It sounds like it could be this issue?:
If so, the good news is there is a workaround (see issue discussion).
On Wed, Jan 17, 2018 at 4:24 PM, Olivier Inizan wrote:
> Dear list,
> I am trying to write a test
I infer you are talking about this Tool Shed repository:
Sadly there is no README file and no copyright statements.
The only clue to the author is one comment is written appears
to be written in Spanish.
What does your config/tool_data_table_conf.xml[.sample] file have?
Can you turn on the debugging as this will will give more information
about the *.loc files. e.g.
On Wed, Oct 18, 2017 at
That's a shame - I don't see anything in the log either at
first reading - it was hoping to see problems with missing
datatypes or sniffers, which might explain this.
Sorry, I am out of ideas.
On Fri, Sep 22, 2017 at 2:41 PM, Pavel Fibich wrote:
> Hi Hans-Rudolf
My first thought would be to double check the Galaxy startup logs
(which normally tell you about the datatypes as they are setup).
That ought to give some clues.
Also check the XML files where the datatypes are defined are
all still fine - do you have any of these and do they look fine?
On Thu, Sep 21, 2017 at 12:50 PM, SAPET, Frederic <
> Hi Peter,
> Good idea, I will keep that in mind for other needs.
> I'm not sure that it will be suitable for what I want to do. Users will
> have to first import database to their history (yet another step
> Thank you for sharing your ideas :)
> De : Laure QUINTRIC [mailto:laure.quint...@ifremer.fr]
> Envoyé : mercredi 13 septembre 2017 13:54
> À : Peter Cock <p.j.a.c...@googlemail.com>; SAPET, Frederic
> *De :* galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] *De
> la part de* Peter Cock
> *Envoyé :* mardi 12 septembre 2017 14:56
> *À :* Laure QUINTRIC <laure.quint...@ifremer.fr>
> *Cc :* Galaxy-dev <firstname.lastname@example.org
I don't think there is any easy to use mechanism for this in Galaxy.
Unfortunately Galaxy loads all the *.loc files at startup and treats
them as global values available to all users equally.
I can't find the email thread, but I recall someone previously trying
to do something with a
Galaxy itself uses samtools for many operations, which is different
from when samtools is called as a dependency of a tool run by the
However, the Docker image ought to take care of that - can you
give more details of which Docker image you are using (URL,
Daniel Blankenberg wrote one (CC'd):
I've never used it in production and don't have enough understanding
e fast response. From reading around elsewhere I'd understood
> that using $PATH_TO_IMAGES was now deprecated? I think I tried it anyway and
> it didn't seem to help. But I might have missed something, so I'd be
> interested to know if it works for you.
> Best wishes
It looks like something important is not showing in the best practise
website, special variable $PATH_TO_IMAGES as per the linked example:
.. image:: $PATH_TO_IMAGES/slop-glyph.png
Let me look into this,
On Wed, Aug 9, 2017 at 2:52 PM, Peter Briggs
> On Thu, Jul 27, 2017 at 11:33 AM, Peter Cock <p.j.a.c...@googlemail.com>
>> Hi Steven,
>> Just in case, you're not talking about my older simpler Galaxy Tool
>> for drawing simple Venn Diagrams, ar
Just in case, you're not talking about my older simpler Galaxy Tool
for drawing simple Venn Diagrams, are you?
This reminds me that I ought to update that tool to
And mere minutes later that change has been accepted,
and will be part of the next release of Planemo.
Thanks for the constructive feedback Matthias!
On Wed, Jul 12, 2017 at 4:24 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Good idea, pull request submitted:
with planemo command --help.
> On 12.07.2017 16:57, Peter Cock wrote:
>> planemo lint --fail_level error sleepwaste.xml
>> The default is to fail if there are warnings.
planemo lint --fail_level error sleepwaste.xml
The default is to fail if there are warnings.
On Wed, Jul 12, 2017 at 3:55 PM, Matthias Bernt <m.be...@ufz.de> wrote:
> Hi Peter,
> I just call planemo l sleepwaste.xml
> On 1
How are you running planemo lint - in particular is it set
to fail if there are any warnings present (like your missing
On Wed, Jul 12, 2017 at 3:52 PM, Matthias Bernt wrote:
> Dear list,
> In order to test the job resubmission feature I wrote a little
> job_name = job_name[:self.restrict_job_name_length]
> return job_name
>> On May 29, 2017, at 11:33 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> Thanks Saravanaraj,
> I will talk to our sysadmin and see if I can change the locale to en_US.UTF-8.
> Thank you very much.
> line 400, in
> job_name = ''.join( x if x in ( string.letters + string.digits + '_' )
> else '_' for x in job_name )
> UnicodeDecodeError: 'ascii' code
Time for more debugging, try inserting something like this inserted
the line above into
(having backed up the file):
log.debug( 'Making job_name, tag was %r, plan to use %r with
underscores replacements' %
On Wed, Mar 20, 2013 at 3:51 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On Mon, Apr 30, 2012 at 4:47 PM, Nate Coraor <n...@bx.psu.edu> wrote:
>> On Apr 25, 2012, at 9:39 AM, Louise-Amélie Schmitt wrote:
>>> Hi everyone,
On Wed, Apr 19, 2017 at 1:17 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> I've emailed the rest of the IUC for their input - adding the old versions
> in bioconda should work, or adding the recent Biopython releases as packages
> on the Tool Shed.
be no good idea because of backward
> On 19.04.2017 13:50, Peter Cock wrote:
> > Just lucky timing, could you try blast_rbh v0.1.11,
> > https://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh/d8d9a9
be great to get the update, but since I have a
> method that is working for the moment there is no need to hurry.
> On 19.04.2017 12:57, Peter Cock wrote:
>> Oh right - I've just been updating ncbi_blast_plus this morning
>> to tr
Oh right - I've just been updating ncbi_blast_plus this morning
to transition to BLAST+ 2.5.0 via either bioconda or the older
legacy Tool Shed.
I can try to update blast_rbh next, which may solve this by
letting you use bioconda.
On Wed, Apr 19, 2017 at 11:52 AM, Matthias Bernt
This just went live on the main tool shed:
You can report issues here or on GitHub at:
On Thu, Dec 8, 2016 at 11:35 AM, Peter Cock <p.j.a.c...@googlemail.com>
software development and open science in the biological research
community (like the Galaxy Community Conference).
(Dr Peter Cock, OBF
2017 at 18:05, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Dear all,
> Recent BOSC meetings have had a strong Galaxy presence, so please do
> consider submitting an abstract and/or attending BOSC 2017 in Prague.
> Thank you,
> Dr. Peter Cock,
ng up email
> aliases? I would need to ask our cluster admins if they could realize this.
> On 10.04.2017 16:39, Peter Cock wrote:
>> This may depend on the cluster setup, and how Galaxy accesses it.
>> What are you using?
This may depend on the cluster setup, and how Galaxy accesses it.
What are you using?
We use SGE (actually Univa Grid Engine) via DRMAA, and had to setup
usern...@example.org email aliases just for this.
On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt wrote:
> Dear list,
I suspect the missing dependency BWA may reflect the switch away
from Galaxy's home-grown packaging system to using Conda -
enabled by default since v17.01,
Newer dependencies will likely next get an old fashioned package
Recent BOSC meetings have had a strong Galaxy presence, so please do
consider submitting an abstract and/or attending BOSC 2017 in Prague.
Dr. Peter Cock,
Bioinformatician at The James Hutton Institute;
Open Bioinformatics Foundation, board of directors, treasurer
.com/api/version` to learn the release of Galaxy you have.
> Thanks for using Galaxy,
> On Wed, Mar 8, 2017 at 7:39 AM Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> Galaxy was originally distributed via the mercurial (hg) version
Galaxy was originally distributed via the mercurial (hg) version
control system, later the git version control system.
Try this (which will work on a very old Galaxy using hg),
$ hg log | head
d writing it will
> automatically run the convert to bigwig command
> Peter Cock
> February 28, 2017 12:21 PM
> It depends on what you mean by automatic. You could
> create a Galaxy Workflow where a tool is run which
> generates the bedgraph file, and then as the next
It depends on what you mean by automatic. You could
create a Galaxy Workflow where a tool is run which
generates the bedgraph file, and then as the next
step it is converted to bigwig.
For this specific task, it might be possible to exploit
the Galaxy datatype definition for bedgraph to allow
t 11:20 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> This went smoother today, and has served to refresh some of the
> details of how the Galaxy's venv etc all work.
> In my TravisCI setup for tool testing I currently "manually" install
> the tool dependencies
On Mon, Feb 13, 2017 at 9:17 AM, Matthias Bernt wrote:
> Dear Martin,
> Thanks for your input. Before answering the raised questions I would like to
> add some more information that I just found:
> I've noticed something odd (to me) which is maybe the source of the problem.
On Fri, Feb 10, 2017 at 3:26 PM, Matthias Bernt wrote:
> Dear galaxy-dev list,
> I'm currently trying to introduce myself to the galaxy server, i.e.,
> learning how to use and administer a galaxy server.
> I have installed galaxy following this excellent tutorial:
Hmm. I wonder if a composite datatype would work here?
On Thu, Feb 9, 2017 at 9:25 AM, Jochen Bick wrote:
> Hi Dan,
> I understand the option with this specific flag. What I mean is that for
t and let yo know how it goes.
> Thank you
> On 01/02/2017 10:10, "Peter Cock" <p.j.a.c...@googlemail.com> wrote:
> Hi Eduardo,
> Certainly when Luobin Yang submitted the early work on the
> PSI BLAST wrapper we need the P
Wed, Feb 1, 2017 at 9:46 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Thanks John - that could explain what's going wrong and offers
> another approach to fixing my TravisCI testing - setting:
> preserve_python_environment = legacy_and_local
akeprofiledb. Does that allow you to remove psiblast from blacklist in
> your repository?
> Thank you
> On Tue, Feb 5, 2013 at 4:28 PM, Peter
rted - there is a config option that is documented
> pretty well in the PR but I missed named it in the sample (fixing it with
> Hopefully this helps and thanks for the bug report!
> On Tue, Jan 31, 2
> On 31/01/17 10:39, Peter Cock wrote:
>> Hi all,
>> A few of my tools have for a long time used Galaxy's own parsing
>> functionality in order to avoid an extern
A few of my tools have for a long time used Galaxy's own parsing
functionality in order to avoid an external dependency. Lately
this has stopped working on my TravisCI testing with planemo
using the Galaxy dev branch (the stable master branch is fine):
Ah - I assumed you meant from the user-facing UI, or the reports page.
I would suggest exploring the advance job metrics options, see e.g.
I've never used it, but perhaps the backend using Collectl
I don't think Galaxy itself will tell you this, in part because the
details would be dependent on the Cluster being used.
I would do that via whatever cluster management system you are running
(e.g. qstat or qmon if using SGE).
By default all the jobs will be submitted by the
Right now this is not possible, and I can't think of any way to
restrict access to system level BLAST databases listed in
the blast*.loc files by user. However, since other Galaxy
tools use *.loc files, someone else may have some ideas.
You might be able to try using a BLAST
I have updated the NCBI BLAST+ wrappers on the Test Tool Shed,
the wrapper is now at v0.2.00:
The main changes is this now depends on BLAST+ 2.5.0, and that is
available via either BioConda or the Tool Shed:
Galaxy itself needs samtools, and this is not handled via the
Tool Shed which only does dependencies of Galaxy Tools.
I don't think the website is clear enough about this,
just points at
On Wed, Nov 23, 2016 at 10:49 AM, Peter Briggs
> Hello Evan, Hans-Rudolf
> I'm just in the middle of doing a similar migration for our local production
> server, and Hans-Rudolf's advice seems sound to me. Definitely moving the
> core Galaxy server has been
Are you asking how Galaxy takes the user-entered parameters
(requested in the tool XML file with tags) and builds a
command line string using the Cheetah-format template defined
in the tag?
At least part of the answer to that is the ToolEvaluator object:
> On Tue, Nov 15, 2016 at 10:06 AM, Peter Cock <p.j.a.c...@googlemail.com>
>> Hello all,
>> Is there a specific issue tracker for the wiki? It seems wrong to
>> open an issue on the
Is there a specific issue tracker for the wiki? It seems wrong to
open an issue on the main GitHub code repository...
e.g. Many of the documentation pages still refer to the legacy
configuration filename universe_wgsi.ini rather than the new
name of config/galaxy.ini
> version="" />
> This tool is not the one trying to be installed.
> On Nov 3, 2016, at 10:28 AM, Peter Cock
> <p.j.a.c...@googlemail.com<mailto:p.j.a.c...@googlemail.com>> wrote:
> I think you may have hit the sa
I think you may have hit the same bug I found recently:
What is line 44 of your integrated_tool_panel.xml file?
On Thu, Nov 3, 2016 at 2:16 PM, Yip, Miu ki wrote:
> Hi all,
> While trying to install tools from the
You might find this work useful for fetching bacteria from the NCBI:
On Tue, Oct 25, 2016 at 12:54 PM, Vos, Michiel wrote:
> Dear Galaxy developers,
> We hereby want to ask if anyone is interested in helping out
You are on the right track, but something in the WAV file has
triggered one of Galaxy's security protections to try to block
uploading of potentially dangerous files. There may be some
settings here you can relax - I've not had to deal with this
On Fri, Oct 21, 2016 at
Using a soft link for this is a common pattern, and should be followed with &&
(ideally using XML CDATA to avoid escaping everything like etc),
and quote the filenames just in case there are any spaces. e.g.
The first example looks OK, very similar to this one of mine for example,
so I am not sure what is breaking:
I would try adding more shell actions to debug
This is an annoyance from the NCBI team, and dealing with the
expired tbl2asn tool is a regular question from Prokka users, eg:
The Tool Shed package for Prokka will need updating - but
luckily Nicola is
I just found this old email by a very similar exception logged as:
There do seem to be some corner cases where missing default
values are not handled nicely.
On Tue, Jan 26, 2016 at 2:38 PM, Matthias De Smet
the command I'm using to run planemo:
> . galaxy_test/.venv/bin/activate
> planemo test --test_data /home/galaxy-functional-testdata --galaxy_root
> galaxy-test/ --skip_venv test.xml
> I'm getting no errors when using the planemo lint tool.
> On Fri, O
Looking at your XML that looks OK.
It might not be important, but how exactly are you running planemo
I'm asking because currently it will not create tool-data/twobit.loc
for you from your sample file - although in that case I would have
expected a different error message:
into the Galaxy core, under Galaxy's open source
licence: Academic Free License version 3.0
On Tue, Sep 20, 2016 at 2:51 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Thanks JJ,
> That's great. We'r
> These can be copied to the iuc owned repositories and I could deprecate
> those under my name.
e tag works:
>> On Thu, Sep 1, 2016 at 8:23 AM, Peter Cock <p.j.a.c...@googlemail.com>
>>> I'm not quite sure what you mean by a "code f
I'm not quite sure what you mean by a "code file", but if you
mean using the tag, here's an example:
I am using a Cheetah syntax for loop to access each entry
in a repeat parameter.
On Thu, Sep 1, 2016 at
>> Peter Cock ha scritto
>>> Thanks Hans-Rudolf,
>>> Yes - you are right. The wiki does li
> Regards, Hans-Rudolf
> On 08/29/2016 05:27 PM, Peter Cock wrote:
>> Hi Martin,
>> I'd like to look into creating new users via the API (where we can
>> control the email address and username format for integration with our
>> cluster), and ha
I'd like to look into creating new users via the API (where we can control
the email address and username format for integration with our cluster),
and have the web-interface forbid users from self-registration.
The read-the-docs site you mentioned in this old email (below) doesn't
That's great Bjoern,
I was thinking we should mention this on the wiki (with a link
to the documentation rather than duplicating it). There are
some existing pages about the tool_dependencies.xml
system - but no obvious top level introduction that I saw?
Are you asking about compatibility staying on the same Galaxy
instance, or the harder problem of compatibility sharing workflows
between Galaxy servers?
Taking data from input Galaxy datasets should be fine, anything else
may not be portable. Even the relatively simple case of
On Tue, Aug 9, 2016 at 6:33 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hello all,
> Recently I've been debugging various problems with my Galaxy tool TravisCI
> tests as part of moving to using "planemo test" rather than the fragile system
> I first create
Recently I've been debugging various problems with my Galaxy tool TravisCI
tests as part of moving to using "planemo test" rather than the fragile system
I first created which mimicked a pre-ToolShed manual install:
On Mon, Aug 8, 2016 at 3:27 PM, Björn Grüning <bjoern.gruen...@gmail.com> wrote:
> Hi Peter,
> Am 08.08.2016 um 15:54 schrieb Peter Cock:
>> On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche <e...@tamu.edu> wrote:
>>> Hi Peter,
>>> The c
On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche wrote:
> Hi Peter,
> The cargo port is the ideal place for this, however it does not support
> manual uploads of files.
You mean https://github.com/galaxyproject/cargo-port
Is that something which might be addressed in
How do tool wrapper developers/packagers go about adding entries
to the Galaxy depot? There isn't a GitHub repository for this is there?
Specifically I want to upload some older MIRA releases, e.g. these
URLs have broken, but I have the original files and checksums:
On Wed, Jul 27, 2016 at 9:34 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Thank Dan, that's what I thought.
> So databases can added to any of the multiple blastdb.loc
> files which Galaxy ought to
Great - I'm glad it was an easy fix.
On Tue, Aug 2, 2016 at 10:36 AM, Mohamed Kassam <k.mam...@gmail.com> wrote:
> Hell Peter
> The CDATA works perfectly thanks again.
> 2016-08-02 11:31 GMT+02:00 Peter Cock <p.j.a.c...@googlemail.com>:
This could be as simple as the & needing to be
escaped as or better escaping the whole
help text using CDATA:
Can you show us your tool XML file? Is it on GitHub?
On Tue, Aug 2, 2016 at 10:26 AM,
When datatypes were moved to the Tool Shed, I
think the idea was to eventually have only a core
set of topic-neutral datatypes (plain text, tabular,
etc) in Galaxy itself. That does seem sensible.
I'm not quite sure why policy has returned to a
larger centralised set - but limitations
I have a work-in-progress branch and pull request here,
The Galaxy TravisCI tests looked fine.
On Mon, Aug 1, 2016 at 11:18 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
I ran this past the IUC first, and the only comments were
Although I wasn't at GCC2017 to discuss this in person,
I understand that the Galaxy Team now encourages
widely used datatypes to be included in the main Galaxy
repository, rather than distributed via the Tool Shed.
For me too, thanks!
On Thu, Jul 28, 2016 at 11:06 AM, Nicola Soranzo <nsora...@tiscali.it> wrote:
> Works for me now.
> On 28/07/16 09:44, Peter Cock wrote:
>> Hello all,
>> The main Tool Shed
The main Tool Shed seems fine, but the Test Tool Shed is not:
> The Tool Shed could not be reached
> You are seeing this message because a request to the
> Tool Shed timed out or was refused. This may be a temporary
> issue which could
> was created during their installation.
> Please let me know if I can provide additional clarification.
> Thanks for using Galaxy,
>> On Jul 26, 2016, at 6:08 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> Hello all,
Can any of the Galaxy Data Manager expects advise please?
-- Forwarded message --
From: Harry Wright <harry.wri...@moredun.ac.uk>
Date: Tue, Jul 26, 2016 at 9:25 AM
Subject: RE: Galaxy Blast
To: Peter Cock <p.j.a.c...@googlemail.
Sorry, I know relatively little about how Galaxy loads the tool XML
files and turns this into the HTML pages. I've mostly searched
the codebase with grep at the command line (also searching
directly on GitHub works pretty well) trying to trace functionality
when I was debugging something.
Are you asking about the XML files which described Galaxy Tools
by listing all the options to show the user, any help text to show the
user, and instructions for how to turn the options picked into a
command line to be executed:
This isn't a very strong example, as it is self-reuse and self-citing,
but anyway - we described some workflows in this book chapter:
Cock and Pritchard (2014)
Galaxy as a Platform for Identifying Candidate Pathogen Effectors.
We re-used a
On Thu, Jul 21, 2016 at 10:35 AM, Shane Sturrock wrote:
> I’m just using the drmaa plugin so I’m guessing I need to either specify a
> job runner for BLAST which sets GALAXY_SLOTS. The documentation isn’t
> entirely clear although it seems I need to create a job_conf.xml
We've not touched anything on the BLAST+ wrapper here for
a while - the command line is always built using:
That means use the environment variable $GALAXY_SLOTS
if set, defaulting to 8 threads if not. See:
Did you mean parameter as in input field shown
to the user? Like a combobox or text field?
Since this happened to come up earlier today, here's
a rejected pull request which added a password
parameter - that ought to give you a rough idea:
which explains the $__user_id__ and $__user_email__ tokens
which can be used in the definition of a tool
wrapper XML file.
From a security point of view, I don't think any tool should have
access to the user's Galaxy
This has been suggested before (with code to do it),
but rejected on security grounds, see:
What would you do with the password when calling
your tool? If you use it directly in the command line
string then it will appear in the Galaxy logs, but
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