[galaxy-dev] Re: Ansible Galaxy using root user for role installation

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: >

[galaxy-dev] Re: Ansible Galaxy using root user for role installation

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

Re: [galaxy-dev] _remove_dead_weakref error even after deleting .venv (Galaxy 18.09)

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

[galaxy-dev] _remove_dead_weakref error even after deleting .venv (Galaxy 18.09)

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

[galaxy-dev] Adding the Ilifu cloud to launch.usegalaxy.org

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

Re: [galaxy-dev] Running Cloudlaunch against a new OpenStack cloud

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

Re: [galaxy-dev] regarding galaxy kickstart

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

[galaxy-dev] Running Cloudlaunch against a new OpenStack cloud

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

[galaxy-dev] Error when trying to update tool vcf_to_alignment in testtoolshed

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

Re: [galaxy-dev] Using Singularity images to resolve dependences in Galaxy 18.05

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

[galaxy-dev] Using Singularity images to resolve dependences in Galaxy 18.05

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.

Re: [galaxy-dev] "Merging tabular data tables with non-matching columns is not allowed"

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

Re: [galaxy-dev] "Merging tabular data tables with non-matching columns is not allowed"

, 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

Re: [galaxy-dev] "Merging tabular data tables with non-matching columns is not allowed"

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

Re: [galaxy-dev] "Merging tabular data tables with non-matching columns is not allowed"

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

Re: [galaxy-dev] Problems installing Galaxy 18.01

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

Re: [galaxy-dev] Problems installing Galaxy 18.01

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

[galaxy-dev] Problems installing Galaxy 18.01

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

Re: [galaxy-dev] Improved DRMAAJobRunner (Peter van Heusden)

. > >> 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? &

Re: [galaxy-dev] Improved DRMAAJobRunner (Peter van Heusden)

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 >

Re: [galaxy-dev] Improved DRMAAJobRunner

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

[galaxy-dev] "Best practice" for maintaining genome list in Galaxy

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:

[galaxy-dev] composite datatypes: uploading and optional files

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

[galaxy-dev] Perl module problem with vcftools in conda + new tool

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

Re: [galaxy-dev] Loading a GUI on galaxy

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,

[galaxy-dev] Travis CI for Galaxy repositories?

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

Re: [galaxy-dev] Parameter Storing in Database

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 <

[galaxy-dev] run-as-user and Galaxy 16.04

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

Re: [galaxy-dev] Building tool dependencies

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

[galaxy-dev] Mapping requirements to conda recipe names (granularity?)

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

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

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

Re: [galaxy-dev] Implementing iRODS with Galaxy

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:

[galaxy-dev] Infinite recursion on conda dependency manager

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:

Re: [galaxy-dev] The state of the MOTHUR merge?

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

[galaxy-dev] The state of the MOTHUR merge?

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 ___

Re: [galaxy-dev] Scaling tools: data available? (Peter van Heusden)

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

Re: [galaxy-dev] planemo update failing on testtoolshed

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

[galaxy-dev] planemo update failing on testtoolshed

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

Re: [galaxy-dev] Scaling tools: data available?

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

[galaxy-dev] novoalign in Galaxy

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: [galaxy-dev] Broken package_perl_5_18, was Re: JBrowse on dev branch: progress

> > 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 > >

Re: [galaxy-dev] JBrowse on dev branch: progress

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.

[galaxy-dev] Plans for workflow & parallelisation work?

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

[galaxy-dev] Scaling tools: data available?

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

Re: [galaxy-dev] Galaxy broken after update to 16.01

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

Re: [galaxy-dev] Trimmomatic doesn't recognise pair collection

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

Re: [galaxy-dev] planemo reports test failure when test succeeds

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 > >

Re: [galaxy-dev] Working on the admin interface: JS vs Mako

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

Re: [galaxy-dev] galaxy job manager with celery and rabbitmq

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

[galaxy-dev] Trimmomatic doesn't recognise pair collection

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

[galaxy-dev] Ansible roles: galaxy_server_dir vs galaxy_home_dir and galaxy_root

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

[galaxy-dev] Job metrics configuration

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)

Re: [galaxy-dev] Job metrics configuration

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

Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

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

Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

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

Re: [galaxy-dev] Tools that make datasets

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: > >&

Re: [galaxy-dev] Tools that make datasets

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:

Re: [galaxy-dev] Tools that make datasets

..@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&

Re: [galaxy-dev] Tools that make datasets

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 -

Re: [galaxy-dev] Failure when preparing job on blastp

/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

[galaxy-dev] Failure when preparing job on blastp

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

Re: [galaxy-dev] Troubleshooting

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

Re: [galaxy-dev] Adding packages for bedtools and ucsc-utils for Trackster?

/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

Re: [galaxy-dev] Nginx Config

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