ices will not 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 Heus
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
`galaxyprojec
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
f
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 the
amount of time to your other 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-dem
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 kic
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 c
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 '/home/pvh/Docum
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
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 previou
alaxy 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 whe
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 and do a `planemo shed_update` I get the error:
Unexpected HTTP status code: 500: {"err_msg": "Error attempting to parse
file t
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 wrote:
> First to answer your q
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 to
I'm trying to use HISAT2 using a Docker-ized Galaxy
(bgruening/galaxy-rna-seq:dev - Galaxy 17.05). I installed the HISAT2 index
builder from the toolshed and built an index for the dm3 genome (resulting
in an index in /galaxy-central/tool-data/dm3/hisat2_index/dm3). When I try
and run HISAT2 with t
rip out everything else in the digest that is not part of the
> >> thread you are responding to.
> >>
> >> Why?
> >> 1. This will keep the subject meaningful. People will have some idea
> >> from the subject line if they should read it or not.
&g
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
> engines.
> For t
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 runner allows to detec
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:
https://galaxyproject.or
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 file
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 using
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, whether it is possible to emb
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 fail
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 <
katherine.beaulieu...@gmai
Hi there
Does anyone have the run-as-user support working with Galaxy 16.04? If so,
could you describe your config?
Thanks,
Peter
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Hi Ulf
What job runner are you using for your setup?
On Fri, 15 Jul 2016 at 10:32 Ulf Schaefer wrote:
> Hi Hans-Rudolf
>
> That was the first thing that came to my mind as well.
>
> But by default you don't seem to get a "job_conf.xml". You just get
> "job_conf.xml.sample_advanced" and "job_con
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 o
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 CONVERTER_bam_to_bigwig_
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 w
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:
https://wiki.galaxyproj
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:
https://gist.github.com/pvanheus/c16a0
On 3 June 2016 at 15:53, Björn Grüning 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 13:37 schrieb Peter van Heu
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
___
Please
emory 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 02/21/2016 11:13 PM, Peter van Heusden
a.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_update -t testtoolshed
> &g
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 split
arily.
>
> 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
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.
Pet
ll 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
>
> Peter
>
> O
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 wrote:
> Thanks Peter
>
> I managed, on the second attempt, to get past the gnu coreutils problem.
> Zipho notic
e removal of
> this line addresses the problem.
>
> I don't think I've seen the problem with 'package_gnu_coreutils_8_22' that
> you describe however so it may be that my hypothesis is not correct.
>
> HTH
>
> Best wishes
>
> Peter
>
>
>
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
effort
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
Hi there Eric and others
I tried to install the JBrowse tool on a dev branch server running on an
Ubuntu 14.04 VM.
It got stuck at the package_gnu_coreutils_8_22 dependency (revision
ac64dfe4b1fb)
- this ended up in "Installing tool dependencies" state.
If I go look at the tool details it highli
Hi Ray
Data Managers are designed to co-exist with manually editing the .loc
files. So don't worry, edit away.
Peter
On 18 February 2016 at 10:00, Raymond Wan wrote:
> Hi Hans-Rudolf,
>
> Thank you for getting back to me!
>
> I did take a peak at those files and they seem self-explanatory. I
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 master branch on our local s
(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.
>
y 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 l
t 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
> wrote:
> > Hi there
> >
> > Zipho and I'd would like to make some changes to the admin
Hi there
Zipho and I'd would like to make some changes to the admin pages, including
the tool info page and the local data page. These are currently rendered
from mako templates - should we change these or is the interface going to
be rewritten in client side / javascript in the near(ish) future?
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 job manager. We found
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 fas
Since ansible
> doesn't provide any ability to write tests, I'm pretty sure I'd
> universally encourage people not to use it as a long running
> configuration management technology - but obviously I don't speak for
> the project on that topic since it is used extensiv
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
ansible-galaxy
tion does worry me - what it does to persisted job state and
> parameter handling is fairly hacky and I'm somewhat surprised we
> haven't encountered more problems. This is part of the reason not why
> this hasn't been documented, but why I feel less bad that it hasn't
> bee
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) f
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 superv
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 anyone
> succesfully instal
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 wrote:
>
>> Since you're using a di
le 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 wrote:
>
>> Sorry, I don't understand - what does the Upload F
idy 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 wrote:
>
>> Just a quick check -
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:
http://pvh.wp.sanbi.ac.za/
> >>
> >> My guess is that since this used to be .extra_files_path perhaps your
> >> Galaxy is too old for .files_path to work?
> >>
> >>
> https://github.com/peterjc/galaxy_blast/commit/2bbbf7f361ada20bf1b5bd777fae6e0cb52c4a38
> >>
> >&g
8
>
> Thanks,
>
> Peter C.
>
> On Tue, Jul 21, 2015 at 3:08 PM, Peter van Heusden
> 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 pre
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 t
rote:
> Peter,
>
> I'm in a hurry ... have a look at
> https://github.com/galaxyproject/tools-iuc/tree/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
pend on these Galaxy
packages, however, and those (bedtools and ucsc-utils) are now installed,
so I'm not sure why it can't pick them up from the shed_tools.
On 18 June 2015 at 09:10, Hans-Rudolf Hotz wrote:
>
>
> On 06/18/2015 09:06 AM, Peter van Heusden wrote:
>
>> Hi
Hi there
I'm trying to visualise some of our genome data using Trackster. Initial
input is 790,000 lines of GFF3. When I try and create the visualisation, I
get errors from two tools:
Convert GFF to Interval Index on data 3
-- an out of memory error - I'll try and fix this by upping the memory
l
Your nginx server doesn't seem to be listening on the HTTPS port, you need
this in the server config:
listen 443 default ssl;
Here's the relevant part of the Galaxy setup I have over here:
upstream galaxy_app {
server localhost:8080;
}
# redirect http to https
server
Wow that's a lot of upstreams... what is your Galaxy configuration?
On 26 November 2014 at 20:26, Nicholas Kline 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 returned.
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