbox tool_path=../shed_tools My current version: parent: 12441:dc067a95261d Added tag

Re: [galaxy-dev] tool trouble

2014-02-28 Thread Greg Von Kuster
/package_bowtie2_2_1_0/017a00c265f1/bowtie2-build [galaxy@eugene galaxy]$ cd shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/ I seem to be missing the .py and .xml files in the shed_tools directory. -Sheldon From: Briand, Sheldon Sent: Friday, February 28, 2014 2:11 PM To: 'Greg Von Kuster

Re: [galaxy-dev] contributing patches to toolshed repos...

2014-02-25 Thread Greg Von Kuster
Hi Brad and Björn, Tickets can currently only be added to the Galaxy Trello Board, so please add them there and we'll move them to the Tool Shed Trello board whenever appropriate. Hopefully we'll soon have the ability for tickets to be submitted to multiple boards. Thanks very much! Greg

Re: [galaxy-dev] Test Tool Shed, nightly tests: Error 'unicode' object has no attribute 'get'

2014-02-24 Thread Greg Von Kuster
Hello Peter, On Feb 24, 2014, at 3:32 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Greg, Good progress - no sign of the unicode error :) I now have the following three repositories shown under Latest revision: installation errors http://testtoolshed.g2.bx.psu.edu/view/peterjc

Re: [galaxy-dev] With regard to Galaxy tools, a repository should only contain one

2014-02-21 Thread Greg Von Kuster
Hi Peter, On Feb 21, 2014, at 9:10 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I've just seen Greg's blog post, The Galaxy Tool Shed: Best Practices for Populating a Repository http://gregvonkuster.org/galaxy-tool-shed-best-practices-populating-repository/ One particular

Re: [galaxy-dev] Test Tool Shed, nightly tests: Error 'unicode' object has no attribute 'get'

2014-02-21 Thread Greg Von Kuster
to the exception handling for displaying the invalid data in the Tool Shed repository's Test runs container. We've corrected the data in the database as well as the bug that produced it, so tonight's test run should not result in this behavior for these repositories. Thanks very much! Greg Von Kuster

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-02-20 Thread Greg Von Kuster
to the Tool Shed and several other Terello cards can be handled. See my inline comments below… On Feb 20, 2014, at 5:30 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Feb 20, 2014 at 9:59 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster g

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-02-19 Thread Greg Von Kuster
Hello Peter, Please see below… On Feb 19, 2014, at 4:41 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Greg, Overnight this has gone back to the previously observed missing data problem (e.g. email of 4th Feb) - no test results at all: http://testtoolshed.g2.bx.psu.edu/view/peterjc

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-02-19 Thread Greg Von Kuster
! Greg Von Kuster On Feb 19, 2014, at 3:49 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Feb 19, 2014 at 8:42 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Peter, Please see below... ... Your above email arrived in my inbox at 4:42 AM EST, and it looks like your repository

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-02-19 Thread Greg Von Kuster
Hi Peter, On Feb 19, 2014, at 6:09 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Wed, Feb 19, 2014 at 9:33 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, Dave B and I just discovered that issue that causes your tests to fail. The problem lies with our current implementation

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-02-18 Thread Greg Von Kuster
Hi Peter, We'll try to get some time to look at your tool_dependencies.xml recipe as soon as possible. Greg Von Kuster On Feb 18, 2014, at 5:47 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Greg, Dave, RE: http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler Same

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-02-17 Thread Greg Von Kuster
-gnu_x86_64_static.tar.bz2 and it looked ok. Let's see what the restults of tonight's test run is for this repository and if there are still problems after your latest changes we'll track them down. Thanks, Greg Von Kuster On Feb 17, 2014, at 6:15 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Sat, Feb 15

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-02-15 Thread Greg Von Kuster
Hi Peter, On Feb 3, 2014, at 7:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Moreover there is a similar problem with the matching repository on the Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr 2014-01-04 showing failed tests for

Re: [galaxy-dev] WARNING:galaxy.datatypes.registry:Overriding conflicting datatype

2014-02-14 Thread Greg Von Kuster
I've gone ahead and made the change in the datatypes registry to use log.debu instead of log.warning, so hopefully this issue is resolved. The changeset in central is 12497:0b0018fa5d20, which has also be grafted to stable. Greg Von Kuster On Feb 13, 2014, at 11:51 AM, Jim Johnson johns

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-02-13 Thread Greg Von Kuster
/blastxml_to_top_descr 2014-01-29 missing blast_datatypes dependency (why?) 2014-01-28 showing failed tests for sambamba_filter (wrong tool) I'll be taking a look at the remaining issues on the following Trello card next. https://trello.com/c/M1rwVWhI/143-nightly-test-runs-1 Greg Von Kuster

Re: [galaxy-dev] Twill compares wrong file; was: Twill comparisons ignore GALAXY_TEST_NO_CLEANUP

2014-02-13 Thread Greg Von Kuster
though we'll have to soon eliminate it due to Javascript. I'm not sure if others agree with this though. Greg Von Kuster On Feb 12, 2014, at 5:46 AM, Peter Cock p.j.a.c...@googlemail.com wrote: I think it ought be possible to refactor the Twill test code to use the same dictionary approach used

Re: [galaxy-dev] WARNING:galaxy.datatypes.registry:Overriding conflicting datatype

2014-02-13 Thread Greg Von Kuster
Hi JJ, On Feb 13, 2014, at 11:00 AM, Jim Johnson johns...@umn.edu wrote: I now have 2 versions of snpeff installed from the toolshed on my galaxy server. Each snpeff version includes an identical datatypes_conf.xml The galaxy server is setting metadata externally. When any job

Re: [galaxy-dev] Twill compares wrong file; was: Twill comparisons ignore GALAXY_TEST_NO_CLEANUP

2014-02-13 Thread Greg Von Kuster
it will require some work to eliminate it completely. Some enhancements to our twill framework will undoubtedly be necessaruy form some time. However, non-trivial enhancements should be thought about carefully. Thanks! Greg Von Kuster On Feb 13, 2014, at 5:46 PM, Björn Grüning bjoern.gruen

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-02-04 Thread Greg Von Kuster
-test-runs-1 Thanks Greg Von Kuster On Feb 3, 2014, at 7:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Jan 30, 2014 at 4:32 PM, Greg Von Kuster g...@bx.psu.edu wrote: On Jan 29, 2014, at 1:18 PM, Greg Von Kuster g...@bx.psu.edu wrote: Peter wrote: http://toolshed.g2.bx.psu.edu

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-02-04 Thread Greg Von Kuster
-test-runs-1 Thanks Greg Von Kuster On Feb 3, 2014, at 7:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Jan 30, 2014 at 4:32 PM, Greg Von Kuster g...@bx.psu.edu wrote: On Jan 29, 2014, at 1:18 PM, Greg Von Kuster g...@bx.psu.edu wrote: Peter wrote: http://toolshed.g2.bx.psu.edu

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-01-30 Thread Greg Von Kuster
Hi Peter, On Jan 29, 2014, at 1:18 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr 2014-01-29 missing blast_datatypes dependency (why?) 2014-01-28 showing failed tests for sambamba_filter (wrong tool) I'll have

Re: [galaxy-dev] Nightly testing status on the (Test) Tool Shed

2014-01-29 Thread Greg Von Kuster
Hi Peter, On Jan 29, 2014, at 12:55 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, Are both the main and test Tool Sheds currently meant to be running nightly tests again? Yes I've not really got back into Galaxy tool testing since Christmas. Most of my tools' test results

[galaxy-dev] The main Galaxy Tool Shed is now running the next-stable branch

2014-01-27 Thread Greg Von Kuster
authorize others (either users or groups) to administer their repository using the new Manage repository administrators option in the Repository Actions pop-up menu. Please report any issues you uncover and we'll get them handled in preparation for the upcoming release. Thanks! Greg Von Kuster

Re: [galaxy-dev] Toolshed throwing error when reading tool's XML

2014-01-20 Thread Greg Von Kuster
, it seems that your repository may not include a required xxx.loc.sample file. Let me know if adding one does not solve the problem. Is your repository in one of the Galaxy team;'s public tool sheds? Greg Von Kuster On Jan 20, 2014, at 2:24 PM, Dooley, Damion damion.doo...@bccdc.ca wrote: I'm

Re: [galaxy-dev] Toolshed throwing error when reading tool's XML

2014-01-20 Thread Greg Von Kuster
the trick, thanks Greg. I only had .loc files in the upload set; didn't know about the .sample version or tool_data_table_conf.xml.sample. One thing, did I miss reading the documentation on this somewhere or is this workshop type knowledge? From: Greg Von

Re: [galaxy-dev] making tools with Galaxy

2014-01-16 Thread Greg Von Kuster
to start is probably: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Greg Von Kuster On Jan 16, 2014, at 5:56 AM, Lionel Chiron lionel.chi...@nmrtec.com wrote: Hi Greg, I'm trying to make a tool in Galaxy for implementing our algorithm for mass spectrometry treatment

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