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
___
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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
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
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
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
to the stable branch when it is
created for the upcoming Galaxy release.
Thanks very much,
Greg Von Kuster
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and other
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
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
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
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
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
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
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
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
-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
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
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
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
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
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
-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
.
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
/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
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
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
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
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
, 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
,
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
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
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
.
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
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
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Please keep all replies on the list by using reply all
in your mail
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
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
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
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
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
!
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
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
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
/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
: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
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
.
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
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
(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
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
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
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
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
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
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
...@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
-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
://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
.
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
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
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
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?
___
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in your mail client
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
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
-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
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
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
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
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
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
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
/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
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
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
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
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
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
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
!
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
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
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
-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
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
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
/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
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
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
-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
-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
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
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
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
, 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
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
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
/guOeL1sF/28-toolshed-add-the-ability-for-a-repository-owner-to-grant-administrative-privileges-on-their-repository-in-the-tool-shed-to-otherThanks,Greg Von KusterOn Jan 14, 2014, at 4:44 PM, Philip Mabon philipma...@gmail.com wrote:Is it possible to permanentlychangethe owner of a Tool in the Tool
, changes should be made within the
Galaxy environment rather than the Tool Shed.
As input regarding this request comes in from the community, perhaps we can
create an appropriate Trello card to capture the direction we should go.
Thanks very much for your request on this!
Greg Von Kuster
On Jan
Perfect thanks!
On Mon, Jan 6, 2014 at 1:16 PM, Dannon Baker dannon.ba...@gmail.com wrote:
Hey Greg,
Sorry about the delay on this over the holidays. I see what you're working
with now. If you install your customizations in a portable manner in
/mnt/galaxyData that should be safe and we'll
Hello Damion,
I believe this issue was corrected in
https://bitbucket.org/galaxy/galaxy-central/commits/3d8841746ce9b65e19a44028dea2eac73a4eddf8
It looks like you are tracking the galaxy-central brach, so if you pull and
update your repository you should get the fix.
Greg Von Kuster
Hello Pieter,
I've added the following Trello card for this issue - we'll take a looke as
soon as possible.
https://trello.com/c/LZ3Lj9ye/125-problem-with-adding-deleting-adding-readme-files
Thanks for reporing this,
Greg Von Kuster
On Dec 30, 2013, at 8:09 AM, Lukasse, Pieter pieter.luka
Just following up on this. So it's ok to do all of my customizations
in /mnt/galaxyData?
Or am I doing something wrong, and I need to figure out how to boot up
into a version that has /mnt/galaxy?
Thanks again,
Greg
On Fri, Dec 20, 2013 at 2:49 PM, greg margeem...@gmail.com wrote:
Yes, I
it on a galaxy cloud instance and then provide the
share string to other researchers.
I did this successfully a year or two ago by installing it to /mnt/galaxyData.
Thanks,
Greg
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