Hello Shaun,
On 7/31/12 09:37:23.000, SHAUN WEBB wrote:
Genome indexing:
1. I realise this is just a beta feature and it will be great when fully
integrated. I tried to generate bowtie2 indexes for an installed build.
I can see the job appear below the table in yellow and it contains the
Derrick,
The deferred_job_queue instance in the job manager object is only
instantiated when the enable_beta_job_managers variable is set to True.
Is it possible that your previous setting of that variable was somehow
reverted?
The KeyError error you mentioned in your previous should be
as
expected.
But the deferred_job_queue error persists. We are running galaxy in the
cluster (SGE) here. Is it possible that Manage local data need to be
configured in the cluster env?
Regards,
Derrick
On Mon, Sep 10, 2012 at 10:59 PM, Dave Bouvier d...@bx.psu.edu
mailto:d...@bx.psu.edu wrote
Kevin,
Correct, converting from 2bit to fasta shouldn't cause any problems.
--Dave B.
On 9/25/12 03:20:14.000, Kevin Y wrote:
Hi,
Thanks for providing the indexes via rsync::
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
We've, noticed that despite soft links pointing to it, there
, Kevin Y wrote:
Thanks Dave,
A question before we go ahead, why are they missing in the first place?
Does the main galaxy not actually need them? are the tools moving away
from fa?
Cheers,
Kevin.
On Tue, Sep 25, 2012 at 11:12 PM, Dave Bouvier d...@bx.psu.edu
mailto:d...@bx.psu.edu wrote
/hg18/srma_index/hg18.fa
So any ideas where to look further?
regards, Andreas
On 01.11.2012 15:36, Dave Bouvier wrote:
Andreas,
When setting up the rsync server, we decided that .fa files would be
excluded from the listing,
since the 2bit format contains the same data but takes up to 75% less
Hemant,
The BWA index format was changed in 0.6.0 to integrate the BWT and
reverse BWT into the same file. I would recommend using BWA 0.5.9 to
generate the index, which does still create .bwt and .rbwt files.
--Dave B.
On 11/7/12 14:32:15.000, Kelkar, Hemant wrote:
We recently upgraded
Adam,
Thank you for the information you provided, this error has been fixed in
changeset 8338:42a6e3f82c0d, which will be included in the next Galaxy
distribution release.
The problem was that the .tar.gz you were uploading contains a tool
wrapper XML, specifically rgGLM.xml, with invalid
Franco,
BEDTools, unlike some other packages, does not require the 'make clean'
shell command to compile. If you remove that line, the dependency should
install without problems.
--Dave B.
On 2012-12-11 21:16, Franco Caramia wrote:
Hi list,
I got the following tool_dependencies.xml file
to make target `all'. Stop.
Same problem as before but this time with the 'all' rule...
I'm not sure what the action type=download_by_url tag does..
Do I need to 'cd' into the unzipped directory?
Thanks,
Franco
On 12/12/12 1:03 PM, Dave Bouvier d...@bx.psu.edu wrote:
Franco,
BEDTools
Peter,
It looks like you have two dashes in your -sid option, whereas the
parser expects just one.
--Dave B.
On 2/11/13 06:56:03.000, Peter wrote:
On Wed, Nov 3, 2010 at 11:48 AM, Peter pe...@maubp.freeserve.co.uk wrote:
On Tue, Nov 2, 2010 at 1:57 PM, Nate Coraor n...@bx.psu.edu wrote:
Jim,
Thanks for spotting that, I've pushed the fix in 8816:e5dcefc328bb.
--Dave B.
On 2/11/13 20:14:13.000, Jim Johnson wrote:
File
'/home/galaxy/gx/prod/galaxy/database/compiled_templates/reports/base/base_panels.mako.py',
line 68 in render_body
__M_writer(unicode(self.javascripts()))
Jorrit,
Thank you for uncovering that issue, I've commited a fix in the stable
branch of galaxy-central at 8887:d5896e8a60fa. To apply that changeset,
you'll need to run the following commands from your Galaxy directory:
$ hg pull -b stable https://bitbucket.org/galaxy/galaxy-central/
$ hg
Tim,
The Galaxy functional test suite's run time can vary significantly
depending on your environment, and we are currently working on a number
of enhancements to the speed of the functional tests.
You can run the functional tests before installing tools and tool
dependencies, and you can
My apologies, that command was incorrect. The correct version is:
$ sh run_functional_tests.sh help
--Dave B.
On 2/22/13 08:47:19.000, Dave Bouvier wrote:
Tim,
The Galaxy functional test suite's run time can vary significantly
depending on your environment, and we are currently working
Shenwiyn,
I have not been able to duplicate that error message in my local
environment, what changeset revision of Galaxy are you running, and how
is your server environment configured?
--Dave B.
On 3/4/13 10:41:36.000, shenwiyn wrote:
Hi,
I want to install our local Galaxy for more
Hello,
I'll respond inline, but your base understanding is correct.
--Dave B.
On 3/5/13 12:17:47.000, Florence Maurier wrote:
Hi,
We are currently installing galaxy on a server. By reading the galaxy
wiki, we found the script run_functional_tests.sh (the principle is
really handy!).
Jorrit,
Thank you for reporting this issue, I've committed a fix in the default
branch at 9077:62bd6fe0e9aa, and it will be updated in stable at our
next release.
--Dave B.
On 3/13/13 18:11:27.000, jorrit poelen wrote:
To add some information to my earlier post -
It seems that the
Johannes,
The internal server error you encountered has been resolved as of
9105:7b5f97700fdc.
The tool shed not letting you delete the flexbar subfolder was a result
of untracked files in the repository path. We have removed those files,
and your repository should now be correct.
Jorrit,
Just to eliminate one possible cause of this behavior, could you confirm
that your local Galaxy instance's universe_wsgi.ini file's
enable_tool_shed_check setting is uncommented and set to True, and the
hours_between_check is also uncommented and set to a value between 1 and 12?
of galaxy instance Z tries again
Thanks for your patience and efforts,
-jorrit
On Mar 26, 2013, at 8:19 AM, Dave Bouvier wrote:
Jorrit,
Just to eliminate one possible cause of this behavior, could you confirm that
your local Galaxy instance's universe_wsgi.ini file's enable_tool_shed_check
Richard,
You can find the code for admin users stopping jobs in
lib/galaxy/web/base/controllers/admin.py, in the jobs method of the
Admin class. Hopefully that will provide the base structure for what you
want to accomplish.
--Dave B.
On 3/27/13 12:02:20.000, Richard Park wrote:
Hey
longer before posting a question next time ; )
-jorrit
On Mar 26, 2013, at 10:41 AM, Dave Bouvier wrote:
Jorrit,
First, allow me to clarify a point of naming:
It's not quite right to say tools in this situation, as tools are only one of
several utilities that a tool shed repository can contain
Jorrit,
While I investigate the root cause of this, have you tried clearing all
cookies for testtoolshed.g2.bx.psu.edu?
--Dave B.
On 3/28/13 17:14:55.000, jorrit poelen wrote:
Hey y'all galaxiers,
Today, I tried to login using the testtoolshed web ui. To make sure that it
wasn't just
in Galaxy instance.
psu tool shed test - unable to test because I could not login to psu test
toolshed
On Mar 28, 2013, at 2:19 PM, Dave Bouvier wrote:
Jorrit,
I may have been a bit unclear in my previous response. Allow me to illustrate
two scenarios:
First scenario:
1. A repository
=menu_options, visible=( trans.user and
( trans.user.requests or trans.app.security_agent.get_accessible_request_types( trans, trans.user )
) ) )
AttributeError: 'User' object has no attribute 'requests'
On Mar 28, 2013, at 2:22 PM, Dave Bouvier wrote:
Jorrit,
While I investigate the root cause
Jorrit,
I've committed a fix for this in 9220:56de0ee7932f, thank you for
helping me track down the issue.
--Dave B.
On 3/28/13 20:30:37.000, Dave Bouvier wrote:
Jorrit,
Thank you for the additional information, following those steps I was
able to reproduce the error and will be looking
Peter,
Yes, it is definitely possible to use a composite datatype in functional
tests, and a number of tools in the Galaxy distribution do so. For
examples on how to define composite inputs, you can look at the tools in
tools/rgenetics/, such as rgGLM.xml or rgHaploView.xml. For the outputs,
Peter,
Thanks for reporting this issue, it looks like there might be a bug in
tool_list.py, which I will be looking into. In the meantime, you should
still be able to run functional tests for your tool by executing
sh run_functional_tests.sh -id tool_id
Where tool_id is the ID you have
David,
While I look into the cause of this error, could you tell me which
revision of Galaxy you're running?
--Dave B.
On 4/11/13 12:51:03.000, David Bonsall wrote:
Dear Galaxy team,
I'm trying to install NCBI + tools on a local instance of galaxy (rep:
8.1546099212f), but I get the
Peter,
The automated testing framework is also running against the test tool
shed. Could you send me a link to the repository that is behaving oddly?
--Dave B.
On 4/12/13 06:42:04.000, Peter Cock wrote:
Hi all,
I'd like to be able to experiment with the new automated testing
recently
Peter,
Thanks for the contribution, I've verified that it works, and it has
been committed in 9395:388e86c30bad.
--Dave B.
On 4/15/13 09:59:46.000, Peter Cock wrote:
On Mon, Apr 15, 2013 at 2:15 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
Thanks for reporting this issue, it looks
:35:40.000, Peter Cock wrote:
On Mon, Apr 15, 2013 at 2:20 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
The automated testing framework is also running against the test tool shed.
Could you send me a link to the repository that is behaving oddly?
e.g. http://toolshed.g2.bx.psu.edu/view
David,
Thank you for reporting this error, which was due to a new tool shed
feature being introduced in -central, which had not yet been wrapped in
a backwards compatibility layer for -dist. As of 9440:bbb229927c68, the
issue should be resolved.
--Dave B.
On 4/11/13 12:51:03.000, David
On Tue, Apr 16, 2013 at 9:16 PM, Dave Bouvier d...@bx.psu.edu
mailto:d...@bx.psu.edu wrote:
David,
Thank you for reporting this error, which was due to a new tool shed
feature being introduced in -central, which had not yet been wrapped
in a backwards compatibility layer for -dist
Peter,
I've committed a fix for this in 9480:a80175a97194, and re-run the
automated testing framework. However, as you will see, the test still
reports an error. This is not due to an issue in your repository, but an
problem on the Galaxy side, as described in the following trello card:
Peter,
Again, thank you for reporting this issue, I've committed a fix in
9470:d056556a1e63 and re-run the testing framework, and the functional
test results page now shows the data for the tmhmm_and_signalp
repository only.
--Dave B.
On 4/16/13 16:47:25.000, Greg Von Kuster wrote:
On 4/22/13 13:31:28.000, Peter Cock wrote:
On Mon, Apr 22, 2013 at 6:24 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
I noticed that the 'version' attribute of the install tag is set to '0.0.1',
while the code currently only supports a version attribute of 1.0. When I
duplicated the tool
Peter,
You are correct, that is related to the issue described in the following
trello card:
https://trello.com/c/KdGX3hkh
We are looking into a fix for that behavior, and I'll keep you posted.
--Dave B.
On 4/23/13 10:11:59.000, Peter Cock wrote:
Hi all,
I'm seeing a unit test failure
Peter,
Our approach has always been to treat each tool shed repository as a
self-contained entity. This means that all required components are
contained in the repository or definitions for obtaining them from
remote repositories are contained in the repository.
You'll notice that several
Peter,
Thank you for reporting this issue, I've committed a fix in
9508:4126ec15fd61.
--Dave B.
On 4/24/13 05:10:55.000, Peter Cock wrote:
On Tue, Nov 23, 2010 at 2:06 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I'm working on a FASTA filter script, as per this email:
Peter,
My recommendation would be to append or prepend the conditional name to
each use parameter's name attribute, then specify the test parameters
like:
param name=useBackbone value=false /
There are good examples of how this is structured in
tools/ngs_rna/cufflinks_wrapper.xml
I've updated the relevant trello card, my plan is to focus on improving
the testing framework over the next few days.
--Dave B.
On 4/24/13 16:15:53.000, James Taylor wrote:
I regard this as a bug or limitation of the test framework, but if not,
things are confusingly inconsistent. If you
Peter,
That was my mistake, I had put that on my todo list, but neglected to
make a trello card. Thank you for the reminder, I've moved the card to
the appropriate section.
--Dave B.
On 4/30/13 06:38:26.000, Peter Cock wrote:
On Wed, Apr 24, 2013 at 6:02 PM, Peter Cock
Mattias,
Thank you for reporting this error, the issue has been resolved, and
downloading zipped files from the main tool shed is working.
--Dave B.
On 5/1/13 08:55:50.000, Greg Von Kuster wrote:
Hello Mattias,
I've created the following Trello card for this and we'll get it fixed asap.
Peter,
Thanks for the data, I am in the process of tracking down the source of
the issue, and I hope to have a fix ready shortly.
--Dave B.
On 2013-05-01 08:52, Greg Von Kuster wrote:
Hi Peter,
I created the following Trello card for this and things will be fixed as a
priority. Thanks
Ilya,
Thank you for reporting this issue, a fix has been committed in
9627:8d8368ab03ff, and the test tool shed has been updated.
--Dave B.
On 5/2/13 13:01:54.000, Sytchev, Ilya wrote:
Hi,
I can't install any tools from the test tool shed into the local Galaxy
instances. I can see the
, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
Thanks for the data, I am in the process of tracking down the source of the
issue, and I hope to have a fix ready shortly.
--Dave B.
Hi Dave,
I see from the Trello card you've made some progress here - but I am
still seeing odd results on the Test Tool
, May 6, 2013 at 1:55 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
Yes, there are a few issues that are causing some repositories not to be
tested correctly. I've discovered the problem, but the solution will require
a bit of work. My goal is to have this resolved as soon as possible.
--Dave B
Peter,
I've updated the test tool shed with new code to also display (sandbox)
in the page title attribute.
--Dave B.
On 5/6/13 14:11:10.000, Peter Cock wrote:
On Mon, May 6, 2013 at 9:55 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On May 2, 2013, at 12:54 PM, Peter Cock wrote:
Branden,
Thank you for reporting this issue, I've committed a fix in
9662:6c462a5a566d. You should be able to re-run your tool migration
after updating to that revision.
--Dave B.
On 5/7/13 11:09:31.000, Branden Timm wrote:
I recently upgraded to the latest galaxy-central, and was
Peter,
A technical issue prevented the tests from automatically running. I've
resolved the issue and started a manual run, you should be seeing test
results within 2-3 hours.
--Dave B.
On 5/8/13 07:09:28.000, Peter Cock wrote:
On Tue, May 7, 2013 at 2:10 PM, Dave Bouvier d...@bx.psu.edu
Adam,
Normally, the Galaxy URL should be automatically determined and set in a
cookie during the repository installation process.
To help track down this issue, could you provide the revision of Galaxy
you're running, and the end of the paster.log file when this error occurs?
--Dave B.
Joachim,
As you discovered, deactivating a repository does not give you the
option to select a new tool panel section. However, if you select the
option to remove the repository from disk, and then reinstall it, you
will be presented with the tool panel section page, where you can
uncheck
Ira,
There is a known issue with resolving tool dependencies when running
functional tests. One workaround is to set the
GALAXY_TOOL_DEPENDENCY_DIR environment variable to the path configured
in your universe_wsgi.ini.
This issue is documented in https://trello.com/c/eVT3QWJF
--Dave B.
Peter,
I have duplicated this discrepancy in my local environment, and will be
looking into the cause. I hope to have it resolved in short order.
--Dave B.
On 5/9/13 06:06:16.000, Peter Cock wrote:
On Thu, May 9, 2013 at 10:59 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, May
to ERROR
Is there something wrong with the way I've defined my tool dependencies
for this tool? Or perhaps it's a bug in the testing framework.
Cheers
Ira
On Thu, May 9, 2013 at 3:10 PM, Dave Bouvier d...@bx.psu.edu wrote:
Ira,
There is a known issue with resolving tool dependencies when
Peter,
As of my latest commit, the automated test results should now match that
of run_functional_tests.sh.
--Dave B.
On 5/9/13 06:06:16.000, Peter Cock wrote:
On Thu, May 9, 2013 at 10:59 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, May 9, 2013 at 10:49 AM, Peter Cock
That is correct, the tests are run nightly, some time after midnight
eastern US time, unless I manually initiate the testing process.
--Dave B.
On 5/10/13 05:36:41.000, Peter Cock wrote:
On Thu, May 9, 2013 at 6:59 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
As of my latest commit
Björn, Peter,
I've created a trello card (https://trello.com/c/QY0Z7L7p) for this
requirement, and will be working on enhancing that feature as my next
priority.
--Dave B.
On 5/10/13 09:59:37.000, Björn Grüning wrote:
Hi Peter,
For defining the 'install script' for some of my tool
Peter,
Yes, jar files are just a directory of .class (and other) files packaged
with the zip algorithm, which has its benefits and drawbacks, as you've
discovered. In the new action type I'm working on, I do intend to
include the option to extract a downloaded file, or leave it as-is,
which
Peter,
As of 9696:b4733e42a2c9, Galaxy now supports an additional tool
dependency installation action called download_file, which downloads a
file from the specified URL and saves it to the current working
directory, without extracting it. The format is:
action
Peter,
That test output does look wrong, but wrong in a way that suggests a new
issue has been uncovered. I'll work on tracking it down as soon as I can.
--Dave B.
On 5/16/13 11:05:56.000, Peter Cock wrote:
On Thu, May 9, 2013 at 6:59 PM, Dave Bouvier d...@bx.psu.edu
mailto:d
Peter,
This issue was a result of untracked hidden files on the filesystem,
which have now been removed.
--Dave B.
On 5/16/13 12:51:59.000, Peter Cock wrote:
Hi all,
Due to some hickups with tar balls, I've been left with an unwanted
empty folder:
Peter,
The most likely cause of this is that there is an issue with some
preceding repositories that hang on installation, causing the build
process to time out and not test later repositories in the list. I am in
the process of working out a solution for that situation.
--Dave B.
On
Peter,
I have implemented a system that will explicitly exclude a defined list
of repositories from the testing framework, so your repositories' tests
should now be running.
--Dave B.
On 5/21/13 06:26:56.000, Peter Cock wrote:
On Mon, May 13, 2013 at 11:09 AM, Peter Cock
Peter,
Thank you for reporting this issue, it has been resolved in
9827:2a630237801f.
--Dave B.
On 5/21/13 06:10:34.000, Peter Cock wrote:
Hi Greg,
There may be an issue with the new feature to mark a specific revision
to skip tool tests. I ticked this earlier this week on this
Peter,
The issue was the same as before, an earlier repository in the list took
longer than 1800 seconds to compile tool dependencies, so the testing
framework canceled the install and test process. I've added that
repository to the exclude list, and implemented a framework to install
and
Joachim,
I'm unable to duplicate that error, what revision of Galaxy and the tool
shed code are you running?
The path mentioned in the error message is a temporary working directory
that is created for downloading and processing files needed for a tool
dependency. Had the installation
I was also able to install the BLAST+ repository and tool dependency
locally, which suggests that the automated testing environment is
causing this issue. I'll have a look at that and update you.
--Dave B.
On 5/30/13 08:45:27.000, Björn Grüning wrote:
Hi Peter,
is it also crashing for
) it
resolves the dependencies just fine.
Any idea what am I doing wrong?
Thanks
Ira
On 10/05/2013, at 12:10 AM, Dave Bouvier d...@bx.psu.edu wrote:
Ira,
There is a known issue with resolving tool dependencies when running functional
tests. One workaround is to set
Peter,
It turns out that the automated functional testing framework was not
actually running. I suggest having a look in the morning, and if there
are still any missing test results, I'll get them resolved then.
--Dave B.
On 6/25/13 02:10:10.000, Peter Cock wrote:
Hi again Dave,
Have
Peter,
It looks like the failed tests container is being populated, but there
is some odd behavior with displaying it. As soon as we've tracked down
the issue, I'll update you.
--Dave B.
On 6/26/13 02:00:30.000, Peter Cock wrote:
On Tue, Jun 25, 2013 at 9:43 PM, Dave Bouvier d
Peter,
The empty failed tests folder issue has been resolved in
10171:eaa5112fefcd, and the test tool shed has been updated to that
revision.
--Dave B.
On 6/26/13 11:34:38.000, Dave Bouvier wrote:
Peter,
It looks like the failed tests container is being populated, but there
is some odd
Björn,
I've uploaded the modified tool_dependencies.xml to devteam's
package_emboss_5_0_0 repository on the test tool shed, and verified that
it works. Again, thank you for your contributions.
--Dave B.
On 7/7/13 18:59:57.000, Björn Grüning wrote:
Hi Greg,
bitbucket has a downtime so I
Peter,
Thank you for reporting this issue, it has been fixed in
10253:27b458743a11, and the test tool shed has been updated to that
revision.
--Dave B.
On 7/23/13 12:29:34.000, Peter Cock wrote:
On Tue, Jul 23, 2013 at 5:20 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Gred,
I'm
Shantanu,
I've yet been unable to reproduce this issue on a local installation of
a tool shed. If I do manage to reproduce it, I will re-open the issue
and find a fix.
--Dave B.
On 7/17/13 16:31:56.000, Greg Von Kuster wrote:
Hello Shantanu,
I've created a Trello card for this - we'll
Peter,
I've created a Trello card where you can track this issue:
https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue
Most of these look like display issues, the test results are correctly
recorded in the database. I hope to have that and the seq_rename and
.
On 7/29/13 12:03:23.000, Dave Bouvier wrote:
Peter,
The issue with seq_rename incorrectly failing functional tests has been
resolved in 10266:fe04978dadac, and the test results will be corrected
the next time the automated testing framework runs. I'm still looking
into the other issues you
Rodolfo,
In order to simplify tracking down this issue, could you provide the
changeset revision of Galaxy that is running on tamu.edu? To retrieve
the revision, execute the following command in your galaxy root directory:
hg id
To clarify, our understanding is that you installed the
at 11:47 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Aug 1, 2013 at 11:43 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Jul 29, 2013 at 5:03 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
The issue with seq_rename incorrectly failing functional tests has been
resolved
Peter,
This should be fixed in 10296:22fb05ea1b47, and clinod should no longer
be in that list after the automated testing framework checks it again.
--Dave B.
On 8/2/13 09:56:25.000, Peter Cock wrote:
Hi again,
Currently under Latest revision: installation errors' my clinod
tool is
.
--Dave B.
On 8/5/13 14:03:14.000, Rodolfo Aramayo wrote:
Dear Dave,
Answers below...
On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier d...@bx.psu.edu wrote:
Rodolfo,
In order to simplify tracking down this issue, could you provide the
changeset revision of Galaxy that is running on tamu.edu
Rodolfo,
--Dave B.
On 8/5/13 15:50:46.000, Rodolfo Aramayo wrote:
Dave,
See below
On Mon, Aug 5, 2013 at 1:55 PM, Dave Bouvier d...@bx.psu.edu wrote:
Rodolfo,
Please keep the thread on the mailing list by using the Reply all option.
Apologies
You should now be able to go
Peter,
The automated build prior to this email was executed incorrectly. I've
resolved that status, and the current test results look correct.
--Dave B.
On 8/8/13 10:30:37.000, Peter Cock wrote:
On Thu, Aug 1, 2013 at 12:11 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Dave,
The
Peter, Björn,
The August Galaxy release is out, and the template_command is now in the
stable repository and branch. Regarding matplotlib and numpy, I
currently only see matplotlib depending on the 74c21f9bdc39 revision of
numpy. Is this still an issue, or has it been resolved?
--Dave B.
Peter,
The problem with testing the installation of package tool dependencies,
especially but not limited to BLAST+, is that the time it takes to
compile them exceeds the timeout for the automated testing framework,
and so it terminates that build step. I am currently working on
enhancing
Peter,
Remnants from previously failed installation attempts seems the most
likely explanation, but I'll try to duplicate that situation locally and
see if there's any underlying issue.
--Dave B.
On 8/14/13 09:51:24.000, Peter Cock wrote:
Hi Greg,
I'm seeing something strange on a
, 2013 at 2:32 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
The problem with testing the installation of package tool dependencies,
especially but not limited to BLAST+, is that the time it takes to compile
them exceeds the timeout for the automated testing framework, and so it
terminates
Lionel,
Thank you for reporting this, the test tool shed is now running again.
--Dave B.
On 8/15/13 03:48:14.000, Lionel Guy wrote:
Good morning Galaxy,
It appears that the test tool shed is down, returning a 502 Bad Gateway
message. The main tool shed is fine.
I'm not sure that this is
Peter,
Thanks for the reminder, they did indeed not run. I'm running them
manually, and you should see updated results within a few hours.
--Dave B.
On 8/15/13 09:19:50.000, Peter Cock wrote:
On Thu, Aug 15, 2013 at 2:09 PM, Dave Bouvier d...@bx.psu.edu wrote:
Lionel,
Thank you
Peter,
I've duplicated the installation error on the scipy tool dependency, and
will be looking into the cause. Thanks for the report.
--Dave B.
On 8/15/13 09:01:17.000, Bjoern Gruening wrote:
Hi Dave,
the bug is unfortunately still present in the latest Galaxy version.
If you try to
Peter,
Judging by the code, the search for valid tools page is intended to
search with greater granularity for valid tool versions, and displays
every tool found with a unique version, whereas the prominent search
page is intended as a general search for repository names matching the
given
Björn,
This has been resolved in 10407:2d64260eb6e3, which is now running on
the test tool shed.
--Dave B.
On 8/14/13 10:48:35.000, Dave Bouvier wrote:
Björn,
Thank you for the report, I've created a trello card to track the
progress of this issue:
https://trello.com/c/ZXgnlXfo/1049
Dear Galaxy admins,
As of 10408:6822f41bc9bb stable/10409:2ca0b65d5005 default, a bug has
been fixed where running functional tests could overwrite some files in
your Galaxy path. If you intend to run functional tests, it is
recommended to update to the relevant revision on the branch you are
Peter,
The fix is now available in both galaxy-dist and galaxy-central.
--Dave B.
On 8/19/13 13:39:29.000, Peter Cock wrote:
On Mon, Aug 19, 2013 at 6:35 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Aug 19, 2013 at 6:25 PM, Dave Bouvier d...@bx.psu.edu wrote:
Dear Galaxy
, Peter Cock wrote:
On Wed, Aug 21, 2013 at 10:54 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Aug 20, 2013 at 9:15 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
I believe this was again due to the installation of an earlier repository
hanging until the testing framework canceled
Curt,
I tried installing the ingtest repository on a local instance of Galaxy,
and the requests python module installed without errors. Which revision
of Galaxy are you trying to install this repository into, and what kind
of environment are you running on that system?
--Dave B.
On
/install
readme
/readme
/package
/tool_dependency
And this worked for me. I'm thinking you may have downloaded after I
made the changes.
-Curt
On 8/21/13 6:01 PM, Dave Bouvier d...@bx.psu.edu wrote:
Curt,
I tried installing the ingtest repository on a local
Björn,
This looks like an issue that was fixed in 10444:ab74f2d80173, can you
confirm that you are running that revision or later locally?
--Dave B.
On 08/26/2013 07:46 AM, Bjoern Gruening wrote:
Hi,
if I try to install a repository via API I get the following error:
Traceback (most
1 - 100 of 165 matches
Mail list logo
