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" wrote:
> I&#x
place
to start is probably:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Greg Von Kuster
On Jan 16, 2014, at 5:56 AM, Lionel Chiron wrote:
> Hi Greg,
>
> I'm trying to make a tool in Galaxy for implementing our algorithm for mass
> spectrometry treatment but
://trello.com/c/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 permanently change the owner of a T
, 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 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 an
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
On
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 wrote:
> Yes, I just launched
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,
If so, how'd you launch
> it?
>
>
> On Fri, Dec 20, 2013 at 2:37 PM, greg wrote:
>>
>> Here's what I'm seeing:
>>
>> ubuntu@ip-10-182-195-79:/$ ls /
>> bin boot dev etc export home initrd.img lib lib64 lost+found
>> media mnt
k to /mnt/galaxy if I remember correctly.
>
> If you're launching your cluster from usegalaxy.org/cloudlaunch, you should
> always be using the latest stuff.
>
>
> On Fri, Dec 20, 2013 at 2:13 PM, greg wrote:
>>
>> Thanks. I was wrong before. I actually do see a
Thanks. I was wrong before. I actually do see a /mnt/galaxyData.
Should I not being seeing that? Am I not on cloudman 2.0?
-Greg
On Fri, Dec 20, 2013 at 1:57 PM, Dannon Baker wrote:
> With the Cloudman 2.0 release, the galaxyData and galaxyTools volumes have
> been merged to a
want to install 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
___
Please keep all replies on the list by u
Hello Kerry,
I've committed a fix for this in 11800:a53f2f700699 to the galaxy-central
branch. Is that the branch you're pulling?
Thanks for reporting this.
Greg Von Kuster
On Dec 18, 2013, at 5:48 PM, Kerry Deutsch
wrote:
>
> Hello -
>
> I pulled down the latest
ependency_definition. This enhancement will be included in the
next-stable branch when it is created in mid-January.
Sorry for the inconvenience this may cause, but after mid-January things should
be in good shape on the main tool shed.
Greg Von Kuster
On Dec 12, 2013, at 5:00 PM, Nicola S
an_keypair.pem ubuntu@` to get more verbose
> logging.
>
>
> On Mon, Dec 16, 2013 at 10:48 AM, greg wrote:
>>
>> I last used cloud launch a year ago with this account. I may have
>> used biocloudcentral though at that point.
>>
>> Is there a work around I can do i
groups -- a known issue that I'm working
> on a fix for.
>
> -Dannon
>
>
>
> On Mon, Dec 16, 2013 at 10:20 AM, greg wrote:
>>
>> Hi guys,
>>
>> I just did a cloud launch of MSG by going here:
>> https://usegalaxy.org/cloudlaunch
&g
.amazonaws.com
ssh: connect to host ec2-54-196-189-227.compute-1.amazonaws.com port
22: Operation timed out
And the same problem when I use the IP address.
I also can't ping the above address nor the IP address. It just says
request time out.
Thanks,
hem over a year ago but I no
longer need them.)
Thanks,
Greg
___
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
this card completed before the Christmas break.
https://trello.com/c/HVGrShnC/60-tool-shed-should-test-installation-of-packages
Greg Von Kuster
On Dec 10, 2013, at 10:59 AM, Peter Cock wrote:
>
> Thanks Greg,
>
> I'm seeing this tool listed under "Latest revision: failing
letting me know about this.
Greg Von Kuster
On Dec 10, 2013, at 10:09 AM, Nicola Soranzo wrote:
> Hi Greg!
> I don't know if it's the same problem, but I've not been able to see
> test results for this repository for a while:
>
> http://toolshed.g2.bx.psu.edu/view/crs
; category.
Thanks for letting us know about this, and please let us know if you discover
other reposiory revisions that require the same correction.
Greg Von Kuster
On Dec 9, 2013, at 5:06 AM, Peter Cock wrote:
> Hi Dave & Greg,
>
> Could you double check how the "Skip autom
t;Repair repository" if it is available.
On Dec 5, 2013, at 4:08 PM, Valeria Parreira Pinto wrote:
> Hi Greg,
>
> I have done at least twice just to double check From Repository actions -
> reset to install
> This is what a I see:
>
>
> Monitor installing tool sh
What happens if you choose "Reset to install" from the "Repository Actions"
menu? You should be presented with a page that shows the repository as
uninstalled, at which time you can attempt to install it again.
On Dec 5, 2013, at 3:11 PM, Valeria Parreira Pinto wrote:
&g
p in the right direction. After making this change, let us know if you
still see problems.
Greg Von Kuster
On Dec 5, 2013, at 12:13 PM, Valeria Parreira Pinto
wrote:
> Hi Greg,
>
> Unfortunately, it is not working...sorry bug you again.
> I know nothing about programming...this is w
Hello Valeria,
The setting for tool_dependency_dir must be an actual path on your local file
system, something like:
tool_dependency_dir = ../tool_dependencies
Make sure that you set the location to a place that is safe for installing
files.
Greg Von Kuster
On Dec 4, 2013, at 3:09 PM
ample entries for the Galaxy data tables that this tool must
use. I'm not sure of the layout of this table for this particular tool, but if
you discover what it should be, you can manually add them into a file named
hmmdb.loc in the ~/tool-data directory in your Galaxy environment.
Greg
Hi Peter,
On Nov 28, 2013, at 12:56 PM, Peter Cock wrote:
> On Thu, Nov 28, 2013 at 5:30 PM, Peter Cock wrote:
>>
>> Thank you - that alerted me to a missing set of out output files for a
>> recently added test, hopefully addressed in this revision:
>> http://testtoolshed.g2.bx.psu.edu/view/p
Hello Peter,
On Nov 28, 2013, at 4:56 AM, Peter Cock wrote:
> On Wed, Nov 27, 2013 at 9:02 PM, Greg Von Kuster wrote:
>>
>> Hello Peter,
>>
>> I've done a significant amount of re-engineering of the
>> Tool Shed's install and test framework over
n top of things that need fixing as we proceed with this new
framework.
Thanks,
Greg Von Kuster
On Nov 27, 2013, at 5:44 AM, Peter Cock wrote:
> On Thu, Nov 21, 2013 at 2:47 PM, Peter Cock wrote:
>> On Thu, Nov 21, 2013 at 2:38 PM, Dave Bouvier wrote:
>>> Peter,
>&
Hi Peter,
On Nov 18, 2013, at 10:33 AM, Peter Cock wrote:
> On Mon, Nov 18, 2013 at 2:24 PM, Dave Bouvier wrote:
>> Peter,
>>
>> It turns out there were two problems. First, the test environment was not
>> resolving the upload tool's dependency on samtools, which I've now
>> corrected.
>
> Ex
ever, it's been on my list for a while to
eliminate fabric if possible so that I have more management of the threads and
process ids during installation. If fabric / subprocess is a problem here, I
can attempt to raise the prority of looking at this.
Greg Von Kuster
On Nov 14, 2013, at
Hi Peter,
On Nov 14, 2013, at 11:27 AM, Peter Cock wrote:
> On Wed, Nov 13, 2013 at 12:03 PM, Greg Von Kuster wrote:
>> Hello Peter,
>>
>> Yesterday we discovered what Björn has communicated and added it to the
>> Trello card for this issue:
>>
>>
dependencies.xml file:
This is all discussed in the following section of the Tool Shed wiki:
http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories
Let me know if this doesn't correct this problem.
Thanks
Hello Peter,
Thanks for reporting this - I've added the following Trello card for this issue.
https://trello.com/c/sN2iLCCn/99-bug-in-install-and-test-framework-1
Greg Von Kuster
On Nov 12, 2013, at 7:07 AM, Peter Cock wrote:
> Hi guys,
>
> I have a new wrapper for samtools i
manifest that was corrected in
this change set. You can just export the capsule again with this latest
changeset.
Please let me know if you encounter any issues.
Thanks,
Greg Von Kuster
On Nov 4, 2013, at 10:54 AM, Greg Von Kuster wrote:
> Hello Ray and Björn,
>
> I'm currently
Please see my inline comments. Thanks!
Greg Von Kuster
On Nov 7, 2013, at 1:33 PM, John Chilton wrote:
> On Thu, Nov 7, 2013 at 1:46 AM, Björn Grüning
> wrote:
>> Am Donnerstag, den 07.11.2013, 00:25 -0600 schrieb John Chilton:
>>
>> My two cents below.
>>
Thanks Björn,
We'll have to digest this a bit and we'll get back to you.
Greg Von Kuster
On Nov 5, 2013, at 4:35 PM, Björn Grüning
wrote:
> Hi Greg,
>
>> Hello Bjoern,
>>
>>
>> On Nov 5, 2013, at 12:13 PM, Bjoern Gruening
>> wrote:
Hello Bjoern,
On Nov 5, 2013, at 12:13 PM, Bjoern Gruening wrote:
> Hi Greg,
>
> I'm right now in implementing a setup_perl_environment and stumbled about a
> tricky problem (that is not only related to perl but also for ruby, python
> and R).
>
> The Problem:
&g
t would be much appreciated as well.
Greg Von Kuster
On Nov 5, 2013, at 12:03 AM, John Chilton wrote:
> Simon,
>
> As you have probably noticed a new stable galaxy was released. It
> includes 95% of what we discussed including this implicit check to see
> if tool shed packag
be available in the next few days.
Thanks,
Greg Von Kuster
On Nov 4, 2013, at 3:46 AM, Björn Grüning
wrote:
> Hi Ray,
>
> there is some work in that direction to easily import and export
> repositories. The export feature is already integrated and should help
> you. You will
ted. Will this
be an appropriate approach to this, or am I missing something here?
Thanks!
Greg Von Kuster
On Nov 2, 2013, at 7:06 AM, Peter Cock wrote:
> On Fri, Nov 1, 2013 at 2:13 PM, John Chilton wrote:
>>
>> Hmmm... I have been thinking a lot about this. I imagine at some
I believe this is fixed in 11184:d2b9f616e66c - at least everyting worked for
me. However, committing to next-stable was a bit tweaky although I think all
is ok. Please let me know if you see any problems.
Thanks!
Greg Von kuster
On Oct 30, 2013, at 4:09 PM, John Chilton wrote:
> I
Thanks John,
I just sent my message as yours arrived - this will help me more quickly
resolve the issue. I'll have a fix soon.
Greg Von Kuster
On Oct 30, 2013, at 4:09 PM, John Chilton wrote:
> I can verify augustus doesn't work correctly any longer, but I do not
> get the
this dependecny the one where you've seen
this problem?
Thabnks,
Greg Von kuster
Tool shed repository 'augustus' tool dependencies
NameVersion TypeStatus Error
AUGUSTUS_SCRIPT_PATHNoneset_environment Never installed
augustus2.7 package Installed
On
epo.
Can you let me know what steps you are taking and the behavior you are seeing
that differs from this?
Thanks!
Greg Von Kuster
On Oct 29, 2013, at 1:03 PM, Bjoern Gruening wrote:
> Hi Greg,
>
> do you mean that patch?
>
> https://bitbucket.org/galaxy/galaxy-central/com
e of days to look at this again if you haven't been
able to discover the cause of the problem.
Thanks,
Greg Von Kuster
On Oct 29, 2013, at 7:00 AM, Peter Cock wrote:
> On Tue, Oct 29, 2013 at 6:23 AM, Lukasse, Pieter
> wrote:
>> Hi Greg,
>>
>> what I mean is that
Hi Pieter,
Perhaps I'm misunderstanding this issue. Can you clarify the problem?
Thanks,
Greg Von kuster
On Oct 25, 2013, at 9:53 AM, "Lukasse, Pieter" wrote:
> Kind of assuming Greg did this yesterday when he replied with only two
> problemsbut you are right
Hello Simon,
On Oct 24, 2013, at 4:06 PM, "Guest, Simon"
wrote:
>
> Hi Greg,
>
> Thanks for the explanation, and the link to that helpful Wiki page.
> And also that code update 4:71c35dbde130 which will help our tool
> test/development cycle.
>
> I
messages for invalid XML
like this as the XMNL parser does not provide much of anything meaningful that
can be passed on in the UI. At some point I may find the chance to incorporate
a validator, but just don't currently have the time.
Greg Von Kuster
On Oct 24, 2013, at 10:46 AM, &qu
psu.edu/view/pieterlukasse/prims_masscomb
>
> There does seem to be something amiss - probably a question
> for Greg.
>
> Peter
>
> ___
> Please keep all replies on the list by using "reply all"
> in your
this issue.
Greg Von Kuster
On Oct 23, 2013, at 11:34 AM, S.D. Hiltemann wrote:
> I updated my Galaxies to the latest version today, and when I try to install
> a toolshed repository which defines an environment variable via the
> tags in the tool_dependencies.xml file, I get an
Hello Simon,
On Oct 23, 2013, at 5:01 PM, Simon Guest wrote:
> We've noticed a funny about resetting repository metadata from the
> toolshed web interface.
>
> My understanding is that this is used to get the toolshed back in sync
> with the underlying mercurial repo, for example after pushing
get it corrected. I should be able to get back to you
tomorrow on this one.
Thanks,
Greg Von Kuster
On Oct 23, 2013, at 11:34 AM, S.D. Hiltemann wrote:
> I updated my Galaxies to the latest version today, and when I try to install
> a toolshed repository which defines an environment va
previousl email).
Thanks,
Greg Von Kuster
On Oct 22, 2013, at 5:48 AM, Peter Cock wrote:
> Hi Dave, Greg,
>
> Based on my tool's overnight test results from the Test Tool Shed,
> something seems to have been broken to do with sniffing datatypes
> on upload.
>
> e.g. using
until it is finished.
https://trello.com/c/QWgsgll8/1203-toolshed-automated-test-framework-fixes
Greg Von Kuster
On Oct 22, 2013, at 5:43 AM, Peter Cock wrote:
> On Mon, Oct 7, 2013 at 7:32 PM, Dave Bouvier wrote:
>> Peter,
>>
>> Thanks for the information, it uncover
FYI:
The Main Tool Shed is now running the next-stable branch and all metadata has
been reset on all repositories. The tentative date of the next Galaxy relesase
is currently November 4. The Main Tool Shed will be updated to the stable
branch at the time of the release.
Greg Von Kuster
Hello Simon,
On Oct 14, 2013, at 6:26 AM, Greg Von Kuster wrote:
> On Oct 13, 2013, at 5:13 PM, Simon Guest wrote:
>
>>
>> I've recently upgraded to the
>> development branch, and I'm getting HTTP 404 errors from the new
>> function get_t
you wanted to run the development
branch, the current behavior for this feature should not keep you from doing so.
Thanks for reporting this.
Greg Von Kuster
On Oct 13, 2013, at 5:13 PM, Simon Guest wrote:
> Hi Greg,
>
> I think this would be yours. I've recently upgraded to
Hello Peter,
I've created teh following Trello card for this:
https://trello.com/c/Vg12cS7o/1174-toolshed-frames-issue-with-readme-file-links
Thanks,
Greg Von Kuster
On Oct 8, 2013, at 10:44 AM, Peter Cock wrote:
> Consider the following sequence:
>
> 1. Goto http://toolshed
Hi Peter,
On Oct 8, 2013, at 11:01 AM, Peter Cock wrote:
> On Tue, Oct 8, 2013 at 3:47 PM, Greg Von Kuster wrote:
>> Hi Peter and others,
>>
>> Peter wrote:
>>> As an aside, I've asked before about why the function tests look
>>> at *.loc rather
Hi Peter and others,
On Oct 8, 2013, at 10:22 AM, Peter Cock wrote:
> Hi Greg, Jean-Frédéric,
>
> I'm returning to this old thread rather than starting a new one,
> since it is nicely aligned with something I wanted to raise.
>
> On Tue, Feb 19, 2013 at 2:23 PM,
Hello Joachim,
What version of Galaxy / Tool Shed code are you using?
On Sep 30, 2013, at 8:05 AM, Joachim Jacob | VIB | wrote:
> Hi Greg,
>
>
> Sorry to dig up this unsolved thread from a few months back.
>
> Recap of the bug: I have developed a small tool. I have
Hi Rico,
This should be fixed in 10742:3de162c29e7e.
Thanks for reporting this,
Greg Von Kuster
On Sep 27, 2013, at 12:18 PM, Richard Burhans wrote:
> Greg,
>
> I was mistaken. It wasn't a GET, it was a POST. Here's the POST request:
>
> POST
> /admin_
hanks,
Greg Von Kuster
On Sep 26, 2013, at 9:49 PM, James Taylor wrote:
> Make the precedence a config option. Otherwise I agree.
>
> In addition, I still like the idea I suggested earlier of dependency provider
> plugins. Then you could (for example) have one that uses 'module
r choose to install thje dependency
from the Tool Shed or manually compile hte dependency and have the
ToolDependency object point to it. In either case,all Tool Shed dependency
definitions (both repository and tool depndencies) would all work as expected
with additional repository installs.
Gr
dependency" in whatever location on disk the admin chooses via a new
UI feature? Or do you have a different idea?
Thanks,
Greg Von Kuster
>
> Whats great is this solves other problems as well. For instance, our
> genomics Galaxy web server runs Debian but the worker nodes run
that he has
updated are currently all owned by the devteam in preparation for a tool
migration stage that he will soon be committiing. Perhaps the atlas tool
dependency can be updated to proved a pre-compiled binary installation.
Greg Von Kuster
On Sep 26, 2013, at 11:10 AM, Peter Cock wrote
oblem.
# Get the information necessary to install each repository.
url = suc.url_join( tool_shed_url,
'repository/get_repository_information?repository_ids=%s&changeset_revisions=%s'
% \
( repository_ids, changeset_revisions ) )
Thanks,
Greg Von
reporting this!
Greg Von Kuster
On Sep 23, 2013, at 12:20 PM, Richard Burhans wrote:
> Greg,
>
> That's part of the issue. Please try the following:
>
> 1) Direct your browser to
> http://toolshed.g2.bx.psu.edu/view/miller-lab/genome_diversity
> 2) Choose "33:5064f618
Hi Peter,
This behavior has been corrected in 10637:216c01ce6625. Thanks for reporting
this.
Greg Von Kuster
On Sep 23, 2013, at 7:09 AM, Peter Cock wrote:
> Hi all,
>
> I think I've found a bug, or at least an area for improvement,
>
> 1. Goto http://testtoolshe
It's a bit unclear what you mean by "private" here, but it's possible to at
least force users to login to use a Tool Shed if you include the following
setting in the [app:main] section your tool_shed_wsgi.ini file.
# Force everyone to log in (disable anonymous access)
requir
@montana:~/galaxy_toolshed/database/community_files/000/repo_200$
Since the issue was not related to the Tool Shed's README utility, is was easy
to "miss" it.
Is the content of the README file now what you expect?
Greg Von Kuster
On Sep 21, 2013, at 6:13 PM, Richard Burhans
Hi Rico,
On Sep 21, 2013, at 5:56 PM, Richard Burhans wrote:
> Greg,
>
> To be more clear, montana has revision 4188853b940b on disk, which is not the
> tip revision, 5064f618ec1c.
Unless I am missing something, montana has revisions 5064f618ec1c on disk:
g2cmnty@montana:~/gal
cific changeset revisions of a repository where this is not the case?
The following URL is not a proper URL for browsing a tool shed repository
Readme file via a browser.
> http://toolshed.g2.bx.psu.edu/repos/miller-lab/genome_diversity/file/5064f618ec1c/README
Greg Von Kuster
On Sep 20, 2013, a
ecember 20, 2012 Galaxy release.
With regard to forward-compatiblity between Galaxy and the Tool Shed, there is
a Trello card here:
https://trello.com/c/cd3hBnnH/30-tool-shed-decoupling-galaxy-and-tool-shed-versions
Greg Von Kuster
On Sep 20, 2013, at 1:00 PM, Richard Burhans wrote:
> Greg,
Hi Rico,
The test tool shed is now running my latest commit - 10629:ab20415126a7. I was
successful with installing the genome diversity repository and all of it's
dependencies using that changeset in my local Galaxy environment (although 3
tool dependencies encountered the following errors whil
Hello Pieter,
The version of mercurial you are using is likely older than version 2.2.3. See:
http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Pushing_changes_to_a_repository_using_hg_from_the_command_line
Can you check this?
Greg Von Kuster
On Sep 13, 2013, at 5:54 AM, "Lu
sults" container when
viewing or managing the repository.
Greg Von Kuster
On Sep 12, 2013, at 7:23 AM, "Lukasse, Pieter" wrote:
> Ok, cool...I get the picture.
>
> One small downside is that then admin has to trust the developer has the
> discipline and sound judgment to co
with a set of rules that
define whether changes to the utility result in a new installable changeset
revision or not.
Greg Von Kuster
On Sep 12, 2013, at 7:14 AM, Bjoern Gruening wrote:
> Hi Pieter,
>
> yes that is possible. Have a look at other repositories. You can only
> ch
%20Shed
This page provides a nice overview of repository features:
http://wiki.galaxyproject.org/ToolShedRepositoryFeatures
See additional specific pages below for each item you've listed:
On Sep 11, 2013, at 11:52 AM, "Lukasse, Pieter" wrote:
> Hi Greg,
>
> I want to
handles
hg push from the command line since I don't have an environment set up that
way. That would be the place to take a look though, and if you discover
problems let me know and we'll apply a patch.
Thanks very much,
Greg Von Kuster
On Sep 5, 2013, at 4:53 PM, "Guest, Simon
Hello Simon,
On Sep 4, 2013, at 5:13 PM, "Guest, Simon" wrote:
> Hi Dave, Greg,
>
> Thanks for your reply.
>
> I'm running a recently checked out stable branch. hg log shows this tip:
> changeset: 10473:c42567f43aa7
> tag: tip
> user:
Hello Simin,
Bjoern is correct - if this is possible (which it looks like it is from your
traceback), then a bug has been introduced somewhat recently. We'll take a
look at this today and get a fix committed. Thanks for reporting this.
Greg Von Kuster
On Sep 4, 2013, at 3:17 AM, B
Hello Bjoern,
I've updated the Trello card with your requests - thanks!
Greg Von Kuster
On Aug 27, 2013, at 3:37 AM, Bjoern Gruening wrote:
> Hi Greg,
>
> I tried to extend my old list [1] but I'm not allowed to edit it. Maybe
> you can add the following items to
Hello Robert,
Is this still a problem? If so, what version of Galaxy are you running?
Greg Von Kuster
On Aug 23, 2013, at 1:47 PM, Robert Baertsch wrote:
> When I click on manage installed tool shed repos on the admin screen, I get
> this error.
>
> Any ideas how to debu
Hello Bjoern,
On Aug 21, 2013, at 1:27 PM, Bjoern Gruening wrote:
> Hi Greg,
>
> seems to work fine!
>
>> Hello Bjoern,
>>
>>
>> On Aug 21, 2013, at 2:51 AM, Bjoern Gruening
>> wrote:
>>
>>> Hi Greg,
>>>
>>&
ng to the tool shed
should work.
Greg Von Kuster
On Aug 21, 2013, at 11:23 AM, Peter Cock wrote:
> Hi all,
>
> I was trying to update this workflow repository on the Test Tool Shed,
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
>
> Attempting
ool shed simply inherits this problem from there.
https://trello.com/c/SqrjrnNg/986-trivial-bug-toolshed-adding-a-user-using-the-grant-authority-to-make-changes-section-of-repository-management-fails-unless-selec
Greg Von Kuster
On Aug 21, 2013, at 9:21 AM, Peter Cock wrote:
> I've made a n
Hello Bjoern,
On Aug 21, 2013, at 2:51 AM, Bjoern Gruening wrote:
> Hi Greg,
>
> a first test seems to work as expected for me, will test again with the
> whole CTB.
Great - thanks!
> If I understood your commit you are searching now for the next valid
> 'insta
Thanks Peter,
As soon as I can get the steps to produce "white ghost", I'll get a fix
committed - I've not been able to produce one yet.
Greg Von Kuster
On Aug 21, 2013, at 5:41 AM, Peter Cock wrote:
> On Tue, Aug 20, 2013 at 8:34 PM, Greg Von Kuster wrote:
>>
Peter and Ross,
I've not been able to reproduce this behavior, most likely because I am not
following the precise steps you've used when you see it. Can you clarify what
you do when you encounter it?
Thanks!
Greg Von Kuster
On Aug 15, 2013, at 4:50 AM, Peter Cock wrote:
>
Thanks for reporting this, Petere - we'll take a look as soon as we get a
chance.
I've created the following Trello card for this issue.
https://trello.com/c/CZeVLNFr/1068-toolshed-bullet-points-not-displayed-in-repository-readme-files
Greg Von Kuster
On Aug 20, 2013, at 6:56 AM,
ry to reproduce the behavior you're
discussing here.
Thanks!
Greg Von Kuster
On Aug 12, 2013, at 10:55 AM, Peter Cock wrote:
> Maybe I should retitle this thread...
>
> On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock wrote:
>> On Mon, Aug 12, 2013 at 3:10 PM, Bjoern Gruening
>
you still encounter this issue.
Thanks,
Greg Von Kuster
On Aug 13, 2013, at 12:49 PM, Bjoern Gruening wrote:
> Hi Dave,
>
> for us I think everything is fixed. But we had a bad bug in the 'single
> revision' implementation of the new 'Tool dependency definition&#
1 AM, Bjoern Gruening wrote:
> On Mon, 2013-08-12 at 16:26 +0100, Peter Cock wrote:
>> On Mon, Aug 12, 2013 at 4:19 PM, Bjoern Gruening
>> wrote:
>>> Hi Peter,
>>>
>>>> Hi Bjoern (& Greg),
>>>>
>>>> RE: http://toolshed.g2.
ry with name package_atlas_3_10 and owner hello.
The raised exception did not allow the upload to succeed, and the
"package_confab_1_0_1" repository remains empty with no changeset revisions.
Revision: -1:
Please let me know if I've misunderstood the steps you used
can be safely updated as well. Of course, tracking central in
Galaxy environments will get the fix as usual.
Thanks very much for reporting this!
Greg Von Kuster
On Aug 15, 2013, at 9:01 AM, Bjoern Gruening wrote:
> Hi Dave,
>
> the bug is unfortunately still present in the late
Hello Bjoern,
I just wanted to let you know I've determined the cause of this issue and
should have a fix for it committed by tomorrow (US Easter Time). I'll let you
know as soon as the fix is committed.
Greg Von Kuster
On Aug 15, 2013, at 9:01 AM, Bjoern Gruening wrote:
same approach. Ive created the following Trello card fvor this
request.
https://trello.com/c/nTArHl8J/1064-toolshed-handle-image-display-in-repository-readme-files
Thanks!
Greg Von Kuster
On Aug 19, 2013, at 1:29 PM, Peter Cock wrote:
> Hi all,
>
> Thanks to Bjoern's recent enhan
Hello Bjoern,
This is a strange error which I have not been able to reprioduce. However,
I've committed a fix that I believe will keep it from reoccurring in changeset
10411:c42567f43aa7. Thanks for reportin ghtis and please let me know if my fix
does not resolve it.
Thanks!
Gre
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