is surely wrong.
> I created an issue for it here:
> On Wed, Oct 10, 2018 at 2:11 PM D K wrote:
>> Sure, I've attached a sample xlsx file and my datatypes_conf.xml file
That sounds very strange - could you share the test file (ideally publicly,
but at least by private email)? Modern MS files do use XML but I don't
understand how it would be recognised as BLAST XML...
It may also be useful to see your Galaxy data types configuration file.
On Wed, 10 Oct
> On 02.10.2018 11:22, Peter Cock wrote:
> > Personally I tend to work with $GALAXY/tool
Personally I tend to work with $GALAXY/tool-data/*.loc (and ignore
the tool shed installed copies in their cryptically named folders) but
this reflects in part the fact that this used to be the only copy of the file,
and that's just what I always did.
If you use a data manager, I don't know which
Hi Peter vH,
I wonder if adding columns is not supported - because some tools
would define the table without the extra column? You might have
to define a new data table instead (with largely the same content).
But to be clear, I am not an expert in this area of Galaxy.
However, it does seem the
also very big? I tested this on the first 10 sequences and it took
> about 10mins. But maybe this is still not faster than running all at once?
> How many cores would you give such a job?
> Cheers Jochen
> On 30.08.2018 16:44, Peter Cock wrote:
> > If there are any limits, it woul
If there are any limits, it would be down to the Galaxy Admin's job
settings - something generic with collections.
Personally I've not done this - I tend to concatenate FASTA files
to make large files with multiple sequences instead.
(And then we have the optional task splitting enabled so that
to use the extra_files_path mechanism (which seems to
> be the simplest for me)
> In any of these cases my next question would be how to create a test using
> such a data as input and output (for output I have seen an example
> Am 16/08/18 18:32 schrieb Peter Cock :
> Defining 20 different text-based formats does not look ideal (if that
> is what you are doing).
> Do you have sample output in the repository? Perhaps at least some of
> these ca
n I can pass the folder to
> downstream tools (and can check for proper input). I hope that subclassing
> txt or tabular will be sufficient.
> On 16.08.2018 17:02, Peter Cock wrote:
>> More details might help - are you just de
More details might help - are you just defining the new datatype as a
subclass in the XML, or do you need to include Python code (e.g. for a
If you want to see some examples of datatypes using Python code which
are available via the Tool Shed, here are two:
You may have found a new Galaxy bug then :(
Could you log an issue here:
(From what you've said, I don't think that this is a problem in the
BLAST+ wrappers themselves)
On Wed, Jul 11, 2018 at 3:20 PM, Matthias Enders <
Good. So is everything resolved now?
On Wed, Jul 11, 2018 at 3:08 PM, Matthias Enders <
> Dear Peter,
> yes we did reload the Blast *.loc files using the admin interface. Our
> Version is 18.05 (based on the Galaxy – Docker image).
Is there anything in the Admin's interface to let you reload the BLAST
If yes, did you try it but it didn't work?
What version of Galaxy do you have?
On Tue, Jul 10, 2018 at 3:11 PM, Matthias Enders <
> Dear Peter,
> up to our
Thanks for getting back to us - this was actually my guess from the
original email - that it was not a blastn error message, but a Galaxy
message before ever calling BLAST.
My guess is you are seeing this issue, or something like it, with
having to restart Galaxy to reload the *.loc files?
There is a setting to enable showing the command line string
and full paths on disk via the "i" icon from a history entry, see
# This option allows users to see the full path of datasets via the
# "View Details"
er I deleted these directories
> the error messages disappeared and tools are running again.
> Cheers, David
> From: Peter Cock <p.j.a.c...@googlemail.com>
> Sent: 24 May 2018 14:22:40
> To: David Lee
> Cc: galaxy-dev
On Thu, May 24, 2018 at 2:14 PM, David Lee wrote:
> I hope somebody can help me with this. I've been maintaining a Galaxy
> installation for the past few months that has suddenly developed a problem
> that I can't undo.
Which version of Galaxy? Can you tell
On Tue, Apr 10, 2018 at 3:28 PM, Jochen Bick wrote:
> Hi Peter,
> I can contact report the issue on github.
I think that would be best.
> It looks like its looking for
> a variable called dataset with is not
galaxy is a release_17.05
> I think the xml is also broken.
> Cheers Jochen
> On 10.04.2018 15:28, Peter Cock wrote:
>> Are you trying to install this?
>> If so,
Are you trying to install this?
If so, it does set out its requirements:
However, your Galaxy would have to be using BioConda to do this.
This could be a special character unicode issue, but my guess
is something has gone wrong with compression.
Can you identify the file on disk (easy via the history "i" for
information icon if this option is enabled; by default Galaxy
does not tell you the file path)?
Then try the Unix command
u can use pip in a conda environemnt to do this manually).
> Hope that helps,
> On 5 March 2018 at 17:51, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> I stand corrected. Looking closer, there are conda packages
>> for both Python 2 and
> tk: 8.6.7-0 conda-forge
> wheel: 0.30.0-py27_2conda-forge
> zlib:1.2.11-0 conda-forge
> So given a recent conda (latest version should work) and the correct channel
Tricky, as I understand it the conda python packages are specific to
the conda version of Python - in this case Python 3 not 2.
It might actually be simpler to fix pal_finder/pal_filter.py to cope
with Python 3 - is the code online somewhere, I could probably cast an
eye over it.
I think you will find this very difficult without including a large
chunk of the Galaxy code in your project for turning a tool
XML file into an object representation.
Although the main features of the tool XML provide a quite
neutral tool description (list of arguments, output
Domaine de Vilvert
> 78352 Jouy-en-Josas
> Le 17 janv. 2018 à 17:39, Peter Cock <p.j.a.c...@googlemail.com> a écrit :
> It sounds like it could be this issue?:
> If so, the good news is there is a workaroun
I *think* this is a problem with your copy of Python 2.7 and a
standard library (hashlib) normally present. Do you know how this
Python was installed? If it was compiled from source, then it may have
been missing a few dependencies, and thus you have ended up with
missing a few normally present
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 <email@example.com
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, 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
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.
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
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
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