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 in 10266:fe04978dadac, and the test results
On Mon, Jul 29, 2013 at 3:10 PM, Dave Bouvier d...@bx.psu.edu wrote:
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
Retitling thread to focus on a regression in the (Tool Shed) test framework
to do with input file types and sniffers.
On Thu, Aug 1, 2013 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
On Thu, Aug 1, 2013 at 1:41 PM, Rodolfo Aramayo raram...@tamu.edu wrote:
On Thu, Aug 1, 2013 at 6:49 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Aug 1, 2013 at 12:38 PM, Rodolfo Aramayo raram...@tamu.edu wrote:
People,
I successfully installed NCBI_Blast_Plus from the toolshed
On Mon, Jul 29, 2013 at 10:27 PM, Nate Coraor n...@bx.psu.edu wrote:
On Jul 29, 2013, at 1:02 PM, Peter Cock wrote:
Hi all,
Is there a target date for the next Galaxy release, or should that
differ, the next update to the main Tool Shed?
Hi Peter,
The next release is planned for August
On Thu, Aug 1, 2013 at 2:47 PM, Rodolfo Aramayo raram...@tamu.edu wrote:
On Thu, Aug 1, 2013 at 8:40 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
I've seen that kind of error from NCBI BLAST+ before - do you
know which of the BLAST tools was this, and what the query
was?
The repo
On Thu, Aug 1, 2013 at 2:58 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
The main tool shed was updated on schedule on Tuesday, July 30.
As Nate stated in his reply to you regarding your question about the target
date for the next Galaxy release, the next-stable branch was created
]; then
Is there an open Trello card for this?
Thanks,
Peter
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to be designed to be called once
for all the work,
Peter
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On Tue, Jul 30, 2013 at 4:39 PM, James Taylor ja...@jamestaylor.org wrote:
I would actually prefer we use $GALAXY_SLOTS.
I like that too, CPUs is a bit of a fuzzy term with multiple cores,
and SLOTS has familiarity from the SGE terminology as well.
Peter
On Tue, Jul 30, 2013 at 4:44 PM, Nate Coraor n...@bx.psu.edu wrote:
On Jul 30, 2013, at 11:40 AM, Peter Cock wrote:
On Tue, Jul 30, 2013 at 4:39 PM, James Taylor ja...@jamestaylor.org wrote:
I would actually prefer we use $GALAXY_SLOTS.
I like that too, CPUs is a bit of a fuzzy term
On Thu, May 2, 2013 at 4:29 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
For what is I think the second time (fortunately this was only on the
Test Tool Shed), I have managed to upload a tar-ball to the wrong
repository:
2:fae4084a0bc0
http://testtoolshed.g2.bx.psu.edu/view
Hi Dave,
Did a Trello card get filled for this problem of failing tests on the Tool Shed?
Thanks,
Peter
On Tue, Jun 11, 2013 at 9:04 AM, Björn Grüning bjo...@gruenings.eu wrote:
Hi,
I also have that error in the latest toolshed:
AssertionError: Attempting to set field 'topology' to value
:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014701.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-July/015710.html
Thanks,
Peter
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On Mon, Jul 29, 2013 at 3:10 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
I've created a Trello card where you can track this issue:
https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue
Thanks Dave.
Most of these look like display issues, the test results are correctly
On Mon, Jul 29, 2013 at 2:49 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Dave,
Did a Trello card get filled for this problem of failing tests on the Tool
Shed?
Thanks,
Peter
For anyone following this issue, on another thread Dave just replied:
Peter,
The issue with seq_rename
if and else statements, for loops too. Try this in
your Galaxy directory to find some real examples:
$ grep ^#if tools/*/*.xml
Peter
P.S. The template language is called Cheetah and is used
outside of Galaxy.
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(since it doesn't
yet have the updates to look for and display *.rst files).
Thanks,
Peter
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On Monday, July 29, 2013, Dave Bouvier wrote:
Peter,
From what I've been able to determine, the tmhmm_and_signalp test results
predate the introduction of the skip tool tests option, and the script to
check repositories for the presence of functional tests and test data has
been updating
tried to play with #filter
directives, but to no avail.
Thanks,
Joachim
That sounds like the Galaxy character sanitation making the change,
things like pipes etc can have unexpected results in command lines.
Have a look at the sanitizer tag for use in the tool's XML file.
Peter
.bx.psu.edu/view/devteam/add_value
Regards,
Peter
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contact details...
Peter
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On Tue, Jul 23, 2013 at 5:24 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Björn,
This one has been applied in changeset 10219:a7edac403b6c, and all of
your patches are now running on the test tool shed.
Thanks
there.
The peek text shown in the history pane (right hand side) is
deliberately short. You can get the full stdout and stderr via the
i icon (well, up to 32kb or something like that).
Peter
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On Tue, Jul 23, 2013 at 2:12 PM, Gromobir gromo...@arcor.de wrote:
On 07/23/2013 02:51 PM, Peter Cock wrote:
On Tue, Jul 23, 2013 at 1:45 PM, Gromobir gromo...@arcor.de wrote:
Hello list,
I have two questions regarding galaxy:
1.) Is it possible to configure the amount of lines listed
On Tue, Jul 23, 2013 at 2:40 PM, Gromobir gromo...@arcor.de wrote:
Hello Peter,
Thanks a lot for your reply. I was talking about the stdout, which can be
displayed after clicking on the i icon.
I went to i-icon - stdout and only the last five lines are displayed
there.
Hmm. Which tool
!
Cheers,
Gromobir
On Tue, Jul 23, 2013 at 3:01 PM, Gromobir gromo...@arcor.de wrote:
There was a tail -n 5 hidden in my xml command. Thank you,
Peter, for guiding me in the right direction.
Any comments concering my other question?
How data files are shown in the central panel depends
tools --
repositories description=This requires Biopython as a dependency.
!-- Leave out the tool shed and revision to get the current
tool shed and latest revision at the time of upload --
repository owner=biopython name=package_biopython_1_61 /
/repositories
Peter
: WARNING are shown to the user.
I suggest that the ToolShed only render like this if the README file
is using the *.rst extension, but otherwise default to plain text (e.g.
no extension or *.txt files).
Thanks,
Peter
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On Tue, Jul 23, 2013 at 5:20 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Gred,
I'm trying to update this repository (initially just to switch my
README file to reStructuredText as the current plain text is
not being rendered nicely):
http://testtoolshed.g2.bx.psu.edu/view/peterjc
, or negative only:
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
Is this a known limitation? Is there a Trello card I should follow?
Thanks,
Peter
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On Mon, Jul 22, 2013 at 3:03 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
This is a known issue - there is a Trello card for it here:
https://trello.com/c/3sAsMYFc/588-toolshed-fix-display-of-conditional-objects-in-display-tool-action
Thanks,
Greg Von Kuster
Thanks Greg - I've
. The input is probably truncated.
(should I make a new post out of this?)
Which version of samtools? There is a bug in the
currently release where that warning is a false alarm:
https://github.com/samtools/samtools/issues/18
Peter
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=viewtarget=KissingerWebServices.pdf
Regards,
Peter
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=float label=p-value cutoff value=0.001 /
/repeat
Thanks for your help in advance
Tim
Would a multi-select column picker work instead? Note that would
not give you any control of the order of the selected rows.
Peter
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the main and test toolsheds, i.e. idot in your case.)
As to the immediate problem, I don't recall experiencing
that myself.
Peter
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On Wed, Jul 10, 2013 at 12:39 PM, Tim-Christoph Roloff
tim.rol...@fmi.ch wrote:
Hi Peter,
I thought about that but the user is expected to choose individual
fold-change and p-value for each of the selected contrasts. I currently
don't see how I would be able to connect the selected items
On Tue, Apr 30, 2013 at 4:30 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Apr 25, 2013 at 3:36 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
OK, I've updated to the latest galaxy-central default branch. Here's
the slightly revised test for ncbi_makeblastdb.xml
Himanshu
Galaxy now saves stdout and stderr on its own (unless it is very large,
in which case that start and end only are kept), and this can be viewed
via the i information icon on each history entry.
Maybe that is enough and you can abandon your old modification?
Peter
add .pdf to it Galaxy won't find it:
output_file = sys.argv[2]
..
pdf_out = output_file + '.pdf'
The tool should just use the filenames Galaxy tells it
(and they will end in .dat regardless of the datatype).
Peter
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Peter
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On Tue, Jul 9, 2013 at 5:53 PM, Robert Baertsch rbaer...@ucsc.edu wrote:
On Jul 8, 2013, at 3:33 PM, Peter Cock wrote:
The tools available in Galaxy are written in a range
of languages including C, Perl, R, etc. Yes, some are in Python,
but of those most are independent of Galaxy and can
.
Peter
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with this with various tools on the
Mac outside of Galaxy usage]
Regards,
Peter
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=venn_list
owner=peterjc toolshed=http://testtoolshed.g2.bx.psu.edu; /
/repositories
I corrected the ame/name error, and re-uploaded a fresh tar-ball which worked,
Revision: 4:25e0ffd4f762
Peter
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On Mon, Jul 8, 2013 at 10:24 PM, Robert Baertsch
robert.baert...@gmail.com wrote:
Peter and Dan,
I like the idea of replacing all open() with galaxy_open() in all tools. You
can tell the format by looking at the first 4 byes (see C code below from
the UCSC browser team). Is there some pythonic
,
Peter
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On Tue, Jun 25, 2013 at 9:43 PM, Dave Bouvier d...@bx.psu.edu wrote:
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
On Wed, Jun 26, 2013 at 10:01 PM, Dave Bouvier d...@bx.psu.edu wrote:
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.
Great - currently all the missing test failures have been resolved
and seq_rename, I am trying to
use an automatically installed dependency on Biopython - so
perhaps there is a silent dependency failure which means the
tests are not being run?
Regards,
Peter
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..it is similar to
txt format with some specific property ..
Reagrds
shashi
So you've followed this:
http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes
Have you tested your sniff method works? Have you checked the
order the file types are tested?
Peter
P.S. Don't forget to CC
automatically recognise a new
file type when uploading data into Galaxy?
Peter
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On Fri, Jun 21, 2013 at 2:21 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Fri, Jun 14, 2013 at 1:40 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
On Jun 13, 2013, at 4:14 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Jun 13, 2013 at 6:34 PM, Greg Von Kuster g
On Fri, Jun 14, 2013 at 1:40 AM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
On Jun 13, 2013, at 4:14 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Jun 13, 2013 at 6:34 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Peter,
Unfortunately, workflows are currently not very
revision (version).
Thanks,
Peter
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://wiki.galaxyproject.org/Events/GCC2013/BoF
Regards,
Peter
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Peter
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Forwarding back to the list which had been offline and
seemed to be missing these two emails...
-- Forwarded message --
From: Greg Von Kuster g...@bx.psu.edu
Date: Thu, Jun 13, 2013 at 6:34 PM
Subject: Re: Portable tool identifiers in workflows
To: Peter Cock p.j.a.c
On Thu, Jun 13, 2013 at 6:34 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Peter,
Unfortunately, workflows are currently not very compatible with
the tool shed - there is a Trello card that details the issues here:
https://trello.com/card/workflow-issues/506338ce32ae458f6d15e4b3/692
or will
be actively involved in the wrapper development and testing.
Thanks all,
Peter
P.S. I will only have intermittent email access from now until
the GCC2013 meeting.
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/bgruening/augustus
Cheers,
Björn
This sounds like the problem I've been having with missing test results.
What is interesting is I can see the augustus failure, which does seem
to support this being at least partly a caching problem. Test failure
below for your reference.
Regards,
Peter
Chilton
see: http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html
We're not making heavy use of rpy in Galaxy yet, but I
hope John's good work switching to rpy2 gets integrated
soon.
Peter
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Uploaded stuff
Peter
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On Wed, Jun 5, 2013 at 12:21 PM, alex.khassa...@csiro.au wrote:
Hi Peter,
Of course I added def get_label(self), as a matter of fact, I copied
get_label() from ToolParameter class. That's why I'm a bit confused.
The get_label function returns a string which is supposed to be displayed
versions of R/BioConductor
given this is important for reproducibility of many more complex
and rapidly developed R tools.
Peter
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or more output files.
e.g. Fetch the human genome as FASTA file, version hg18. But in that
case you'd be better off just defining the file within a shared data library.
Perhaps you could give an example of the kind of tool you are interested in?
Thanks,
Peter
On Wed, Jun 5, 2013 at 4:37 PM, Michael E. Cotterell
mepcotter...@gmail.com wrote:
Peter,
Thanks for getting back to me.
I'm working on an existing project where my predecessors have added a tool
that enables a user to add REST and SOAP Web services as usable tools within
Galaxy
PANAMA_results.csv
$output1/command
In cases like this where the underlying tool is too inflexible to accept an
output filename, I would personally use a wrapper script which can handle
moving things to the desired location, and raising a clear error if the file
was not created.
Peter
preference? If so, could the Tool Shed be enhanced
to allow a default stem for the URL (rather than the current
host name) to show these URLs instead?
(Personally I find the usegalaxy.org based URLs more presentable
compared to toolshed.g2.bx.psu.edu which feels less permanent.)
Thanks,
Peter
account, so I cannot apparently search that way)
Yes - sadly the best we can do as non-members is filter cards
(pop out panel on right hand side) but that only looks at the titles.
Peter
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=Webamp;PAGE_TYPE=BlastDocsamp;DOC_TYPE=Download
/readme
/package
/tool_dependency
Peter
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to need the executable flag set.
Peter
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On Thu, May 30, 2013 at 3:46 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
It turns out the issue was due to an overzealous firewall rule blocking
outgoing FTP connections on the host running the automated tests. I've
opened outgoing FTP and started a test for ncbi_blast_plus.
--Dave B
On Wed, May 22, 2013 at 8:05 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
On Wed, May 22, 2013 at 6:47 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
I have implemented a system that will explicitly exclude a defined list
of
repositories from the testing framework, so your repositories
On Fri, May 24, 2013 at 4:58 PM, Dave Bouvier d...@bx.psu.edu wrote:
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
On Wed, May 22, 2013 at 9:26 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, May 20, 2013 at 3:05 PM, Peter Cock wrote:
On Mon, May 20, 2013 at 2:47 PM, Greg Von Kuster wrote:
Peter wrote:
I've copied the blast_datatypes from the main tool shed to the test
tool shed with all
On Fri, May 24, 2013 at 11:18 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Greg,
Something is still amiss with this dependency and/or the Tool
Shed display. These two are currently listed under Latest revision:
installation errors but don't show any errors or test failures:
http
installation errors.
Thanks,
Peter
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of file
That first plus line should give the new comment, i.e.
!-- Revision 4:f9a7783ed7b6 on the main (and test) tool shed is
v0.0.14 which added BLAST databases --
Regards,
Peter
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On Thu, May 23, 2013 at 4:58 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Peter,
On May 23, 2013, at 4:49 AM, Peter Cock wrote:
On Wed, May 22, 2013 at 9:59 PM, Greg Von Kuster g...@bx.psu.edu wrote:
As an aside, the XML comment line seems not to show up properly
in the HTML diff view
.
commandIntersectBed -a $inputreads -b $inputgenes .../command
I presume there are more options to your command, e.g. output files ;)
Peter
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On Wed, May 22, 2013 at 6:47 PM, Dave Bouvier d...@bx.psu.edu wrote:
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.
Looks good - and now I have some
On Mon, May 20, 2013 at 3:05 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
On Mon, May 20, 2013 at 2:47 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Peter wrote:
Right now the single biggest class of test failures amongst my tools on
the Test Tool Shed is a missing dependencies
*
Repository dependencies
Tool shedNameOwnerChangeset revisiontesttoolshed.g2.bx.psu.edublast2go
peterjc9ef0d4ecb9d5ErrorNone
Do you see this too? Have I hit a problem with the error capturing?
Thanks,
Peter
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/2b35b5c4b7f4
Revision: 18:2b35b5c4b7f4
Regards,
Peter
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On Mon, May 13, 2013 at 11:09 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
I remain puzzled why I am seeing seemingly stochastic missing test
results.
Hi Dave,
This continues - although I have been making progress with the
tests for some of my tools. Currently there are a number
On Mon, May 20, 2013 at 2:47 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hello Peter,
Sorry for the delay on this - I was out of the lab last Friday.
On May 17, 2013, at 10:16 AM, Peter Cock wrote:
Hi Greg,
Do you guys have a rough plan for when inter-ToolShed dependencies
if listed
later in the script (just as any unknown actions are currently ignored).
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/6e7694a0ae00
(I'm about to try and fix this tool_dependencies.xml file)
Peter
On Mon, May 13, 2013 at 10:34 AM, Peter Cock p.j.a.c...@googlemail.com wrote
in handle_directory_changes
for undesirable_dir in undesirable_dirs:
NameError: global name 'undesirable_dirs' is not defined
Peter
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On Fri, May 17, 2013 at 12:37 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
Thanks for letting me know and sorry about the inconvenience. I've fixed
this in 9763:9c06caa86e2a which is now on the test tool shed.
Greg Von Kuster
Great - that works for me now :)
Peter
possible, I'll use the new [2]
'latest revision' ability instead:
repository name=blast_datatypes owner=devteam /
Thanks,
Peter
--
[1]
https://bitbucket.org/galaxy/galaxy-central/commits/842a78530fcd87670198d55d96d9adbdfc53483e
[2]
https://bitbucket.org/galaxy/galaxy-central/commits
On Thu, May 9, 2013 at 6:59 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
As of my latest commit, the automated test results should now match that
of run_functional_tests.sh.
--Dave B.
Hi Dave,
This problem seems to have returned since then (unless this time
instead of missing test
/mnt/galaxy/galaxy-central/tools/plotting/venn_list.py
/mnt/galaxy/galaxy-central/database/files/000/dataset_1.dat tabular
Some Proteins
/mnt/galaxy/galaxy-central/database/files/000/dataset_2.dat fasta
Rhodopsins /mnt/galaxy/galaxy-central/database/files/000/dataset_3.dat
Thanks,
Peter
Thanks :)
On Thursday, May 16, 2013, Dave Bouvier wrote:
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
On Mon, May 13, 2013 at 8:35 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, May 13, 2013 at 11:42 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
...
This would explain the behaviour I am seeing with effectivet3 and
other tools on the Tool Shed - despite the tool_dependencies.xml
://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem
You may be suffering from the same missing test results problem
as me, see the long thread Missing test results on (Test) Tool Shed:
http://dev.list.galaxyproject.org/Missing-test-results-on-Test-Tool-Shed-td4659531.html
Peter
On Tue, May 14, 2013 at 10:39 AM, Ira Cooke iraco...@gmail.com wrote:
Hi Peter,
Yes that's most likely part of it ... thanks for the link to that thread.
I think I am suffering from the same issue.
... but I'm also assuming when my test results come back I'll still
need to figure out where
On Fri, May 10, 2013 at 2:30 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Fri, May 10, 2013 at 1:51 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
The automated testing framework consists of a series of scripts that run in
a certain order, so between one script and the next, there may
Shed if
the new download_file action is used).
Regards,
Peter
$ hg diff
diff -r 65a81aead95e
lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py
--- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py Sun
May 12 11:52:55 2013 -0400
+++ b/lib/tool_shed/galaxy_install
On Mon, May 13, 2013 at 10:34 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Fri, May 10, 2013 at 8:11 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Dave,
that was fast.
Thanks a lot!
Björn
Thanks Dave,
I see this also should fix handling of JAR files
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