From the syntax I can see pbs-python still uses a Python 2 style
print, it will need updating for Python 3.
I suggest opening an issue on the repository, and seeing what the
author says. I would guess the Python 2 to 3 changes will be fairly
easy, but worry that there have been other changes to Ga
That seems a good compromise within conda, since BioConda
wouldn't want the binary package itself to be too big.
(I'm doing something similar with some real sample data for
a tool, putting it up on Zenodo. Of course, this is optional for
my tool - your use case is different.)
The Galaxy Data Mana
I don't have any advise from the BLAST DB side, but I would
expect the same solution to work with any *.loc file and the
file system it points at.
Peter
On Mon, May 20, 2019 at 10:50 AM Schäfer, Richard
wrote:
>
> Hello,
>
> I want to integrate a Docker container as a tool in Galaxy. This works
Christopher filed this as https://github.com/galaxyproject/galaxy/issues/7068
On Mon, Dec 3, 2018 at 4:01 PM Previti
wrote:
>
> Ok, I submitted it, hope somebody can help with this.
>
> Cheers,
> Christoper
>
> On 12/3/18 3:20 PM, Nicola Soranzo wrote:
>
> Hi Christopher,
> can you please submit
hich is surely wrong.
>
> I created an issue for it here:
> https://github.com/galaxyproject/galaxy/issues/6849
>
> M.
>
>
>
> 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.
Peter
On Wed, 10 Oct 20
shed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/tool_data_table_conf.xml
> ->
> tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/diamond_database.loc
>
> Best,
> Matthias
>
>
> On 02.10.2018 11:22, Peter Cock wrote:
> > Personally I tend to work wi
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 I
ery 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
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 G
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
> somewhere).
>
> Cheers,
> Matthias
>
>
>
>
>
ned in the xml file?
>
> Best,
> Matthias
>
>
>
> 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
>
. Then I can pass the folder to
> downstream tools (and can check for proper input). I hope that subclassing
> txt or tabular will be sufficient.
>
> Cheers,
> Matthias
>
>
>
> On 16.08.2018 17:02, Peter Cock wrote:
>>
>> More details might help - are you ju
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
sniffer)?
If you want to see some examples of datatypes using Python code which
are available via the Tool Shed, here are two:
https://github.com/peterjc/ga
You may have found a new Galaxy bug then :(
Could you log an issue here:
https://github.com/galaxyproject/galaxy/issues
(From what you've said, I don't think that this is a problem in the
BLAST+ wrappers themselves)
Peter
On Wed, Jul 11, 2018 at 3:20 PM, Matthias Enders <
m.end...@german-seed-
Good. So is everything resolved now?
Peter
On Wed, Jul 11, 2018 at 3:08 PM, Matthias Enders <
m.end...@german-seed-alliance.de> wrote:
> 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).
>
>
>
> Mit
Is there anything in the Admin's interface to let you reload the BLAST
*.loc files?
If yes, did you try it but it didn't work?
What version of Galaxy do you have?
Peter
On Tue, Jul 10, 2018 at 3:11 PM, Matthias Enders <
m.end...@german-seed-alliance.de> wrote:
> Dear Peter,
>
>
>
> up to our g
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?
https:
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
https://docs.galaxyproject.org/en/master/admin/options.html#expose-dataset-path
# This option allows users to see the full path of datasets via the
# "View Details" optio
ectories
> the error messages disappeared and tools are running again.
>
>
> Cheers, David
>
>
> From: Peter Cock
> Sent: 24 May 2018 14:22:40
> To: David Lee
> Cc: galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Conda proble
On Thu, May 24, 2018 at 2:14 PM, David Lee wrote:
> Hi,
>
>
> 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 what version of conda it is u
On Tue, Apr 10, 2018 at 3:28 PM, Jochen Bick wrote:
> Hi Peter,
>
>
>>
>> https://github.com/CollardT/Ballgown-Wrapper
>
> 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 defined in the input part.
>
>
;
> I think the xml is also broken.
>
> Cheers Jochen
>
> On 10.04.2018 15:28, Peter Cock wrote:
>> Are you trying to install this?
>>
>> https://toolshed.g2.bx.psu.edu/view/theo.collard/ballgown_wrapper/05977e96375b
>>
>> If so, it does set out its req
Are you trying to install this?
https://toolshed.g2.bx.psu.edu/view/theo.collard/ballgown_wrapper/05977e96375b
If so, it does set out its requirements:
bioconductor-ballgown
r-dplyr
r-optparse
However, your Galaxy would have to be using BioConda to do this.
Thi
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 "he
you can use pip in a conda environemnt to do this manually).
>
> Hope that helps,
> Marius
>
> On 5 March 2018 at 17:51, Peter Cock wrote:
>>
>> I stand corrected. Looking closer, there are conda packages
>> for both Python 2 and 3, e.g.
>>
>> https://ana
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
> order
> it should work.
&
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.
Peter
On Mon, M
Hi Jochen,
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 filenam
> Is it correct ?
>
> Thanks again Peter.
>
> Olivier
>
>
>
> Olivier INIZAN
> olivier.ini...@inra.fr
> Unité Mathématiques & Informatique Appliquées du Génome à l'Environnement
> Plateforme bioinformatique Migale
> Bâtiment 233
> Domaine de Vilvert
>
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 Pyt
It sounds like it could be this issue?:
https://github.com/galaxyproject/planemo/issues/530
If so, the good news is there is a workaround (see issue discussion).
Peter
On Wed, Jan 17, 2018 at 4:24 PM, Olivier Inizan wrote:
> Dear list,
>
> I am trying to write a test with a param type "select"
I infer you are talking about this Tool Shed repository:
https://toolshed.g2.bx.psu.edu/view/fabad/sparql_uniprot/
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.
Based on https://toolshed.g2.bx.ps
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.
https://github.com/galaxyproject/galaxy/pull/3095
https://github.com/galaxyproject/galaxy/pull/3099
Peter
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.
Peter
On Fri, Sep 22, 2017 at 2:41 PM, Pavel Fibich wrote:
> Hi Hans-Rudolf and Peter,
>
> thank you f
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?
datatypes
On Thu, Sep 21, 2017 at 12:50 PM, SAPET, Frederic <
frederic.sa...@biogemma.com> wrote:
> 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
aring your ideas :)
>
>
>
> Fred
>
> De : Laure QUINTRIC [mailto:laure.quint...@ifremer.fr]
> Envoyé : mercredi 13 septembre 2017 13:54
> À : Peter Cock ; SAPET, Frederic
>
>
>
> Cc : Galaxy-dev
> Objet : Re: [galaxy-dev] Displaying tool select list according
;
>
>
> Fred
>
>
>
> *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
> *Cc :* Galaxy-dev
> *Objet :* Re: [galaxy-dev] Displaying too
Hi Laure,
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 si
Galaxy itself uses samtools for many operations, which is different
from when samtools is called as a dependency of a tool run by the
Galaxy user.
However, the Docker image ought to take care of that - can you
give more details of which Docker image you are using (URL,
version, etc)?
Thanks,
Pet
Hi David,
Daniel Blankenberg wrote one (CC'd):
https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blastdb
http://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_example_blastdb_ncbi_update_blastdb
I've never used it in production and don't have enough understanding
ound 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
>
> Peter
>
>
&g
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,
Peter
On Wed, Aug 9, 2017 at 2:52 PM, Peter Briggs
wrote:
> Dear devs
>
> I've been updati
n sets. Each set is represented by entries in a column e.g.
>
> #SET1 SET2 SET3
> A GA
> B HB
> C AG
> D BH
> E CX
> F DZ
>
> I hope this helps.
>
> Thanks
> Sam
>
Hi Steven,
Just in case, you're not talking about my older simpler Galaxy Tool
for drawing simple Venn Diagrams, are you?
https://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list
This reminds me that I ought to update that tool to w
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!
Peter
On Wed, Jul 12, 2017 at 4:24 PM, Peter Cock wrote:
> Good idea, pull request submitted:
>
> https://github.com/galaxyproject/pla
--help.
>
> Best,
> Matthias
>
>
> On 12.07.2017 16:57, Peter Cock wrote:
>>
>> Try:
>>
>> planemo lint --fail_level error sleepwaste.xml
>>
>> The default is to fail if there are warnings.
>>
>> Peter
>>
>>
>> On Wed, Jul
Try:
planemo lint --fail_level error sleepwaste.xml
The default is to fail if there are warnings.
Peter
On Wed, Jul 12, 2017 at 3:55 PM, Matthias Bernt wrote:
> Hi Peter,
>
> I just call planemo l sleepwaste.xml
>
> Best,
> Matthias
>
>
> On 12.07.2017 16:54, Pete
How are you running planemo lint - in particular is it set
to fail if there are any warnings present (like your missing
citation warning)?
Peter
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 tool for
> galax
#x27;'.join( x if x in ( string.ascii_letters + string.digits
> + '_' ) else '_' for x in job_name )
> if self.restrict_job_name_length:
> job_name = job_name[:self.restrict_job_name_length]
> return job_name
>
> -Raj
>
>&g
ELEPHONE="en_US.iso885915"
> LC_MEASUREMENT="en_US.iso885915"
> LC_IDENTIFICATION="en_US.iso885915"
> LC_ALL=
>
> I will talk to our sysadmin and see if I can change the locale to en_US.UTF-8.
>
> Thank you very much.
> -Raj
>
>
>> O
nfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
> line 132, in queue_job
> job_name = self._job_name(job_wrapper)
> File
> "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
> lin
Time for more debugging, try inserting something like this inserted
the line above into
/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py
(having backed up the file):
log.debug( 'Making job_name, tag was %r, plan to use %r with
underscores replacements' % (g
On Wed, Mar 20, 2013 at 3:51 PM, Peter Cock wrote:
> On Mon, Apr 30, 2012 at 4:47 PM, Nate Coraor wrote:
>> On Apr 25, 2012, at 9:39 AM, Louise-Amélie Schmitt wrote:
>>
>>> Hi everyone,
>>>
>>> I just wanted to ask how the extra_file_path is handled i
BLAST+ 2.5.0.
Peter
On Wed, Apr 19, 2017 at 1:17 PM, Peter Cock 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.
>
> For blast_rbh just nee
idea because of backward
> compatibility?
>
> Cheers,
> Matthias
>
>
>
>
>
> 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/d8d9a9069586
> >
he update, but since I have a
> method that is working for the moment there is no need to hurry.
>
> Best,
> Matthias
>
>
>
> On 19.04.2017 12:57, Peter Cock wrote:
>>
>> Oh right - I've just been updating ncbi_blast_plus this morning
>> to transition to
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.
Peter
On Wed, Apr 19, 2017 at 11:52 AM, Matthias Bernt wrote:
>
This just went live on the main tool shed:
https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/
You can report issues here or on GitHub at:
https://github.com/peterjc/galaxy_blast/issues
Thanks,
Peter
On Thu, Dec 8, 2016 at 11:35 AM, Peter Cock wrote:
> Hello all,
>
> I hav
bioinformatics
software development and open science in the biological research
community (like the Galaxy Community Conference).
http://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/
https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md
Regards,
Peter
(Dr Peter Cock, OBF
urer.
On Wed, 8 Mar 2017 at 18:05, Peter Cock 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,
>
> Peter
>
> Dr. Peter Cock,
> B
il
> aliases? I would need to ask our cluster admins if they could realize this.
>
> Best,
> Matthias
>
>
>
> 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.
Peter
On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt wrote:
> Dear list,
>
> I'm just star
Hi Bryan,
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,
https://docs.galaxyproject.org/en/master/admin/conda_faq.html
Newer dependencies will likely next get an old fashioned package
on
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,
Peter
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,
>
> Martin
>
> On Wed, Mar 8, 2017 at 7:39 AM Peter Cock wrote:
>>
>> Galaxy was originally distributed via the mercurial (hg) version
>> control system, later the git version control
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
changeset: 17125:e837a68e8d14
tag: tip
parent: 17121:7a4e3a661a76
parent: 17124:46a4
ly 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
> step it is converted to bigwig.
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
auto
017 at 11:20 AM, Peter Cock 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, and thus am using pip
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.
> My galaxy install
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:
>
> https://github.com/marten
Hmm. I wonder if a composite datatype would work here?
https://wiki.galaxyproject.org/Admin/Datatypes/Composite%20Datatypes
Peter
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
> example the file format b
.
>
> Thank you
>
> Eduardo
>
> On 01/02/2017 10:10, "Peter Cock" wrote:
>
>
> Hi Eduardo,
>
>
> Certainly when Luobin Yang submitted the early work on the
> PSI BLAST wrapper we need the PSSM datatype to be defined,
> but as you note, tha
On Wed, Feb 1, 2017 at 9:46 AM, Peter Cock 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
>
> or:
>
> preserve_python_environment = a
ou to remove psiblast from blacklist in
> your repository?
>
> https://github.com/peterjc/galaxy_blast/blob/13d5b6deca0663d7f1301428574720
> b19aea1380/.tt_blacklist
>
>
> Thank you
>
> Eduardo
>
>
> On Tue, Feb 5, 2013 at 4:28 PM, Peter Cock <[hidden email]>
ere is a config option that is documented
> pretty well in the PR but I missed named it in the sample (fixing it with
> https://github.com/galaxyproject/galaxy/pull/3521/files).
>
> Hopefully this helps and thanks for the bug report!
>
> -John
>
>
> On Tue, Jan 31, 2017 at
org/bioconda/galaxy_sequence_utils
>
> Cheers,
> Nicola
>
>
> 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 external dependency. Lat
Hi all,
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):
e.g.
https://travis-ci.org/peterjc/p
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.
https://github.com/galaxyproject/galaxy/blob/dev/config/job_metrics_conf.xml.sample
I've never used it, but perhaps the backend using Collectl
(http://collec
Hi Katherine,
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 Galax
Hello Mohamed,
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 databa
Hello all,
I have updated the NCBI BLAST+ wrappers on the Test Tool Shed,
the wrapper is now at v0.2.00:
https://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/
The main changes is this now depends on BLAST+ 2.5.0, and that is
available via either BioConda or the Tool Shed:
https://too
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,
https://wiki.galaxyproject.org/Admin/GetGalaxy
just points at
https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies
Whi
On Wed, Nov 23, 2016 at 10:49 AM, Peter Briggs
wrote:
> 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 relatively straightforward.
>
>
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:
https://github.com/galaxyproject/galaxy/
alaxyproject/galaxy-site.
>
> -Dannon
>
> On Tue, Nov 15, 2016 at 10:06 AM, Peter Cock
> wrote:
>>
>> Hello all,
>>
>> Is there a specific issue tracker for the wiki? It seems wrong to
>> open an issue on the main GitHub code repository...
&
Hello all,
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
Problem pages inc
quot;" />
>
> This tool is not the one trying to be installed.
>
> Thanks,
> Miuki
> On Nov 3, 2016, at 10:28 AM, Peter Cock
> mailto:p.j.a.c...@googlemail.com>> wrote:
>
> I think you may have hit the same bug I found recently:
>
> https://gith
I think you may have hit the same bug I found recently:
https://github.com/galaxyproject/galaxy/issues/3084
What is line 44 of your integrated_tool_panel.xml file?
Peter
On Thu, Nov 3, 2016 at 2:16 PM, Yip, Miu ki wrote:
> Hi all,
>
> While trying to install tools from the toolshed via the bro
You might find this work useful for fetching bacteria from the NCBI:
https://github.com/kblin/ncbi-genome-download
Peter
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 to repair and
> updat
Hi Steve,
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
myself.
Peter
On Fri, Oct 21, 2016 at 8:
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.
https://github.com/galaxyproject/tools-iuc/blob/master/tools/trinity/run_de_analysis.xml
Hi Pierre,
The first example looks OK, very similar to this one of mine for example,
so I am not sure what is breaking:
https://github.com/peterjc/pico_galaxy/blob/133aea82c02adf5509134c415565ada99c519312/tools/effectiveT3/tool_dependencies.xml
I would try adding more shell actions to debug this
This is an annoyance from the NCBI team, and dealing with the
expired tbl2asn tool is a regular question from Prokka users, eg:
https://github.com/tseemann/prokka/issues/96
https://github.com/tseemann/prokka/issues/139
The Tool Shed package for Prokka will need updating - but
luckily Nicola is al
I just found this old email by a very similar exception logged as:
https://github.com/galaxyproject/galaxy/issues/2987
There do seem to be some corner cases where missing default
values are not handled nicely.
Peter
On Tue, Jan 26, 2016 at 2:38 PM, Matthias De Smet
wrote:
> Wow, great tip! Th
sing 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.
>
> Thanks!
>
> On Fri, Oct 7, 2016 at 2:06 AM,
Hi DK,
Looking at your XML that looks OK.
It might not be important, but how exactly are you running planemo
test?
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:
https://
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