this problem?
Thanks best wishes
Peter
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On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Thanks Dave,
The good news is yes, the tests are running again on the
Test Tool Shed (although not the main Tool Shed yet), and
many of my tools now have successful test results from
last night.
e.g. My new basic
On Wed, Nov 19, 2014 at 9:36 AM, Peter Briggs
peter.bri...@manchester.ac.uk wrote:
Hello
I'm trying to make a new repository on the public toolshed at
https://toolshed.g2.bx.psu.edu/
but I keep getting the internal server error page.
I was also unable to log out, or even to see the front
Hello Bjoern
Thanks, seems to be okay now (on the main toolshed) - I can log out, log
back in, and create and populate my new repository now.
Thanks, best wishes
Peter
On 19/11/14 10:57, Björn Grüning wrote:
Hi Peter,
can you try again? I'm able to browse the ToolShed and reset metatada
Thanks - uploading tar-balls to the Test Tool Shed is working again :)
Peter
On Wed, Nov 19, 2014 at 2:34 PM, Nate Coraor n...@bx.psu.edu wrote:
Hi all,
Sorry for the service interruption. The Tool Shed should be back now,
and the underlying disk usage problem has been alleviated, so
multiple files to be treated together as
a composite dataset?
Peter
On Wed, Nov 19, 2014 at 3:32 PM, John Chilton jmchil...@gmail.com wrote:
Well there is at least one person using this functionality -
http://dev.list.galaxyproject.org/Problem-to-upload-data-to-Galaxy-when-using-pbed-file-format
Thanks John,
Fingers crossed we'll get some more detailed logs in a day or two :)
Peter
On Wed, Nov 19, 2014 at 5:48 PM, John Chilton jmchil...@gmail.com wrote:
Hey Peter,
Dave is out this week - so I have tried to fumble around and see if I
could make some progress on this. I found some
, but a virtualenv is not viable for existing
Galaxy installations - which may also come to have this problem if
their system copy of paramiko is updated?
I'm not familiar with paramiko or markupsafe, but if there is a conflict
it would be good to have a direct fix.
Peter
something about a conflict between
MarkupSafe and paramiko (assuming this is the real problem).
Peter
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On Tue, Nov 18, 2014 at 1:24 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Nov 18, 2014 7:26 AM, John Chilton jmchil...@gmail.com wrote:
I will admit to not actually understanding Galaxy's dependency management
but I think virtualenv is exactly the advice people who do understand it
give
On Tue, Nov 18, 2014 at 5:51 PM, Nate Coraor n...@bx.psu.edu wrote:
Peter,
Unless you've made modifications to Galaxy that depend on external
libraries, switching to a virtualenv for the server itself should be
pretty safe. Tools themselves can still run without using the/any
virtualenv
version installed).
Also it would seem there is a bug in the resolve method assuming that
e.arg will always have (at least) two entries?
Thanks,
Peter
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Hi Sam,
On Thu, Nov 13, 2014 at 6:25 AM, Aysam Guerler aysam.guer...@gmail.com
wrote:
Hey Peter,
I have modified the data selectors appearance by adding a single select
field as default option. It resembles the previous functionality now and I
think its an improvement.
Great. I won't
://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer
The bad news is there are many unexpected failures with:
Exception: History in error state.
I'm sure you'll learn more once you look over the logs,
Thank you,
Peter
On Wed, Nov 5, 2014 at 6:21 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter
for automatic batch jobs).
Is there any draft documentation on these changes being prepared
to go into the next release notes? This is the sort of thing local
Galaxy Admins would appreciate to anticipate local user queries.
Thanks,
Peter
On Thu, Nov 6, 2014 at 12:45 PM, Aysam Guerler aysam.guer
OK, so this should work then... :)
Thanks Dave,
Peter
On Mon, Nov 3, 2014 at 7:06 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
For the automated indexing of bam files, Galaxy uses the samtools version
linked to as default under tool-dependencies/samtools/
This should normally be 0.1.19
results from the Tool Sheds ...
http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-November/020792.html
Thanks,
Peter
On Tue, Nov 4, 2014 at 8:38 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
OK, so this should work then... :)
Thanks Dave,
Peter
On Mon, Nov 3, 2014 at 7:06 PM, Dave
are still rare, and
would mean we can see the test results on the Tool Shed :)
Please ask if you'd like advice on Tool Shed packaging.
Thanks,
Peter
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On Tue, Nov 4, 2014 at 2:44 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I'm looking for a little advice on the pre-existing SAM/BAM filtering
tools already in the Galaxy Tool Shed (to avoid reinventing the wheel).
As I mentioned on another thread, I'm working on a wrapper
Authors prompt feedback on their updates,
but also catch regressions where changes in Galaxy break
a previously working tool.
Regards,
Peter
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* Read Group 1
* Read Group 2
[Add new Read Group]
Is this a deliberate change? If so, why?
Peter
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installed
wrapper for samtools 1.1 and Galaxy's attempts to automatically call
samtools to index any BAM output file? Would the tool environment
put samtools 1.1 on the (local) $PATH which would then break setting
the metadata as part of the same job?
Regards,
Peter
I have solved this by commenting out the apparently harmless test:
https://github.com/peterjc/pico_galaxy/commit/f3d4261846566a86f9c85a158fb95877ca8bc7c5
Peter
On Wed, Oct 29, 2014 at 5:39 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I'm getting the following exception
, or are the change rights a subset of
the admin role?
Peter
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/issues/62
- http://bugs.python.org/issue11489
Any thoughts? What does Galaxy write to these job-associated JSON
metadata files?
Thanks,
Peter
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was this allowed the tool author some control
over the appearance/order that the tools will be shown in the
Galaxy left hand pane.
Thanks,
Peter
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Thanks,
https://github.com/biopython/biopython/pull/385
You can't (yet) do this via the BLAST wrappers.
You would have to pull out the full sequences using the
makeblastdb wrapper, then edit them with another Galaxy
tool. Or work directly from the FASTA file if you have it.
Peter
On Wed, Oct
Hi Matthias,
Can you file an issue here about adding this here please?
https://github.com/peterjc/galaxy_blast
Thanks!
Peter
On Tue, Oct 21, 2014 at 10:36 AM, Matthias Enders
m.end...@german-seed-alliance.de wrote:
Hello all,
I use the ToolShed NCBI Blast+ Wrappers
(https://toolshed.g2
command template, e.g.
-num_threads \${GALAXY_SLOTS:-8}
Note the colon minus is the special bash syntax, here the default
value is 8 (not minus 8) if $GALAXY_SLOTS is not set. Also note
in the command XML you must escape the dollar sign.
Peter
to debug?
Thanks,
Peter
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To search Galaxy
(every month).
I would suggest both (easy if it is just a link, a tiny bit of copy and paste
if not), but that wasn't an option on the Google form.
Peter
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also seems to have
the same problem.
Regards,
Peter
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yesterday.
Ciao,
Stef
There's a chance it is the same root problem as this issue which
I hit a couple of hours ago (again internal server error):
http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-October/020614.html
Peter
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OK good - my issue with the ToolShed work now too :)
On Wed, Oct 8, 2014 at 11:44 AM, Stef van Lieshout
stefvanliesh...@fastmail.fm wrote:
Ok, works for me again. Just a little hiccup I guess...
Stef
- Original message -
From: Peter Cock p.j.a.c...@googlemail.com
To: Stef van
On Wed, Oct 8, 2014 at 9:22 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
From the new tools information Dave Compiled for the last Galaxy Update
https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contributions
I had a look at galaxyp's filter_by_fasta_ids: Extract
this.
As it stands right now, this ToolShed repository would not get a
gold star approval rating :(
Peter
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release.
Thanks again, best wishes
Peter
On 01/10/14 18:09, John Chilton wrote:
Sorry this has been sitting in my inbox for a while - because I wanted
to try to fix it before the next release but I don't think it is going
to happen.
Generically - it doesn't surprise me that Galaxy can handle
wishes
Peter
Ps this is in galaxy-dist changeset 14355:007f6a80629a
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Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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. a collection of FASTA
files).
If the directory has some structure then the composite
datatype is probably most suitable, e.g. an HTML file with
a collection of image files; or a BLAST database made up
of several binary files.
Peter
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://wiki.galaxyproject.org/Learn/AdvancedWorkflow/VariablesEdit
Peter
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the the value in the tests? I've tried both
param name=operations_0.operation.name' value=... /
and
param name=operations_0|operation|name' value=... /
in my tests, but neither form seem to change the exception from the tests.
Any suggestions are greatly appreciated!
Peter
--
Peter
I'm wondering if anyone can point out what it is that I'm missing. No
doubt it's blindingly obvious, but I just can't see it.
Thanks again for any help
Peter
--
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Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161
also for the tip off about using the API test framework, I just
gave it a try and it looks a bit cleaner than the Twill version. I will
switch to using that from now on.
Thanks so much for your help,
Best wishes
Peter
On 17/09/14 14:00, John Chilton wrote:
Hello Peter,
For both of your
Hi Calvin,
The extension is really the Galaxy datatype name, so
put quikrdb here. The actual filename on disk will be *.dat
once loaded into Galaxy.
More examples, e.g.
https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatypes/datatypes_conf.xml
Peter
On Fri, Sep 12, 2014
not been processed,
and I think it is as simple as you've used invalid syntax in your
command tag. I think you need to remove the extra spaces to have:
#if ...
Not:
# if ...
Then it might work?
Peter
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On Wed, Sep 10, 2014 at 7:55 PM, Nate Coraor n...@bx.psu.edu wrote:
Hi Peter,
This was due to a bug I introduced last week, which I've just fixed in
d1f6d05. Sorry for the trouble.
--nate
Thanks - I'll check back in a day or two once the tests have
run again.
Peter
requests.packages.urllib3.connectionpool: DEBUG: GET
/api/histories/993bad2fe35335db/contents/7fbe67cfae825002/provenance?key=edc04240db9605fb7edc7bab44d3404c
HTTP/1.1 200 None
Any thoughts?
Thanks,
Peter
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You might be able to do this by accepting a collection of
SAM/BAM files as input instead. This is a quite new feature
in Galaxy, see:
https://wiki.galaxyproject.org/News/2014_06_02_Galaxy_Distribution
Peter
On Wed, Sep 3, 2014 at 10:00 AM, Philippe Moncuquet
philippe.m...@gmail.com wrote:
Hi
-when-gt-tags-for-lt-conditiona-gt-parameters-tc4659704.html#none
This probably deserves to be tracked with a Trello Card...
Peter
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, if not there are bound to be other Java examples
in the ToolShed.
Peter
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Do you mean a SAM/BAM file sorted by read name?
If so, try samtools sort -n ... instead.
Peter
On Thu, Aug 28, 2014 at 12:53 PM, Alistair Chilcott
alistair.chilc...@utas.edu.au wrote:
Hello all,
My users are trying to use a tool called bismark and it requires an unsorted
SAM file for one
Ah - I missed this was on the Galaxy list, sorry.
I think that Galaxy automatically coordinate sorts bam files,
which is generally a good thing bar cases like yours. This
problem has undoubtedly come up before - an unsortedbam
datatype may be needed...
Peter
On Thu, Aug 28, 2014 at 1:35 PM
folders on sourceforge... are you
using the Test Tool Shed here (since I have not yet
released the MIRA 4 wrapper on the main ToolShed)?:
https://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
Regards,
Peter
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On Fri, Aug 22, 2014 at 8:18 PM, Marija Atanaskovic
ma...@unimelb.edu.au wrote:
Hi Peter,
I don¹t know what the stdout and stderr information was. I click on it but
nothing comes up.
I installed from the main toolshed:
http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
Yes, I did
On Fri, Aug 22, 2014 at 8:00 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Fri, Aug 22, 2014 at 9:39 AM, Marija Atanaskovic
ma...@unimelb.edu.au wrote:
Also I can’t install Mira 4. This is the message I receive.
Any suggestions.
Getting Internal Server Error is unhelpful - I can't
/view/peterjc/blast_rbh
Thanks,
Peter
P.S. it would be nice to be able to sort the Repositories I
own lists etc by date (particularly for my typical workflow
of posting an update to the TestToolShed, waiting for a
green light from the tests, and then pushing this to the
main ToolShed
On Mon, Aug 18, 2014 at 11:16 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
Are the main and test tool-sheds currently meant to
be running the tool functional tests every 48 hours?
I created and updated these repositories last week,
but they have yet to be tested:
https
On Wed, Aug 13, 2014 at 7:22 PM, Eric Rasche rasche.e...@yandex.ru wrote:
Hi Peter,
I'm working on composite datatypes now (for PacBio SMRT cells). In the
datatype I know I'll have files with variable names (e.g. .1, .2, .3) and
after using the blast datattype as reference material, I noticed
On Mon, Jul 28, 2014 at 9:43 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Jul 28, 2014 at 8:28 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear Nate, dear Peter
Sorry for the delay in replying.
I can import both HTML and blastdb from a history to a data library. If
I try
there is somewhere in the
database to go poking to reset things.
Thanks,
Peter
P.S. this is with the latest Galaxy from galaxy-central.
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file's
datatype in this way?
Peter
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To search
/admin_toolshed.py which in turn is
(eventually) pulled from the repository model I think.
Peter
On 12/08/2014 20:03, John Chilton wrote:
I think your tool has an XML error in it (the in_graph_filename param
is not being closed) - I imagine this would prevent Galaxy from
displaying the tool
Hi Geert,
Which tool is this?
Peter
On Thu, Aug 7, 2014 at 9:00 AM, Geert Vandeweyer
geert.vandewey...@uantwerpen.be wrote:
Hi,
I get an installation error on the python 2.7 package in the test toolshed.
I used the 'contact owner' function, but wanted to mention it here too
that anything other than MS Excel could be
confused by quirks in the Excel format, e.g. multiple ways
to record dates: http://support.microsoft.com/kb/180162
I would personally save each tab of the Excel sheet as tab
separated data, and import those into Galaxy.
Peter
On Mon, Aug 4, 2014 at 1:56 PM
On Mon, Aug 4, 2014 at 4:28 PM, Eric Rasche rasche.e...@yandex.ru wrote:
Hi Peter,
On 08/04/2014 09:25 AM, Peter Cock wrote:
Hi Mert,
Most of the Galaxy tools dealing with tables of data use tabular
format (tab separated variables), not csv (comma separated
variables). CVS is a horrible
from running my tool which was not shown?
Thanks,
Peter
On Wed, Jul 30, 2014 at 6:07 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
I believe part of the problem is that the install and test framework is
unable to resolve the dependency on blast+ 2.2.29 because it is defined as a
repository
On Thu, Jul 31, 2014 at 5:21 PM, bjoern.gruen...@googlemail.com
bjoern.gruen...@gmail.com wrote:
Hi Peter,
2014-07-31 10:57 GMT+02:00 Peter Cock p.j.a.c...@googlemail.com:
Hi Dave,
You are right that on closer inspection I've mixed tool_dependencies.xml
and repository_dependencies.xml
detailed log available which might help debug this?
Thanks,
Peter
As an aside, this looks like the Test Tool Shed is still using the
Twill backend for the functional tests?
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red error message about metadata... see below (both main
and test toolsheds affected).
Regards,
Peter
[1] https://bitbucket.org/galaxy/galaxy-central/pull-request/440/
[2]
https://github.com/peterjc/galaxy_blast/commit/9d2e3906915895765ecc3f48421b91fabf2ccd8b
--
Uploading on the Test Tool
On Wed, Jul 30, 2014 at 11:52 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear Nate, dear Peter
Again, sorry for the delay in replying.
Yes I can. It looks like this
[galaxy@srv ~]$ cat /galaxy/database/files/081/dataset_81002.dat
[galaxy@srv ~]$ ls /galaxy/database/files/081
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
On Wed, Jul 30, 2014 at 12:12 PM, John Chilton jmchil...@gmail.com wrote:
Hey Peter,
Opps sorry about that and thanks for the bug report. The tool
On Mon, Jul 28, 2014 at 8:28 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear Nate, dear Peter
Sorry for the delay in replying.
I can import both HTML and blastdb from a history to a data library. If
I try to get the data out of the library into anothre history, I am
successful
set:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set
Peter
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On Mon, Jul 28, 2014 at 12:23 PM, Wolfgang Maier
wolfgang.ma...@biologie.uni-freiburg.de wrote:
On 28.07.2014 12:22, Peter Cock wrote:
This is standard behaviour to prevent special characters being used
to construct malicious command lines. It can be configured within
your tool definition
.
Note using the *.loc files makes the databases available to
all the Galaxy users, while with a Data Library you can
control access to specific groups/roles.
Regards,
Peter
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Interesting hypothesis - you may well be right.
Galaxy guys - who is the expert to talk to on this and/or where
in the code should we be looking?
Thanks,
Peter
On Wed, Jul 23, 2014 at 11:22 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear Peter
Thanks for your reply.
I can import
database templates, refreshing this every few schema bumps
should be enough.
Thanks,
Peter
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there is room for some speed up.
Regards,
Peter
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On Tue, Jul 22, 2014 at 1:15 PM, Eric Rasche rasche.e...@yandex.ru wrote:
Hi Peter,
On July 22, 2014 3:15:41 AM CDT, Peter Cock p.j.a.c...@googlemail.com wrote:
Given how close you can get now for minimal effort,
this seem unnecessary.
http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci
Set yourself as an administrator, and you can import the files
from disk (and link to them if you wish to avoid a copy) as part
of a data library. See:
https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
Peter
On Tue, Jul 22, 2014 at 3:52 PM, Mark Lindsay m.a.lind
to generate it was going to be my next question too ;)
I'm impressed with Eric's zeal to automate things. Having a script
for making the SQLite template would be good - under git in the
same repository?
Peter
P.S. The schema version 120 template works great, thanks!:
https://travis-ci.org/peterjc
(sniffing, splitting ...)
should be also versioned, or? What happend if I have two stockholm.py files
in my system?
Potentially you might need/want to define those as two different
Galaxy datatypes?
@Peter, can we create a striped-down, python only biopython egg? All parsers
should be included
through greps, globs, and finds. Though I'll hold off on that
for a better solution.
I'd manually install the Python dependencies as part of the Python
used to run Galaxy itself?
Peter
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On Fri, Jul 18, 2014 at 5:14 PM, Dave Bouvier d...@bx.psu.edu wrote:
John, Peter,
The buildbot builders are already using the api interactor for both
functional tests and the install and test framework.
--Dave B.
Great news.
When did that happen? Did it cause any regressions (and
can/did
On Thu, Jul 17, 2014 at 1:58 PM, Calogero Zarbo za...@fbk.eu wrote:
Hello Peter,
Thanks for your answer.
I tried your come but I am still not able to make it work the way I want.
I mean that in the workflow design page, when I switch the parameter, it
doesn't change the graphical list
of all, get it working in the normal tool usage mode (tested by hand).
Then I would get it working with functional tests.
Finally I would test it by hand in the workflow editor, at which point any
problem is probably Galaxy's fault ;)
Peter
/mira_datatypes
I have to do this manually with some sed magic in my TravisCI
automated set setup, see:
http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-tools.html
Peter
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, but that
is an overhead I would like to omit ... any other ideas?
I would love to discuss that issue further, maybe a hangout with Greg and
Peter?
Thanks John for your input,
Bjoern
This could be high level, e.g. other sequence file formats repository
covering GenBank, EMBL, SwissProt plain text
On Thu, Jul 17, 2014 at 5:55 PM, Eric Rasche rasche.e...@yandex.ru wrote:
Not a problem Peter, it's a somewhat subtle bug to have, and there isn't
a lot of documentation on the wiki about writing new datatypes (though I
plan to fix that soon).
That particular error message could stand
on the ToolShed:
Earlier, Björn Grüning bjoern.gruen...@gmail.com wrote:
Imho datatypes should be handled like Tool dependency definitions.
There should be only one installable revsion.
This is something Greg will have to comment on - there may be
ramifications I'm not seeing.
Peter
On Thu, Jul 17, 2014 at 6:28 PM, Eric Rasche rasche.e...@yandex.ru wrote:
Am 17.07.2014 18:51, schrieb Peter Cock:
One reason I have been meaning to do some of these is familiarity with
many of these formats from looking after/writing parsers in Biopython.
Peter, similar case here
Good point Greg.
Let's refine this slightly then, a new special ToolShed repository type for
a *single* datatype definition. That avoids this problem :)
(This does not help with suites of very closely related datatypes -
like different
kinds of BLAST database.)
Peter
On Thu, Jul 17, 2014 at 6
on the output
file (which could be text, html, tabular, blastxml) using the output
datatype's merge method.
I had to work out a lot of this from reading the code and queries
on the mailing list.
Peter
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.
We want you to tell us which format you want to try
parsing it as.
Sorry,
Peter
(Speaking as the Bio.SeqIO maintainer for Biopython)
On Thu, Jul 17, 2014 at 7:45 PM, Eric Rasche rasche.e...@yandex.ru wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Let's pretend for a second that I'm
On Thu, Jul 17, 2014 at 8:20 PM, Eric Rasche rasche.e...@yandex.ru wrote:
On 07/17/2014 02:11 PM, Peter Cock wrote:
You could do something like that, and we already have
Biopython packages in the ToolShed which can be listed
as dependencies :)
If my module depends on the biopython from
of a meta-entry depending on other smaller
specific datatype defining ToolShed repositories. But it hasn't reached the
top of my personal TODO list yet ;)
Peter
On Wed, Jul 16, 2014 at 1:47 PM, Björn Grüning
bjoern.gruen...@gmail.com wrote:
Hi Eric,
please have a look at:
https://github.com
/master/tools/seq_filter_by_id
Peter
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On Wed, Jul 16, 2014 at 7:44 PM, Saket Choudhary sake...@gmail.com wrote:
Thanks Peter, I guess I should then rely on API based tests.
If it is just the order, make sure the order of the output files in the test
is consistent with that in the outputs and it make be OK with Twill...
I wonder
/emboss_datatypes
However that doesn't answer your question :(
Peter
On Mon, Jul 14, 2014 at 7:31 PM, Eric Rasche rasche.e...@yandex.ru wrote:
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I'm trying to add a new datatype to my galaxy instance for genbank
files, however I'm running into various issues
Hi Saket,
From memory the Twill tests are fragile with the output file order in the XML.
John was discussing switching the default from the Twill to API backend,
not sure when that is happening though...
Peter
On Tue, Jul 15, 2014 at 9:31 AM, Saket Choudhary sake...@gmail.com wrote:
I
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