[galaxy-dev] Removing set_metadata_externally from wiki documentation?

Hello all, We're currently looking at changing our Galaxy setup to link user accounts with Linux user accounts for better cluster integration (running jobs as the actual user on SGE). As part of this, we've tried setting up a fresh installation on a new VM which has thrown up some issues. First o

Re: [galaxy-dev] errors installing tool dependencies...

Hi Edgar, I am not sure about this one. Please try setting 'new_file_path' in your galaxy.ini to an absolute path, try again and check whether something changes. Martin On Mon, Jan 25, 2016 at 9:23 AM Fernandez Edgar < edgar.fernan...@umontreal.ca> wrote: > Hello Martin, > > > > Thank you! > >

Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS

Thanks, Bjoern! For my local install of Galaxy, logging in as a user worked and the icon is showing up (although I still had to manually go and change permissions on all the mako templates in ./database/compiled_templates directory). But our production instance of Galaxy (also v15.07 on CentOS 6.7

Re: [galaxy-dev] BED12 Data Format

Hi Lance, FWIW, there is an existing bedstrict and bed12 (and bed6) datatypes in Galaxy. The strict datatypes are currently usually created by implicit datatype converters and are most often used by some external display applications that need standards conforming files. bed6/12 are subclasses

Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS

Hi, can you please check this setting? https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample#L270 Thanks, Bjoern Am 25.01.2016 um 15:46 schrieb Oksana Korol: > Thanks, Bjoern! > > For my local install of Galaxy, logging in as a user worked and the icon > is showing up (alth

[galaxy-dev] Python on cluster for setting metadata after jobs complete

On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock wrote: > Hello all, > > We're currently looking at changing our Galaxy setup to link user accounts > with Linux user accounts for better cluster integration (running jobs as the > actual user on SGE). As part of this, we've tried setting up a fresh > in

Re: [galaxy-dev] Retain the dbkey specified for an input dataset through a Galaxy workflow?

I’ve disovered that this issue is related to tools rather than workflows, and specifically with tools that produce dataset collections on output. In the "job.finish()" method, metadata that includes the input dataset’s dbkey setting is generated correctly for output datasets that are not part o

[galaxy-dev] external_chown_script.py and the local job runner

On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock wrote: > Hello all, > > We're currently looking at changing our Galaxy setup to link user accounts > with Linux user accounts for better cluster integration (running jobs as the > actual user on SGE). As part of this, we've tried setting up a fresh > in

Re: [galaxy-dev] Python on cluster for setting metadata after jobs complete

The script generated to call Galaxy is here: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/metadata.py#L838 The job template stuff that setups of the environment the job runs in is here: https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/jobs/runners/util/job_scr

Re: [galaxy-dev] external_chown_script.py and the local job runner

On Mon, Jan 25, 2016 at 3:26 PM, Peter Cock wrote: > On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock > wrote: >> Hello all, >> >> We're currently looking at changing our Galaxy setup to link user accounts >> with Linux user accounts for better cluster integration (running jobs as the >> actual user

Re: [galaxy-dev] external_chown_script.py and the local job runner

On Mon, Jan 25, 2016 at 3:33 PM, John Chilton wrote: > On Mon, Jan 25, 2016 at 3:26 PM, Peter Cock wrote: >> On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock >> wrote: >>> Hello all, >>> >>> We're currently looking at changing our Galaxy setup to link user accounts >>> with Linux user accounts for

Re: [galaxy-dev] Python on cluster for setting metadata after jobs complete

Thanks John, On Mon, Jan 25, 2016 at 3:29 PM, John Chilton wrote: > The script generated to call Galaxy is here: > > https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/metadata.py#L838 > > The job template stuff that setups of the environment the job runs in is here: > > https:

Re: [galaxy-dev] errors installing tool dependencies...

Hello Martin. I changed the setting “new_file_path” like you said and the same error occurs (with the full path obviously). I check that the full path exists. And is rwx for the galaxy user. Any other ideas I could try? Edgar Fernandez System Administrator (Linux) Direction Générale des Technolo

Re: [galaxy-dev] errors installing tool dependencies...

No wait my mistake: the path doesn’t exists: [Errno 2] No such file or directory: '/home/galaxy/galaxy-prod/database/tmp/tmp-toolshed-mtdb6vbEI/bowtie2-2.2.6/bowtie2-2.2.6/' Because you have twice "bowtie2-2.2.6" in the full path… Is that normal? Edgar Fernandez System Administrator (Linux) Direc

[galaxy-dev] Creating cluster_files_directory (default database/pbs)

On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock wrote: > Hello all, > > We're currently looking at changing our Galaxy setup to link user accounts > with Linux user accounts for better cluster integration (running jobs as the > actual user on SGE). As part of this, we've tried setting up a fresh > in

[galaxy-dev] Question about FastqMcf installed from the Galaxy toolshed

Hi Galaxy team, One of our users requested for FastqMcf to be installed on our Galaxy server as they want to use it to remove duplicate reads in their FASTQ file. However, the

Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS

It's un-commented in both local and production. Still there is no icon in production. Cheers, Oksana On Mon, Jan 25, 2016 at 9:52 AM, Björn Grüning wrote: > Hi, > > can you please check this setting? > > > https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample#L270 > > Thanks

Re: [galaxy-dev] errors installing tool dependencies...

That was my second guess, I wasn't sure whether it should create that dir structure. Are you installing this package at this revision? And what system are you installing it on? https://toolshed.g2.bx.psu.edu/view/iuc/package_bowtie_2_2_6/0d9cd7487cc9 M. On Mon, Jan 25, 2016 at 11:17 AM Fernandez

Re: [galaxy-dev] external_chown_script.py and the local job runner

I think the problem is more that it is configured globally and not per-destination. The real user stuff should all be per-destination and not globally configured - since it should be possible to have like a dedicated cluster for Galaxy jobs that just run jobs normally and a general purpose cluster

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

Hi, We are reading the source code for galaxy job manager. We found that the job manager works like amqp. We want to know why galaxy implements the job manager using rabbitmq and celery. What is the difference between them? Thanks! Best regards, forest__

Re: [galaxy-dev] external_chown_script.py and the local job runner

On Mon, Jan 25, 2016 at 4:44 PM, John Chilton wrote: > I think the problem is more that it is configured globally and not > per-destination. The real user stuff should all be per-destination and > not globally configured - since it should be possible to have like a > dedicated cluster for Galaxy j

[galaxy-dev] Want to Contribute in galaxy project

Hello Developers, I am Manish Bisht. I am in second year of my engineering in information technology. I want to provide the code for Galaxy Project. I have created many projects outside of my college projects. You can see all at https:// github.com

Re: [galaxy-dev] errors installing tool dependencies...

Hi Edgar, this smells like an old fixed bug, what version of Galaxy are you running? Cheers, Nicola On 25/01/16 14:22, Fernandez Edgar wrote: Hello Martin, Thank you! Your instructions for my problem with Perl package worked. For the URL of hmmer, it is wrong and I will report it like you

Re: [galaxy-dev] errors installing tool dependencies...

Hi Edgar, indeed your bug was fixed long ago, please see http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html You should really move to the GitHub repository and update to the latest 15.07 or (better) to 15.10 . Cheers, Nicola On 25/01/16 17:09, Fernand

Re: [galaxy-dev] Creating cluster_files_directory (default database/pbs)

Peter - Nate and I are in agreement that the goal is to eliminate that directory, so I don't want to put effort into automating its creation. https://github.com/galaxyproject/galaxy/issues/1576 If you wish to open a PR that does this though, I would be happy to merge this. The best place to ensu

Re: [galaxy-dev] errors installing tool dependencies...

How would I safely make the transition from mercurial to github without my installation? Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 • Bur. : 1-514-343-6111 po

Re: [galaxy-dev] errors installing tool dependencies...

Edgar, check 'How to migrate a Galaxy instance from Mercurial Bitbucket to Git GitHub' at https://wiki.galaxyproject.org/Develop/SourceCode Thanks M. On Mon, Jan 25, 2016 at 12:29 PM Fernandez Edgar < edgar.fernan...@umontreal.ca> wrote: > How would I safely make the transition from mercurial t

Re: [galaxy-dev] Creating cluster_files_directory (default database/pbs)

Thanks John, The long term vision you outline makes a lot of sense; I've just added a note to the wiki to try to help anyone else running into this: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster?action=diff&rev1=51&rev2=52 Peter On Mon, Jan 25, 2016 at 5:27 PM, John Chilton w

Re: [galaxy-dev] Want to Contribute in galaxy project

Hi Manish, thank you very much for your interest in Galaxy project! I would first look here to check the beginner's dev overview: https://wiki.galaxyproject.org/Develop/GettingStarted And once you feel somewhat comfortable you can check the beginner friendly issues on GitHub here: https://github

Re: [galaxy-dev] Python on cluster for setting metadata after jobs complete

On Mon, Jan 25, 2016 at 3:44 PM, Peter Cock wrote: > Thanks John, > > On Mon, Jan 25, 2016 at 3:29 PM, John Chilton wrote: >> The script generated to call Galaxy is here: >> >> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/metadata.py#L838 >> >> The job template stuff that

Re: [galaxy-dev] Python on cluster for setting metadata after jobs complete

On Mon, Jan 25, 2016 at 5:50 PM, John Chilton wrote: > On Mon, Jan 25, 2016 at 3:44 PM, Peter Cock wrote: >> Thanks John, >> >> On Mon, Jan 25, 2016 at 3:29 PM, John Chilton wrote: >>> The script generated to call Galaxy is here: >>> >>> https://github.com/galaxyproject/galaxy/blob/dev/lib/galax

Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS

This gets tricky, can you check if the visualisations are loacted under this path and do double-check the filetypes? The icon is only displayed with the correct datatype. Am 25.01.2016 um 17:37 schrieb Oksana Korol: > It's un-commented in both local and production. Still there is no icon > in prod

Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS

It get even trickier... I just double-checked my local install, and I didn't have visualization_plugins_directory uncommented, and yet, it works on local install >This gets tricky, can you check if the visualisations are loacted under >this path If you mean phyoviz and other plugin code from