s well. I 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
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 wrote:
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:
Both Galaxy Tool Sheds have been updated with this fix.
Greg
On Jul 30, 2014, at 7:14 AM, Peter Cock 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
>
>
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 wrote:
> ... that might be a Greg question. The tool shed isn't going to use
> the citation inf
ed 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
ool Shed's 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 wrote:
> Hi Björn,
>
>
> On Jul 22,
Hi Björn,
On Jul 22, 2014, at 6:01 PM, Björn Grüning wrote:
> Hi Greg,
>
> thanks for the clarification. Please see my comments below.
>
>> On Jul 20, 2014, at 3:22 PM, Peter Cock wrote:
>>
>>> On Sun, Jul 20, 2014 at 6:23 PM, Björn Grüning wrote:
&g
cently installed one right?
>
> It would also resolve this https://trello.com/c/oTq2Kewd problem - where
> unsniffable binary datatypes are treated as sniffiable if there was ever an
> installed version that was some sniff-able datatype.
>
> -John
>
> On Jul 17,
circular
dependency relationships.
Either of the above 2 scenarios 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
Here's a Trello card for this:
https://trello.com/c/s8tfbW4x
On Jul 17, 2014, at 1:38 PM, Peter Cock 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 :)
&g
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
wrote:
> Hi Greg,
>
> not in the current, in version "2014-05-14"
would no
longer be available.
Greg
On Jul 17, 2014, at 1:30 PM, Peter Cock wrote:
> On Thu, Jul 17, 2014 at 6:10 PM, Björn Grüning
> wrote:
>>
>> ... but the problem will stay the same ... one [datatype definition]
>> repository
>> can have multiple versions ...
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).
I
-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 wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Hi Greg,
>
> Sorry about that, to
Hello Eric,
Please use Biostar or the Galaxy dev mail list rather than individual email
addresses in order to ensure faster responses. Pleasse see my responses below.
On Jul 14, 2014, at 10:20 AM, Eric Rasche wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
>
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
wrote:
> Hi
>
> There's a bug in the
ng the tool from your local Tool Shed.
Import 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 wrote:
> Hi All,
>
> I am playing around with putting a tool in te
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 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
evelopment environment setup that makes use of any existing repositories.
There was some work done 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 he
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 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
&g
e, ot mark 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 wrote:
> Is there any way to access a list of repository updates
e-owned-by-devteam
Thanks,
Greg Von Kuster
On Jun 4, 2014, at 9:59 AM, Jan Kanis 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 rep
:
hg 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
wrote:
> Hi,
>
> I installed the GATK2 wrapper f
Galaxy admin UI.
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
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 wrote:
> Hi Eric,
>
> I was sure there was a Trello card for this, but I can't find it right no
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 wrote:
> On Tue, May 27, 2014 at 3:39 PM, Greg Von Kuster wrote:
>> Hi peter,
>>
>> It seems that
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 wrote:
> Hi Greg, Dave,
>
> I just tried to upload an updated tar-ball to the Test Too
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
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 Ma
https://trello.com/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 wrote:
> Hi guys,
>
> I just noticed two of my tools on the main ToolShed were listed under
>
being
out.
I've added 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 wrote:
> Hi guys,
>
> I updated this new tool on Wednesday last week, b
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
Gre
tool panel, the Tool Shed installation process doesn't either. However,
if the ability to do this is needed, we can open a Trello card for it. Just
let us know.
Thanks,
Greg Von Kuster
On May 23, 2014, at 1:33 PM, Evan Bollig wrote:
> I am using the new_tool_panel_section_label op
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
should be clarified
with the upcoming release notes.
Greg Von Kuster
On May 23, 2014, at 8:56 AM, "Langhorst, Brad" 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://git
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, 201
You can contact the tool author to report this problem. In the meantime, to
use the tool, you'll have to install the flexbar dependency manually and make
sure it can be found in the environment in which the tool is executed.
Greg Von Kuster
On May 19, 2014, at 10:07 PM, "ruiwang.
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&quo
d be fixed 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 wrote:
> Hi Dave et al,
>
> Yesterday I
urial
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 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
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 wrote:
> Thanks for the response. I have made some progress, but I don't se
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 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
alert you 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 repl
hanks!
Greg Von Kuster
On Apr 3, 2014, at 10:24 AM, Björn Grüning 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,
> Bj
I should have handled the import in the same commit, but did so in the
following changeset. It will eliminate the problematic
prior_installation_required="False" attribute from the tag when a
capsule is being imported.
changeset: 12944:59bd7349a128
tag: tip
user:
/commits/773578e65580e3488fadc144739d82f86d9b30f3
Greg Von Kuster
On Apr 3, 2014, at 7:53 AM, Greg Von Kuster 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 A
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 wrote:
> Hi JanakiRam,
>
> I will take Greg into CC. He is the main Tool Shed developer, maybe we
> spotted a
nstalled
tools.
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
wrote:
> Hi,
>
> Thanks for reply. I composed a details email for better clarity.
>
> when r
As Janaki replied below, see:
http://wiki.galaxyproject.org/Admin/RunningTests?action=show&redirect=Admin%2FRunning+Tests
On Mar 27, 2014, at 7:15 AM, Janaki Rama Rao Gollapudi
wrote:
> Hi,
>
> I have added tests to tool dependency xml, but how should I run these tests,
> can you please help
(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
wrote:
> Hi Greg,
>
> The setting was not in my universe_sample file. I added it, set log_info to
> DEBUG and restarted galaxy.
>
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
wrote:
> hi Greg,
>
> I don't have that setting in my universe. S
s for each repository.
#manage_dependency_relationships = True
Greg Von Kuster
On Mar 25, 2014, at 11:08 AM, Geert Vandeweyer
wrote:
>
> Dear all,
>
> I'm wondering if the following behaviour is normal. Since I reinstalled the
> latest galaxy distribution, every restart hangs
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"
wrote:
> Hi,
>
> Not
y workflow 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" wrote:
> Hi Bjoern,
>
> I think you may have misunderstood me. What I mean is : ins
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
his 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
>>
>>
>>
>>
Hi Pete,
Here is the recipe for installing homer from this repository:
http://toolshed.g2.bx.psu.edu/view/kevyin/homer
http://biowhat.ucsd.edu/homer/configureHomer.pl
perl ./configureHomer.pl -install
./
$INSTALL
d.
>
> 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:
eldon"
wrote:
> $ hg summary
> parent: 12441:dc067a95261d
>
> From the tool_dependencies.xml:
>
>
>name="package_tophat2_2_0_9" owner="devteam"
> prior_installation_required="False" toolshed
> ="http://toolshed.g2
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
in walk
> names = listdir(top)
> TypeError: coercing to Unicode: need string or buffer, NoneType found
>
> -Sheldon
>
> From: galaxy-dev-boun...@lists.bx.psu.edu
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
> Sent: Thursday, March
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"
wrote:
> Hi,
>
> T
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
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 wrote:
> Yes, both the test and main Galaxy Tool Sheds are temporarily unavailable due
> to a hardwar
s the Tool Sheds are
available.
Greg Von Kuster
On Mar 17, 2014, at 1:17 PM, changyu wrote:
> Is http://toolshed.g2.bx.psu.edu/ down?
> ___
> Please keep all replies on the list by using "reply all"
> in your mail clien
ult in all tool dependencies installed into a single location.
Greg Von Kuster
On Mar 6, 2014, at 5:41 PM, "Wang, Xiaofei" 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, packa
contains tools
for display in the tool panel. I think you may be confusing Galaxy tools with
tool dependencies.
>
> Thanks!
> -Sheldon
>
> -Original Message-
> From: Briand, Sheldon
> Sent: Monday, March 03, 2014 2:16 PM
> To: 'Greg Von Kuster'
> S
Hi Peter,
On Mar 6, 2014, at 1:07 PM, Peter Cock wrote:
> On Thu, Mar 6, 2014 at 5:24 PM, Peter Cock wrote:
>> On Thu, Mar 6, 2014 at 4:53 PM, Greg Von Kuster wrote:
>>> On Feb 20, 2014, at 10:20 AM, Greg Von Kuster wrote:
>>>>> On Thu, Feb 20, 2014 at
Hello Peter,
On Feb 20, 2014, at 10:20 AM, Greg Von Kuster wrote:
>
>> On Thu, Feb 20, 2014 at 9:59 AM, Peter Cock
>> wrote:
>>> On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster wrote:
>>>> Your installation recipe for mira attempts to download a binary
Hi Peter,
On Mar 4, 2014, at 5:19 AM, Peter Cock wrote:
> On Mon, Mar 3, 2014 at 6:33 PM, Greg Von Kuster wrote:
>> On Mar 3, 2014, at 1:13 PM, Peter Cock wrote:
>>
>>> Hi Guys,
>>>
>>> Is this stuff on the wiki?
>>
>> Not complete
" action on each repository,
> is that it?
>
Yes.
> Thanks,
>
> Peter
>
>
> On Mon, Mar 3, 2014 at 5:58 PM, Greg Von Kuster wrote:
>> Many thanks, Björn for your very kind words. The Tool Shed
>> would not be what it is without your hard work as well.
with newly discovered
issues!
Greg Von Kuster
On Mar 3, 2014, at 12:02 PM, Björn Grüning 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
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 wrot
_0/017a00c265f1/bowtie2-align-debug
> ./galaxy-dist/dependancies/bowtie2/2.1.0/devteam/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_
m guessing that I need to uninstall the tool and wipe some
> postgres entries.
I strongly advise not manually changing inaything in your 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.
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 m
Hello Peter,
On Feb 24, 2014, at 3:32 AM, Peter Cock 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://te
#x27;re seeing
above is due 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 fo
Hi Peter,
On Feb 21, 2014, at 9:10 AM, Peter Cock 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 point that caught
Hi Geert,
Thanks for letting us know - I've added the folllowing Trello card for this and
we'll get it fixed asap.
https://trello.com/c/65DOL7PL/160-repository-package-libpng-owned-by-devteam-on-main-tool-shed-bug
Greg Von Kuster
On Feb 20, 2014, at 5:10 PM, Geert Vandeweyer
wr
ed 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 wrote:
> On Thu, Feb 20, 2014 at 9:59 AM, Peter Cock wrote:
>> On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster wrote:
>>> Your insta
Hi Peter,
On Feb 19, 2014, at 6:09 PM, Peter Cock wrote:
> On Wed, Feb 19, 2014 at 9:33 PM, Greg Von Kuster wrote:
>> Hi Peter,
>>
>> Dave B and I just discovered that issue that causes your tests to fail.
>>
>> The problem lies with our current implementat
they link, problems occur. Again, this behavior is
intermittent depending on the Pyhton version ( and perhaps the os ).
In any case, we have a fix for out move_directory_files which Dave is now
committing. So your tests should pass with tonight's run - Let's hope!
Thanks Peter!
Greg
Hello Peter,
Please see below…
On Feb 19, 2014, at 4:41 AM, Peter Cock 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/
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 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 wrote:
> On Sat, Feb 15
Hi Peter,
On Feb 3, 2014, at 7:01 PM, Peter Cock 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 proteomics_search_tandem_1
> 2013
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
so 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 wrote:
Hi JJ,
On Feb 13, 2014, at 11:00 AM, Jim Johnson 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 runs, (in may
twill framework even 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 wrote:
>
> I think it ought be possible to refactor the Twill test code to use
> the same di
escr
>> 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/M1rwV
WhI/143-nightly-test-runs-1
Thanks
Greg Von Kuster
On Feb 3, 2014, at 7:01 PM, Peter Cock wrote:
> On Thu, Jan 30, 2014 at 4:32 PM, Greg Von Kuster wrote:
>> On Jan 29, 2014, at 1:18 PM, Greg Von Kuster wrote:
>>> Peter wrote:
>>>> http://toolshed.g2.bx.psu.edu/vi
WhI/143-nightly-test-runs-1
Thanks
Greg Von Kuster
On Feb 3, 2014, at 7:01 PM, Peter Cock wrote:
> On Thu, Jan 30, 2014 at 4:32 PM, Greg Von Kuster wrote:
>> On Jan 29, 2014, at 1:18 PM, Greg Von Kuster wrote:
>>> Peter wrote:
>>>> http://toolshed.g2.bx.psu.edu/vi
Hi Peter,
On Jan 29, 2014, at 1:18 PM, Greg Von Kuster 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_filte
Hi Peter,
On Jan 29, 2014, at 12:55 PM, Peter Cock 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 look sensible, but
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!
It's discussed in the following page of the Tool Shed wiki.
https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#Installing_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance
On Jan 20, 2014, at 7:27 PM, "Dooley, Damion" wrote:
> That advice did the tric
1 - 100 of 906 matches
Mail list logo
