On Thu, Nov 7, 2013 at 4:51 PM, Peter Cock wrote:
> Hi Michiel,
>
> Did you finish wrapping samtools idxstats? I can't see it on the Tool Shed...
>
> If not, I may tackle this shortly.
>
> Peter
I've implemented a 'samtools idxstats' wrapper, which seems
Hello all,
On our main Galaxy tracking galaxy-dist using DRMAA/SGE,
jobs submitted to the cluster and queued and waiting (qw)
are correctly shown in Galaxy as "grey" pending entries in
the history.
With my test instance tracking galaxy-central (along with a
new visual look and new icons), such jo
On Mon, Nov 11, 2013 at 6:55 PM, John Chilton wrote:
> Hey Peter,
>
> Does your universe_wsgi.ini have "enable_quotas = True" set?
>
> -John
No,
$ grep enable_quotas universe_wsgi.ini
(nothing)
I had suspected the quotas might not be working...
If the default is not to enable quotas, then th
Hi guys,
I have a new wrapper for samtools idxstats with a working
unit test via run_functional_tests.sh run locally or on TravisCI:
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-November/017406.html
However, this tool
On Tue, Nov 12, 2013 at 2:37 PM, John Chilton wrote:
> This sounds a lot like this;
> http://dev.list.galaxyproject.org/galaxy-cant-find-binaries-in-tp4662442p4662444.html.
>
> When using the local job runner (as the test framework likely does), I
> believe samtools needs to be on Galaxy's path. I
On Tue, Nov 12, 2013 at 3:12 PM, John Chilton wrote:
> On Tue, Nov 12, 2013 at 3:32 AM, Peter Cock wrote:
>> On Mon, Nov 11, 2013 at 6:55 PM, John Chilton wrote:
>>> Hey Peter,
>>>
>>> Does your universe_wsgi.ini have "enable_quotas = True&q
On Wed, Nov 13, 2013 at 10:43 AM, Björn Grüning
wrote:
> Hi Peter,
>
> sorry for coming late to this thread.
>
> I may be wrong, but you are only specifying a repository_dependecies.xml
> file. You probably only need to rename it to tool_dependencies.xml file,
> otherwise the tool can not import i
On Tue, Nov 12, 2013 at 7:13 PM, Ben Gift wrote:
> I'm working with a lot of data on a cluster (condor). If I save all the
> workflow intermediate data, as Galaxy does by default (and rightfully so),
> it fills the drives.
>
> How can tell Galaxy to use /tmp/ to store all intermediate data in a
>
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:
>
> https://trello.com/c/sN2iLCCn/99-bug-in-install-and-test-framework-1
>
> ...
>
> becomes the following in your renam
On Tue, Nov 12, 2013 at 3:33 AM, Dave Bouvier wrote:
> Peter,
>
> Thanks for bringing this to our attention, we're working on fixing a number
> of issues with the test framework, and hope to have more information for you
> tomorrow.
>
> --Dave B.
Hi Dave,
Good news, the BLAST+ tests appear to h
On Thu, Nov 14, 2013 at 5:13 PM, Nate Coraor wrote:
> Bash is easily obtained on these systems and I think the extra functionality
> available in post-Bourne shells ought to be allowed. I also question how
> many people are going to run tools on *BSD since most underlying
> analysis tools tend to
On Wed, Oct 30, 2013 at 4:03 PM, Peter Cock wrote:
> Hello all,
>
> This is just to announce I am working on a wrapper for
> "CLC Assembly Cell" which is the CLCbio commercial
> command line assembly tool suite.
> http://www.clcbio.com/products/clc-assembly-cell
On Thu, Nov 14, 2013 at 4:35 PM, Peter Cock wrote:
>
> Hi Dave,
>
> Good news, the BLAST+ tests appear to have all passed on the Test Tool Shed,
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/f2478dc77ccb
>
> ...
>
> Over on the main Tool Shed, the b
On Sun, Nov 17, 2013 at 8:30 AM, John Chilton wrote:
> On Thu, Apr 25, 2013 at 9:36 AM, Peter Cock wrote:
>> ...
>>
>> As noted in my last email, for some reason when running the test case,
>> the input FASTA file is being included on the command line TWICE.
>> C
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.
Excellent.
On a closely related point, I understand Galaxy likes to store
On Mon, Nov 18, 2013 at 3:31 PM, Eric Kuyt wrote:
> Hi Peter,
>
> After installing the clc testing galaxy wrapper I noticed there are still
> some static paths in the wrapper.
> I'm in favor of expecting binaries in the system path, but maybe that's a
> matter of taste.
Yes - while waiting for an
On Mon, Nov 18, 2013 at 12:35 PM, Peter Cock wrote:
> On Sun, Nov 17, 2013 at 8:30 AM, John Chilton wrote:
>> With these change, I was able to write working functional tests for
>> your tool using the template you outlined in the Trello card. ...
>> I discovered no probl
On Mon, Nov 18, 2013 at 4:02 PM, John Chilton wrote:
> On Mon, Nov 18, 2013 at 9:55 AM, Peter Cock wrote:
>> On Mon, Nov 18, 2013 at 12:35 PM, Peter Cock
>> wrote:
>>> On Sun, Nov 17, 2013 at 8:30 AM, John Chilton wrote:
>>>> With these change, I was able t
Hi Greg,
On Mon, Nov 18, 2013 at 4:02 PM, Greg Von Kuster wrote:
> On Nov 18, 2013, at 10:33 AM, Peter Cock wrote:
>> On a closely related point, I understand Galaxy likes to store all
>> BAM files co-ordinate sorted and indexed - when a tool produces
>> a BAM file where
On Mon, Nov 18, 2013 at 4:23 PM, Eric Kuyt wrote:
> Hi Peter, it turns out we only have a workbench licence, the clc_assembler
> packaged with the workbench is called ./clc_assembler_ilo
>
> which has the man page below, do you think this is the same binary as the
> clc-assembly-cell assembler?
>
Hello all,
It is my recollection that under the "Admin" panel, "Manage jobs"
page, there used to be a toggle control to lock the submission
of new jobs. This was very helpful in preparation for scheduling
a system shutdown (e.g. for hardware or software updates).
However, I no longer see this opt
On Mon, Nov 11, 2013 at 5:29 PM, Peter Cock wrote:
> On Thu, Nov 7, 2013 at 4:51 PM, Peter Cock wrote:
>> Hi Michiel,
>>
>> Did you finish wrapping samtools idxstats? I can't see it on the Tool Shed...
>>
>> If not, I may tackle this shortly.
>>
>&g
On Thu, Nov 21, 2013 at 8:30 AM, Hans-Rudolf Hotz wrote:
> Hi Peter
>
> No, you are not imagining things. It has been removed. I guess, this was the
> commit:
>
> https://bitbucket.org/galaxy/galaxy-central/commits/445b212b1c6d/
>
>
> Though, we used this features very often in the early days, I d
On Wed, Nov 20, 2013 at 7:10 PM, Dooley, Damion wrote:
> I'm doing a 1 step generic reporting tool along the lines of the "BLAST
> XML to tabular" script by Peter. I was just about to ask about this line,
> which looked pretty much like a bug:
>
> sallseqid = ";".join(name.split(None,1)[0
On Mon, Nov 4, 2013 at 10:33 AM, Peter Cock wrote:
>
> More "missing test results", yet listed under "Latest revision:
> failing tool tests":
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
> http://testtoolshed.g2.bx.psu.e
On Thu, Nov 21, 2013 at 10:02 AM, Peter Cock wrote:
> Similarly over on the Main Tool Shed (where I have not yet
> updated these two tools).
I currently have three tool repositories on the Main Tool Shed
listed under "Latest revision: failing tool tests" yet with no
test
On Thu, Nov 21, 2013 at 6:11 PM, Peter Cock wrote:
> On Thu, Nov 21, 2013 at 5:59 PM, Dooley, Damion
> wrote:
>> I hear you, re. guessing about data - it just sounded like this would be a
>> rare case. Is it happening on particular database searches? Now that I
>> loo
Hello all,
I would like to modify the default ZIP bundle behaviour
for composite datatypes, which currently insists on
creating an HTML "main" file. To do this I think the current
monolithic _archive_composite_dataset function needs
to be refactored in file lib/galaxy/datatypes/data.py
I would li
On Mon, Nov 25, 2013 at 7:47 PM, John Chilton wrote:
> On Mon, Nov 25, 2013 at 11:59 AM, Peter Cock
> wrote:
>> Hello all,
>>
>> I would like to modify the default ZIP bundle behaviour
>> for composite datatypes, which currently insists on
>> creating an HTML
On Mon, Nov 25, 2013 at 10:37 PM, Peter Cock wrote:
> On Mon, Nov 25, 2013 at 7:47 PM, John Chilton wrote:
>> On Mon, Nov 25, 2013 at 11:59 AM, Peter Cock
>> wrote:
>>> Hello all,
>>>
>>> I would like to modify the default ZIP bundle behaviour
&g
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,
>>
>> About three weeks ago, we began to focus a higher priority on fixing the
>> nightly functional test runs.
>
> And we're starting to see
On Wed, Nov 27, 2013 at 4:23 PM, John Chilton wrote:
> Hey Peter,
>
> It looks like ext will be undefined in your default implementation of
> _archive_main_file - is this going to cause an error or am I missing
> something?
Whoops, yes - I was primarily testing the subclassed version.
> If this
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 the past 2
> weeks, so the results you are seeing are probably a
> reflection of some broken peices during the time fra
Hello all,
FAO: Administrators of local Galaxy instances using the NCBI BLAST+ wrappers.
Over on the galaxy_blast repository I have been updating the
NCBI BLAST+ wrappers (including unit tests) to work with the
current release, NCBI BLAST+ 2.2.28 (aka BLAST 2.2.28+):
https://github.com/peterjc/ga
On Thu, Nov 28, 2013 at 5:16 PM, Greg Von Kuster wrote:
> Hello Peter,
>
> On Nov 28, 2013, at 4:56 AM, Peter Cock wrote:
>
> Hi Greg,
>
> Things look much better today on the Test Tool Shed, with
> most of my tools under "Latest revision: all tool tests pass&qu
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/peterjc/ncbi_blast_plus/1b8a92016045
>
> But its
On Thu, Nov 28, 2013 at 7:34 PM, Greg Von Kuster wrote:
> Hi Peter,
>
>> But its not all good news - another test is now listed as failing, but with
>> missing test results:
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
>
> The bad data shoud now be eliminated, an
On Fri, Nov 29, 2013 at 3:26 PM, Jim Johnson wrote:
> Peter,
>
> It's good news that the description field is available in tabular format.
> That has been the primary reason for using the xml format.
Yes.
> The tabular format allows use of the task parallel feature.
We already support parallel
On Mon, Dec 2, 2013 at 4:50 AM, Karen Miga wrote:
> Hi Greg,
>
>Thanks for the feedback. I cannot seem to find information for
> hmmdb.loc. When I look in the associated xml file it looks like it could
> be removed completely (does one need a precompiled HMM Database? I do not
> remember usi
On Sun, Dec 1, 2013 at 7:10 PM, Björn Grüning wrote:
> Peter wrote:
>> Great. I'll probably merge the c25 branch and push that
>> to the Test Tool Shed next week (adding the descriptions
>> as a new 25th column to the default extended tabular
>> output).
>
> +1
> The 24 column output will be replac
On Sun, Dec 1, 2013 at 7:10 PM, Björn Grüning
wrote:
> Hi,
>
>> On Fri, Nov 29, 2013 at 3:26 PM, Jim Johnson wrote:
>> > Peter,
>> >
>> > It's good news that the description field is available in tabular format.
>> > That has been the primary reason for using the xml format.
>>
>> Yes.
>>
>> > Th
On Mon, Dec 2, 2013 at 6:50 PM, John Chilton wrote:
> Peter,
>
> I have pushed your patch along with a fix for the ext problem into
> galaxy-central. I don't think the fix will modifies the behavior in
> such a way that your implementation will be affected but let me know
> if I have broken some
On Mon, Dec 2, 2013 at 3:37 PM, Peter Cock
wrote:
> On Sun, Dec 1, 2013 at 7:10 PM, Björn Grüning
> wrote:
>>>
>>> Great. I'll probably merge the c25 branch and push that
>>> to the Test Tool Shed next week (adding the descriptions
>>> as a
On Wed, Dec 4, 2013 at 4:21 PM, Peter Cock wrote:
>
> On Mon, Dec 2, 2013 at 3:37 PM, Peter Cock wrote:
> > On Sun, Dec 1, 2013 at 7:10 PM, Björn Grüning
> > wrote:
> >>>
> >>> Great. I'll probably merge the c25 branch and push that
> >>&g
Peter Cock wrote:
>>>
>>> I've been working on this using JJ's work on column picking
>>> in the BLAST XML to tabular tool - viewable here:
>>>
>>> ...
>>>
>>> I'm considering splitting the column picker into three,
Hi Dave & Greg,
Could you double check how the "Skip automated testing of tools in
this revision" setting is being used on the Test Tool Shed?
e.g.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/ee10017fcd80
Test runs
Automated test environment
Not tested
Licensing issues rest
On Tue, Dec 10, 2013 at 2:46 PM, Greg Von Kuster wrote:
> Hello Peter,
>
> There are several "flags" for each repository revision that determine if and
> how
> the revision is tested. If tested, flags also detemine which category the
> latest
> revision falls into when clicking on the links in
On Mon, Nov 18, 2013 at 4:29 PM, Peter Cock wrote:
> On Mon, Nov 18, 2013 at 4:23 PM, Eric Kuyt wrote:
>> Hi Peter, it turns out we only have a workbench licence, the clc_assembler
>> packaged with the workbench is called ./clc_assembler_ilo
>>
>> which has the man pa
the upgrade...any help is appreciated!
>
> Thanks and regards,
>
> Pieter.
>
> -Original Message-
> From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:
> galaxy-dev-boun...@lists.bx.psu.edu ] On Behalf Of Peter
> Cock
> Sent: donderdag 31 oktober 2013 11:54
>
On Wed, Dec 18, 2013 at 12:51 PM, Lukasse, Pieter wrote:
> Hi Peter,
>
> I know that ;) Still I am curious about the possible solution. Any ideas?
>
> Regards,
>
> Pieter.
Could you clarify the nature of the problem - is it failing to
even start as in the situation I reported at the start of thi
On Thu, Nov 28, 2013 at 5:13 PM, Peter Cock wrote:
> Hello all,
>
> FAO: Administrators of local Galaxy instances using the NCBI BLAST+ wrappers.
>
> Over on the galaxy_blast repository I have been updating the
> NCBI BLAST+ wrappers (including unit tests) to work with the
>
On Fri, Jan 10, 2014 at 3:45 AM, wrote:
> Hi,
> I have a tool that works well. However, when I download the results, the
> results are zipped up but included into the zip file is the *.html file
> (with the same name as the tool output) do you know how I can stop this from
> being zipped up?
On Tue, Jan 14, 2014 at 2:17 PM, Pasquale Notarangelo
wrote:
> Hi all,
> we are two new galaxy users.
>
> We have developed 2 new tools and we would connect them into a new workflow.
>
> We are able to import both tools and to link them into a workflow but we
> aren't able to pass the output of th
Hello all,
For those interested in more flexible tabular output from BLAST+,
please try out the wrappers on the *Test* Tool Shed which I have
also just updated to wrap BLAST+ 2.2.29 as well:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
One open question is should the interface
On Fri, Jan 17, 2014 at 8:34 AM, Bossers, Alex wrote:
> Peter,
> We will definitely give them a try.
Great.
>
> I never understood why the tabular outputs did have an option to include
> the defline/hit decryption.
That was a long standing gripe of mine too, fixed in BLAST+ 2.2.28 and
availabl
Hi guys,
I'm currently trying to update the blast_datatypes on the main
tool shed (thanks Nicola for the reminder),
http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
Having clicked "upload" it is stuck at:
"[Warning] Upload a single file or tarball. Uploading may take a while,
depending
On Tue, Jan 21, 2014 at 6:19 PM, Peter Cock wrote:
> Hi guys,
>
> I'm currently trying to update the blast_datatypes on the main
> tool shed (thanks Nicola for the reminder),
> http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes
>
> Having clicked "upload
On Tuesday, January 28, 2014, Ketan Maheshwari
wrote:
> Is there a data type in Galaxy that identifies executables uniquely, eg.
> from the executable bit in the file perms or some other way?
>
> Thanks,
>
Galaxy's data types are for data files - runnable tools/executables
are handled via XML to
On Tue, Jan 28, 2014 at 8:26 PM, Ketan Maheshwari wrote:
>
> Is it possible to write a type file "bin_or_exe" which can detect the
> executable bit of data before they are part of Galaxy's indexed data.
>
> Thanks,
> Ketan
You haven't convinced me this is a good idea, but I would try this
by defi
Hi all,
Are both the main and test Tool Sheds currently meant to be running
nightly tests again?
I've not really got back into Galaxy tool testing since Christmas.
Most of my tools'
test results look sensible, but there seem to be some issues still, e.g.
http://testtoolshed.g2.bx.psu.edu/view/pe
On Thu, Jan 30, 2014 at 4:32 PM, Greg Von Kuster wrote:
> 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
On Fri, Jan 31, 2014 at 10:52 AM, Geert Vandeweyer
wrote:
> Hi,
>
> I'm looking for the correct syntax to achieve the following:
>
>
> outtype == "0" || outttype == "2"
>
>
> outtype == "1" || outttype == "2"
>
>
> I tried the above, with and without parentheses, but it creat
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/view/peterjc/blastxml_to_top_descr
>>> 2014-01-29 missing blast_datatypes dependency (why?)
>>> 2014-01-28 showing failed tests for samba
The BLAST+ binaries support multi-threaded operation, which is handled
via the $GALAXY_SLOTS environment variable. This should be set
automatically by Galaxy via your job runner settings, which allows you to
(for example) allocate four cores to each BLAST job.
In addition, the BLAST+ wrappers also
Hi all,
Something very handy for tool developers running functional tests
is if the environment variable GALAXY_TEST_NO_CLEANUP
is set, run_functional_tests.sh doesn't remove the test output.
This is great when debugging why a test is failing.
However, I was having trouble with failures like this
On Tue, Feb 11, 2014 at 3:41 PM, Dave Bouvier wrote:
> Peter,
>
> Thanks for pointing this out, I've applied your changes in
> 12478:15fc8675064e on the default branch.
>
>--Dave B.
Thanks Dave,
RE: http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-February/018154.html
https://bitbucket.org/
On Tue, Feb 11, 2014 at 4:42 PM, Peter Cock wrote:
> On Tue, Feb 11, 2014 at 3:41 PM, Dave Bouvier wrote:
>> Peter,
>>
>> Thanks for pointing this out, I've applied your changes in
>> 12478:15fc8675064e on the default branch.
>>
>>--Dave B.
>
On Tue, Feb 11, 2014 at 5:09 PM, Peter Cock wrote:
> On Tue, Feb 11, 2014 at 4:42 PM, Peter Cock wrote:
>> On Tue, Feb 11, 2014 at 3:41 PM, Dave Bouvier wrote:
>>> Peter,
>>>
>>> Thanks for pointing this out, I've applied your changes in
>
On Thu, Feb 13, 2014 at 7:51 AM, Björn Grüning
wrote:
> Am Mittwoch, den 12.02.2014, 10:46 + schrieb Peter Cock:
>>
>> ...
>>
>> However, at only 5kb the FASTA file is small and fine to bundle -
>> but the BAM (49kb), log (123kb) and MAF (764kb) quickly add
&g
On Thu, Feb 13, 2014 at 1:58 PM, Daniel Blankenberg wrote:
> Hi all,
>
> I just wanted to point out that there are several different ways to
> compare the history output item to a test file beyond the default
> "diff", including contains, re_match, sim_size, etc, this is set by
> the "compare" att
On Thu, Feb 13, 2014 at 4:22 PM, Greg Von Kuster 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 s
On Sat, Feb 15, 2014 at 12:25 PM, Greg Von Kuster wrote:
> 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/b
On Sat, Feb 15, 2014 at 12:32 PM, Peter Cock wrote:
> On Sat, Feb 15, 2014 at 12:25 PM, Greg Von Kuster wrote:
>> On Feb 3, 2014, at 7:01 PM, Peter Cock wrote:
>>>
>>> Returning to the MIRA4 problem, I got a meaningful test
>>> failure which I fixed (I hadn&
On Mon, Feb 17, 2014 at 10:26 AM, Thomas Green wrote:
> Galaxy devs,
>
> ...
>
> So after a bit of tweaking and getting used to the structure of the code I
> got something which seemed to work - I have possible a few fixes which
> others might find useful mainly to give better feedback in the log.
On Mon, Feb 17, 2014 at 2:57 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> It looks like you made some changes to your tool dependency
> recipe since the last test run.
Yeah, the mira de novo test was missing the test-data input files.
But I didn't touch mirabait or the install XML instructions.
>
On Mon, Feb 17, 2014 at 3:08 PM, Peter Cock wrote:
> On Mon, Feb 17, 2014 at 2:57 PM, Greg Von Kuster wrote:
>> Hi Peter,
>>
>> It looks like you made some changes to your tool dependency
>> recipe since the last test run.
>
> Yeah, the mira de novo test was
On Tue, Feb 18, 2014 at 11:41 AM, Greg Von Kuster wrote:
> Hi Peter,
>
> We'll try to get some time to look at your tool_dependencies.xml recipe as
> soon as possible.
>
> Greg Von Kuster
Great.
Re:
https://trello.com/c/HVGrShnC/60-tool-shed-should-test-installation-of-packages
Additional act
Hi all,
I just updated my development server, and ran into what looks
like a missing dependency:
$ ./run.sh
...
galaxy.jobs.manager DEBUG 2014-02-18 11:58:06,422 Starting job handler
galaxy.jobs INFO 2014-02-18 11:58:06,422 Handler 'main' will load all
configured runner plugins
galaxy.jobs.runner
On Tue, Feb 18, 2014 at 12:00 PM, Peter Cock wrote:
> Hi all,
>
> I just updated my development server, and ran into what looks
> like a missing dependency:
>
> $ ./run.sh
> ...
> galaxy.jobs.manager DEBUG 2014-02-18 11:58:06,422 Starting job handler
> galaxy.jobs I
Hi John,
Fix confirmed - nice timing, I just finished my lunch break :)
Thanks!
Peter
On Tue, Feb 18, 2014 at 12:35 PM, John Chilton wrote:
> That should be fixed now, sorry about that.
>
> -John
>
> On Tue, Feb 18, 2014 at 6:07 AM, Peter Cock
> wrote:
> > On Tue,
Hi all,
Earlier today I updated my development server, which uses SQLite,
and ran the update schema script (now at v118). With hindsight
there could have been a warning that I missed - because afterwards
despite updating to the galaxy-central tip, trying to use any of
the tools failed with an SQL
On Tue, Feb 18, 2014 at 1:40 PM, Dannon Baker wrote:
> On Tue, Feb 18, 2014 at 8:30 AM, Peter Cock
> wrote:
>>
>> This fixed the history_dataset_association.extended_metadata_id
>> error - so is the most likely explanation a failed schema update?
>> Might a stale mi
Hi all,
If anyone is interested, I've just wrapped a little Python script
I'd prepared early for use in Galaxy for a fairly common need -
"back translating" a protein alignment into a nucleotide alignment
by threading the unaligned sequence.
We're testing this locally, and barring any major issue
On Fri, Sep 13, 2013 at 9:54 AM, Peter Cock wrote:
> Hi all,
>
> I've sent this to both the Galaxy and Biopython developers lists,
> and hope this will make sense to both groups. If you've not heard
> of Galaxy, start here: http://galaxyproject.org - while the easy to
>
On Tue, Feb 18, 2014 at 2:20 PM, Federico Zambelli
wrote:
> Hi,
>
> something strange happens with Cufflinks in our Galaxy server. When a user
> deletes a running Cufflinks job in fact the associated Cufflinks process(es)
> are not terminated. Apart from unneccessary CPU usage, this prevents other
On Tue, Feb 18, 2014 at 5:19 PM, Saba Sehrish wrote:
>
> Hi,
>
> We are trying to add a new tool to our local galaxy instance with the
> following requirements.
>
> When a user clicks on the tool in side panel from tools list, a table should
> appear where the first element in each row is a clicka
On Tue, Feb 18, 2014 at 6:14 PM, Saba Sehrish wrote:
> I am using *.loc files, to create a bunch of tables I need, but I want to
> display complete tables (e.g. from .loc file) with clickable elements
> for users so that their input could be captured.
>
> For example if in my .loc file I have the
On Tue, Feb 18, 2014 at 7:13 PM, Saba Sehrish wrote:
>
> On Feb 18, 2014, at 12:23 PM, Peter Cock
> wrote:
>
> > On Tue, Feb 18, 2014 at 6:14 PM, Saba Sehrish wrote:
> >> I am using *.loc files, to create a bunch of tables I need, but I want
> to
> >>
On Tue, Feb 18, 2014 at 9:59 PM, Saba Sehrish wrote:
>
> On Feb 18, 2014, at 3:22 PM, Peter Cock wrote:
>>
>> OK - so no deep changes to the Galaxy parameter data
>> model etc would be needed (which is good news), 'just'
>> a new table rendering of a *.loc
On Tue, Feb 18, 2014 at 11:41 AM, Greg Von Kuster wrote:
> Hi Peter,
>
> We'll try to get some time to look at your tool_dependencies.xml recipe as
> soon as possible.
>
> Greg Von Kuster
>
>
Hi Greg,
Overnight this has gone back to the previously observed missing
data problem (e.g. email of 4t
Hi all,
I'm looking for examples of tools which take multiple input
files (one or more, determined at run time) and produce
multiple output files (one for each input file). Any
specific suggestions?
I have a number of sequence filtering/renaming tools
where this might be useful - in some cases ta
Hi all,
I was recently wondering how it might be possible for
an output from tool A to be used as a parameter when
calling tool B (without modifying tool B to take a data
configuration file or anything like that).
To clarify, I'm thinking about simple parameters like
a single integer/float/string
On Wed, Feb 19, 2014 at 2:16 PM, John Chilton wrote:
> Hey Peter,
>
> Have you seen this solution?
>
> https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
>
> It always seems to get mentioned when this topic is brought
> On Feb 19, 2014 10:08 AM, "Carlos Borroto" wrote:
>>
>> Hi Peter,
>>
>> I used the current functionality here:
>> http://toolshed.g2.bx.psu.edu/view/cjav/split_by_barcode
>>
>> The code for the underlining tool is available here:
>> https://github.com/cjav/ngs-tools
>>
>> Hope it helps,
>> Carlo
On Wed, Feb 19, 2014 at 8:42 PM, Greg Von Kuster wrote:
>
> Hello Peter,
> Please see below...
>
> ...
>
> Your above email arrived in my inbox at 4:42 AM EST, and
> it looks like your repository in question was not yet tested.
Ah. That would partly explain things - perhaps coupled with
a cache
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 implementation supporting the
> action tag, which is used in your recipe.
> This tag ultimately uses Python's os.li
,
On Thu, Feb 20, 2014 at 2:56 AM, Greg Von Kuster wrote:
> Hi Peter,
>
> On Wed, Feb 19, 2014 at 9:33 PM, Greg Von Kuster wrote:
>>>
>>> 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!
>>
>
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 and if that
>> fails, it echoes an error, but still performs actions..
>
> Ah - I can see that no
Hi Greg & Dave,
Now that moving symlinks has been fixed, something new
happened on the MIRA4 tests yesterday:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
It seems one test run has been split in two - the early section
at 13:11:20 includes the tests run for mira_4_0_de_novo
and
Hi guys,
Yesterday I made a small tweak to the BLAST+ packages to fix a bash syntax
error in the fall back action:
https://github.com/peterjc/galaxy_blast/commit/4b2fa1fbf485c4630cb6dc0beaf7286cb103bd71
I uploaded this update to the Test Tool Shed packages (all four, BLAST+
2.2.26, 2.2.27, 2.2.2
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