allow a
> remote root login, which is correct. There are SSH ways to accomplish the
> same thing, but depend on trust at both ends. The defaulting by Ansible is
> reprehensible, but usually should be expected to fail.
>
>
> On Mon, Feb 15, 2021 at 5:15 AM Peter van Heusden wrote:
>
Hi there
I found I had this problem too, when the `become: true` applied to the
whole Galaxy play. My current top level playbook (at
https://github.com/pvanheus/masters_galaxy_ansible/blob/master/galaxy.yml#L25)
now applies `become: true` as it is needed, and does not apply it to the
g the tool directories for changes is enabled. In certain cases this
can lead to an exception.
Peter
On Tue, 11 Dec 2018 at 17:15, Peter van Heusden wrote:
> Hi there
>
> I'm trying to run Windowmasker in Galaxy and receiving the following error:
>
> "computing the genome length
Hi there
I'm trying to run Windowmasker in Galaxy and receiving the following error:
"computing the genome length
pass 1
pass 2
optimizing the data structure
Traceback (most recent call last):
File
"/tools/software/galaxy/galaxy1/database/jobs/006/6476/set_metadata_bUlLkt.py",
line 1, in
Hi there
While I will continue to work on getting a Cloudlaunch server running
locally, could the Ilifu cloud (http://www.ilifu.ac.za/) be added as an
option on https://launch.usegalaxy.org/catalog ? What details would be
required?
And then - what are the requirements for adding appliances to
questions, as I can
> get more answers in person and relay them to you.
>
> Best,
> Alex Mahmoud
>
>
> On Oct 18, 2018, at 3:45 PM, Peter van Heusden wrote:
>
> Hi there
>
> I'd like to set up cloudlaunch to be able to set up on-demand Galaxy
> servers and associa
I don't have an answer to your 2. but Galaxy Kickstart sets up Galaxy
controlled by supervisord. So you can restart e.g. the Galaxy web front end
with:
sudo supervisorctl restart galaxy:galaxy_web
On Tue, 16 Oct 2018 at 08:16 Rui Wang wrote:
> Hi Folks,
>
> I spent sometime playing with the
Hi there
I'd like to set up cloudlaunch to be able to set up on-demand Galaxy
servers and associated clusters on the new Ilifu OpenStack cloud. From
looking around the repositories it looks like Cloudlaunch is at least 2
components:
1. The cloudlaunch server
2. The UI - either cloudlaunch-ui or
Hi there
I had a failed updated (network problem) of the sanbi-uwc tool
vcf_to_alignment and now when I try and do an update I get:
$ planemo shed_update --shed_target testtoolshed
cd '/home/pvh/Documents/code/SANBI/tools-sanbi-uwc/tools/vcf_to_alignment'
&& git rev-parse HEAD
cd
umentation is here ;)
>
> https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L484
>
> Also the Docker compose image is can also use Singularity if you want to
> reverse engineer it :)
>
> Ciao,
> Bjoern
>
> Am 19.09.2018 um 10:12 schrieb
Hi there
Is it possible to use Singularity images to resolve dependencies in Galaxy
18.05? If so is there documentation somewhere?
I have a Galaxy server where for at least some of the dependencies conda
will not be a good option so I would like to be able to use singularity if
at all possible.
ODO entry here:
>
>
> https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#data-managers
>
> Peter C.
>
> On Mon, Sep 17, 2018 at 10:56 PM Peter van Heusden
> wrote:
>
>> A bit more tracing leads me to suspect that what is happening is that
, 17 Sep 2018 at 13:23 Peter van Heusden wrote:
> Thanks - which is probably because of the previous failures with
> `shed_update` - which relate back to the topic of my original email. I
> suspect that failure from `planemo shed_update` has led to this "not
> installable" s
at revision 5 and 6 are not installable, they both
> have "*This revision can be installed:* False" . If you instead select
> revision 3 it is installable.
>
> Cheers,
> Nicola
>
>
> On 17/09/18 11:51, Peter van Heusden wrote:
>
> I'm following up on my previous emai
server perhaps caching something?
Peter
On Sat, 15 Sep 2018 at 09:57 Peter van Heusden wrote:
> Hi there
>
> I'm working on a data manager to keep track of the reference data
> collection used by the SHAPEIT2 tool. I had to add a column to the data
> manager but when I try an
It is rather too unwieldy to paste here.
Note that while the says [program:web], there is only one section in the
supervisord configuration. The server is running in a uWSGI + Mules
configuration.
Thanks!
Peter
On Mon, 19 Mar 2018 at 11:17 Peter van Heusden <p...@sanbi.ac.za> wrote:
> First
were some last minute bugfixes to the
> release_18.01
> prior to the release, so if the checkout is a few days old an upgrade (and
> an uninstall/install cycle) might help.
>
> Also you mentioned the lack of the upload_store in nginx in nginx, you
> need to install nginx-extras, not nginx.
&g
Hi there
My newly installed Galaxy 18.01 server seems to be unable to install bowtie
(the devteam version). I'm documenting my installation progress at:
http://pvh.wp.sanbi.ac.za/2018/03/18/galaxy-18-01-install/
As noted in the last paragraph:
"My next test was to try and install the bowtie2
.
> >> 2. Not doing this greatly increases the number of emails that match
> >> search queries, but that aren't actually informative.
> >>
> >> Today's Topics:
> >>
> >> 1. Re: any introduce for how Mako and JavaScript work ingalaxy?
&
On Sat, 8 Jul 2017 at 11:56 Matthias Bernt wrote:
> Hi Peter,
>
> > Code looks interesting. This is for Univa Grid Engine?
>
> In its current state its tailored for the Univa Grid Engine. But the drmaa
> library code that is based on job_info() and wait() should run on all grid
>
Code looks interesting. This is for Univa Grid Engine?
In terms of the upload jobs, are those not designed to be run as 'local'
jobs and not with the 'real user' setting?
On Fri, 7 Jul 2017 at 17:32 Matthias Bernt wrote:
> Dear list,
>
> I have implemented a new DRMAA job
Hi there
Is there current "best practice" for maintaining a collection of reference
genome data in a Galaxy server? I.e. filling in the dbkeys.loc and
all_fasta.loc table and associated data. I know of the following
discussions on this topic:
1. The data integration page:
Hi there
We've got a composite datatype (neostore) for Neo4j databases. Currently
the upload is disabled because to upload you need to select each individual
file of the database directory (which is tedious). Is there a more
efficient way to upload composite datatypes? E.g. as a tar.gz or zip
Hi there
I'm trying to add a wrapper for the vcftools vcf-consensus tool. There is
an existing tool collection for vcftools in tools-devteam, so I'm add it
there. Wrapper is at:
https://github.com/pvanheus/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus
I tested this
Hi
Galaxy supports visualisation plugins and then it also supports interactive
environments. I don't know how WEKA VisualizaPanel works - is it a web
application? Does it require a server?
On Fri, 26 Aug 2016 at 20:52 Lijo John wrote:
> Hello All,
> I want to know,
Hi everyone
We maintain a tools collection on Github for tools that are not yet (or
will never be) added to tools-iuc:
https://github.com/SANBI-SA/tools-sanbi-uwc
I tried copying the .travis.yml from tools-iuc to our repository, and it
largely works, except for the planemo upload part, which
You mean the stuff for the tool-data tables? As I understand it, it is
loaded in:
lib/galaxy/tools/data/__init__.py
There's a ToolDataTableManager and a TabularToolDataTable (with associated
TabularToolDataField).
Peter
On Fri, 5 Aug 2016 at 20:46 Katherine Beaulieu <
Hi there
Does anyone have the run-as-user support working with Galaxy 16.04? If so,
could you describe your config?
Thanks,
Peter
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your
Actually, for recent Galaxy, I'd recommend making a conda recipe for
UMI-tools and contributing it to bioconda:
https://bioconda.github.io/
Then your tool can just depend on this and the conda dependency resolver
(default in Galaxy since 16.01) can find it. Others can comment on the
recent work
Hi there
I'm trying to satisfy requirements on our RNA-seq oriented Galaxy server at
SANBI using conda/bioconda. There's a disconnect between the names used in
tool dependency tags and the names of conda recipes though, for example:
1) the BAM to BigWig converter (tool ID
Hi Katherine
I presume this is related to the tool described here (
https://biostar.usegalaxy.org/p/18319/)? I think there is general interest
in the creation of a tool like this - see the recent email from Miu ki Yip.
If you could share the code and XML (e.g. via GitHub) perhaps we could
assist
Hi Miuki
There's two aspects to iRODS and Galaxy. Firstly, there is the Galaxy
object store which can store objects in iRODS. This is entirely hidden from
the user and they have no idea that their datasets are in iRODS. Some work
on that happened earlier in this year, see:
Hi there
I've got a package in our lab conda channel (its still in testing phase)
called goget. This is specified as a requirement for the build_ctb_gene
tool like this:
goget
When the tool runs, I see infinite recursion on the conda side:
June 2016 at 15:53, Björn Grüning <bjoern.gruen...@gmail.com> wrote:
> Me finishing my re review and pressing the merge button.
> I tend to merge as it is at the moment and do some small adjustments
> afterwards ... This weekend Peter, this weekend! :)
>
> Am 03.06.2016 um 13
PR #429 on tools-iuc contains the updated MOTHUR toolsuite for Galaxy.
https://github.com/galaxyproject/tools-iuc/pull/429
It *looks* like it is ready to merge - what is still needed before it
merges into tools-iuc?
Thanks!
Peter
___
n program to log cpu% and memory of
> another executable, then analyze.py might do. Its in
> https://github.com/Public-Health-Bioinformatics/kipper/tree/master/RDP-test
> -case along with a few scripts that show examples of its use.
>
> Damion
> >>
> >> On 02
lob/master/tools/splitfasta/splitFasta.xml
>
> Cheers,
> Bjoern
>
> Am 18.03.2016 um 20:03 schrieb Peter van Heusden:
> > Hi there
> >
> > I'm trying to update a newly created tool on the test tool shed and I
> > get this error:
> >
> > $ planemo shed_updat
Hi there
I'm trying to update a newly created tool on the test tool shed and I get
this error:
$ planemo shed_update -t testtoolshed
cd '/home/pvh/PycharmProjects/split_fasta_chunks' && git rev-parse HEAD
cd '/home/pvh/PycharmProjects/split_fasta_chunks' && git diff --quiet
Could not update
ily.
>
> https://github.com/erasche/galactic-radio-telescope
>
> I'd be very, very interested in finishing this project up.
>
> Cheers,
> Eric
>
>
> On 02/21/2016 11:13 PM, Peter van Heusden wrote:
>
> Hi there
>
> We're researching the resource (CPU time and
Hi there
We're busy integrating novoalign in our local Galaxy - there doesn't seem
to be a tool around for this, but I recall some people saying they were
using (single threaded) novoalign with Galaxy. Does anyone know if tool XML
has already been written? If not, we'll just have to write it.
>
> Re the failing install of 'package_perl_5_18', I've investigated further
> now and have submitted a patch which seems to fix the problem:
>
> https://github.com/galaxyproject/tools-iuc/pull/616
>
> Not sure if this is of any immediate help,
>
> Best wishes
>
>
Ok, second attempt, perl install died with the same error, so I suspect
you're right about the cause. Eric?
Peter
On 22 February 2016 at 11:41, Peter van Heusden <p...@sanbi.ac.za> wrote:
> Thanks Peter
>
> I managed, on the second attempt, to get past the gnu coreutils problem.
Hi there
I see from the PR landing in Galaxy and the comments on things like
issue #1701 (https://github.com/galaxyproject/galaxy/issues/1701) that
there's lots of work happening on the workflow side of Galaxy. This is an
area of interest at SANBI too, so we'd like to coordinate development
Hi there
We're researching the resource (CPU time and memory) requirements for RNA
STAR at the moment. Specifically, we'd like to build up a database of input
size to resource usage so that we can use this to feed a dynamic
destination mapper (currently our STAR configuration uses a thumbsuck for
Mattias, what does your supervisord config look like? Specifically, does it
contain an environment variable to direct the Galaxy handler to the correct
virtualenv?
Peter
On 9 February 2016 at 16:03, Matthias De Smet
wrote:
> Hi all,
>
>
> We were tracking the galaxy
rlying Galaxy infrastructure when using the head of the dev branch).
>
> Best wishes
>
> Peter
>
>
> On 22/01/16 13:53, Peter van Heusden wrote:
>
>> Hi there
>>
>> I've got Trimmomatic installed (from the toolshed) into our local Galaxy
>> server (server is la
t; (Btw this referenced above used planemo 0.22.2 but I've seen it in older
> versions too.)
>
> I don't think I've ever seen planemo report a 'passed' test as 'failed',
> but generally I check the HTML to verify whether the failures are real or
> not.
>
> Best wishes
>
>
and JavaScript could be used to
> build up the tables in
> templates/webapps/tool_shed/repository/common.mako.
>
> -John
>
>
> On Mon, Feb 1, 2016 at 11:51 AM, Peter van Heusden <p...@sanbi.ac.za>
> wrote:
> > Hi there
> >
> > Zipho and I'd would li
Galaxy implements the job manager using rabbitmq and celery? Surely you
mean Galaxy *does not* implement celery (at this point). As far as I know
it is planned for the future.
Peter
On 25 January 2016 at 15:37, 杜云飞 wrote:
> Hi,
> We are reading the source code for galaxy
Hi there
I've got Trimmomatic installed (from the toolshed) into our local Galaxy
server (server is latest commit on the dev branch from GitHub). It refuses
to see a dataset pair as a valid input, however.
I've tested this with two types: firstly a pair made out of 2 individual
datasets (both
Hi there
We've just finished provisioning a new Galaxy server here using the
ansible-galaxy and ansible-galaxy-extras roles, with some extra roles from
Nate and our own creation. In the ansible-galaxy role Galaxy's install
location is set using the galaxy_server_dir variable, but in
Hi there
I'm trying to understand how the job metrics configuration works. Reading
through various examples, it looks like it works together with the dynamic
destination support.
First on the dynamic destination support, this works, as I understand it,
by importing modules (files ending in .py)
ented than other stuff I have done that also hasn't been
> documented :|.
>
> -John
>
> On Mon, Jan 11, 2016 at 1:56 PM, Peter van Heusden <p...@sanbi.ac.za>
> wrote:
> > Hi there
> >
> > I'm trying to understand how the job metrics configuration works. Read
Hi Makis, I recently implemented something like this using uWSGI with a
nginx frontend. Would you consider using uWSGI instead of your current
approach?
On 4 Dec 2015 09:40, "Makis Ladoukakis" wrote:
> Sorry for bumping my own question but I didn't get any replies. Has
I've written up my experiences in a blog:
http://pvh.wp.sanbi.ac.za/2015/12/04/faster-galaxy-with-uwsgi/
The only Galaxy side changes were the ones mentioned on the Scaling page.
The Bad Gateway message means that Apache can't talk to the uWSGI so what
is the state of uWSGI?
Are you using
hough I'm not really sure what the difference is
> between __name__ and __designation__. They both seem to have the same
> effect in my example.
>
> Thanks for your help.
>
> Steve
>
>
> On 21 October 2015 at 16:49, Peter van Heusden <p...@sanbi.ac.za> wrote:
>
>&
Just a quick check - did you refresh your history to confirm that the
dataset *is* empty? We had the same thing at SANBI but it turns out that
Galaxy creates an empty output collection and then only populates it
sometime after job completion (this is a know UI bug).
See:
..@mq.edu.au> wrote:
> Thanks Peter,
> I did see that proviso somewhere but no, refreshing doesn't help.
>
> That page was one of those that I referred to getting to this point.
>
> Steve
>
> On 20 October 2015 at 18:33, Peter van Heusden <p...@sanbi.ac.za&
ust an example of a tool that works - the file that it
> writes out is put into that directory, so I assume that's where my files
> should end up too.
>
> Steve
>
> On 20 October 2015 at 21:12, Peter van Heusden <p...@sanbi.ac.za> wrote:
>
>> Sorry, I don't understand -
/2bbbf7f361ada20bf1b5bd777fae6e0cb52c4a38
Thanks,
Peter C.
On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden p...@sanbi.ac.za
wrote:
Hi there
I'm trying to use the blastp tools from the ncbi_blast_tools, but
every
time
I try and run a job I get the following error
Hi there
I'm trying to use the blastp tools from the ncbi_blast_tools, but every
time I try and run a job I get the following error:
Traceback (most recent call last):
File /net/
datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/lib/galaxy/jobs/runners/__init__.py,
line 163, in
Hi Lionel
Sounds like Galaxy does not know what format your FASTQ file is. When you
click on it, what format does it show? Is it simple fastq? And how did you
get it into Galaxy?
You might need to manually specify the format by clicking on the Edit
Attributes button (the pencil icon) and select
/master/tools/jbrowse
Developed by IUC member Eric Rasche.
Cheers,
Bjoern
On 18.06.2015 10:00, Peter van Heusden wrote:
I've tried that - I've added the Environment Modules for the relevant
tools to the local_env.sh file, so they're there in the environment when
Galaxy runs. These tools
Wow that's a lot of upstreams... what is your Galaxy configuration?
On 26 November 2014 at 20:26, Nicholas Kline nx...@case.edu wrote:
Hi,
I am trying to setup a local production Galaxy running on Ubuntu,
Nginx, PostgreSQL, and ProFTD.
When visiting http://localhost, 502 Bad Gateway is
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