[galaxy-dev] Release of Galaxy 22.05

Dear Community, We are pleased to announce the release of Galaxy 22.05. - Developer and admin release announcement . - User release announcement

[galaxy-dev] Release of Galaxy 22.01

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 22.01. - Developer and admin release announcement . - User release announcement

[galaxy-dev] Re: Cannot update tool on toolshed

Hi Petr, Have you tried using `planemo lint` to check that your tools are structurally correct and `planemo shed_update` ( https://planemo.readthedocs.io/en/latest/publishing.html) to upload repositories ? I'm afraid the upload interface of the tool shed currently only works if there are no

[galaxy-dev] Release of Galaxy 21.09

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 21.09. - Developer and admin release announcement - User release announcement

[galaxy-dev] Re: Galaxy install problems

for the job (still CLI): > > Failed to find job_plugin of type slurm, available types include ['LSF', > 'Slurm', 'SlurmTorque', 'Torque'] > > Luc, > > > Luc Cornet, PhD > Bio-informatician > Mycology and Aerobiology > Sciensano > > - Ma

[galaxy-dev] Re: Galaxy install problems

t ? > > Thanks, > Luc > > > Luc Cornet, PhD > Bio-informatician > Mycology and Aerobiology > Sciensano > > - Mail original - > De: "Marius van den Beek" > À: "Luc Cornet" > Cc: "HelpGalaxy" , "Baurain Denis&qu

[galaxy-dev] Re: Galaxy install problems

OK, > > Sure but can you please tell me how to get these pulsar application logs ? > > Thanks > Luc > > > Luc Cornet, PhD > Bio-informatician > Mycology and Aerobiology > Sciensano > > ----- Mail original - > De: "Marius van den Beek&

[galaxy-dev] Re: Galaxy install problems

10 > amqp_publish_retry_interval_step: 10 > amqp_publish_retry_interval_max: 60 > > > Thanks for your help, > Luc > > > ---- > Luc Cornet, PhD > Bio-informatician > Mycology and Aerobiology > Sciensano > > - Mail original - > De:

[galaxy-dev] Re: Galaxy install problems

Hi Luc, I'm sorry to hear that you're struggling to set up Galaxy to your liking. Let me start by pointing out that usegalaxy.org uses slurm with DRMAA, this is certainly going to be more performant and reliable than the CLI plugin. There is little maintenance necessary, so maybe that is why

[galaxy-dev] Release of Galaxy 21.05

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 21.05. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/21.05_announce.html and user facing release notes are at

[galaxy-dev] Release of Galaxy 21.01

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 21.01. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/21.01_announce.html and user facing release notes are at

[galaxy-dev] Release of Galaxy 20.09

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 20.09. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/20.09_announce.html and user facing release notes are at

[galaxy-dev] Re: Expose local filesystem to Galaxy?

Hi Sandra, if the goal is to import data into galaxy from disk you can designate an area as `user_library_import_dir` (see https://docs.galaxyproject.org/en/master/admin/options.html#user-library-import-dir) and configure user_library_import_dir_auto_creation,

[galaxy-dev] Release of Galaxy 20.05

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 20.05. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/20.05_announce.html and user facing release notes are at

[galaxy-dev] Re: Checkboxes issue (could not find an answer in the forum)

Hi, This was a bug on the dev branch a few weeks ago that was fixed by https://github.com/galaxyproject/galaxy/pull/9667. I would advise against deploying from the dev branch if this is supposed to become a production server. The last stable release is 20.01 at the moment. Best, Marius On Fri,

[galaxy-dev] Release of Galaxy 20.01

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 20.01. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/20.01_announce.html and user facing release notes are at

[galaxy-dev] Re: trouble running the new galaxy instance

Hi Jochen, can you post out the full logs ? Jul 15 10:23:11 green-galaxy galaxy[5957]: yaml.scanner.ScannerError: mappin...e Jul 15 10:23:11 green-galaxy galaxy[5957]: in "/opt/galaxy/galaxy/config/gal...0 probably means that you have syntax error in galaxy.yml, but the full logs will tell you

[galaxy-dev] Re: Error during tool installation: "inotify instance limit reached"

Hi Christopher, you might want to turn off `watch_tools` if you are using it, this is only needed when using the pretty-much undocumented feature where you dump tools into a directory without registering them in any tool_conf.xml file. All other tool reloading happens by another means.

[galaxy-dev] Re: Workflow assigning columns on output causes "Uncaught exception in exposed API method"

Hi Peter, thanks for the report, I've opened a pull request to fix this at https://github.com/galaxyproject/galaxy/pull/8023. We'll backport this to 18.09 after acceptance. As a (terrible) workaround you could download the workflow and change the section that looks like ```

[galaxy-dev] Re: tool installation problem

Hi Matthias, It might just have been deactivated, in which case you can either activate or uninstall the repo in the admin panel -> Manage tools -> Advanced Search -> Deactivated or Uninstalled. Hope that helps, Marius On Tue, 26 Mar 2019 at 15:59, Matthias Bernt wrote: > Dear list, > > I

Re: [galaxy-dev] Question using sftp to upload file to galaxy

Hi Rui, there's a fairly complete explanation and example in in https://docs.galaxyproject.org/en/latest/admin/special_topics/ftp.html Hope that helps, Marius On Mon, 28 Jan 2019 at 07:35, Rui Wang wrote: > Hey Folks, > > I tried a few times with different configurations, but none worked. Did

Re: [galaxy-dev] tools gone after switching to galaxy.yml

Hi Matthias, if your previous config had a separate database for tools you need to use that. This is controlled by the install_database_connection setting. Best, Marius On Wed, 19 Dec 2018 at 13:53, Matthias Bernt wrote: > Dear list, > > just tried to switch to galaxy.yml, which worked in

Re: [galaxy-dev] number of elements in collections and multiple-true-params

Hi Matthias, I think you're right in that len($input_type.input_bam) is inconsistent, we can implement __len__ for the collection case, but that is not done yet. That said, unless your example is a toy example for a more complex scenario the switch seems unnecessary, a multiple="true" data

Re: [galaxy-dev] Error after creating dataset list of bam files in v18.05

Dear Christopher, You need to copy the shipped datatypes_conf.xml.sample to the appropriate location(s) for your installation. Best, Marius On Tue, Oct 23, 2018, 11:08 AM Previti < christopher.prev...@dkfz-heidelberg.de> wrote: > Dear all, > > We're in the process of testing version 18.05

Re: [galaxy-dev] can't create user on a new instance

Hi Rui, The session token is used to prevent certain kinds of attacks. Your browser may still have a session token for the old instance. You can delete the cookies for this address in your browser and you should be issued a new and valid token. Hope that helps, Marius On Thu, Oct 11, 2018, 7:12

Re: [galaxy-dev] Issue with deseq2

Hi Christopher, due to the old version of Galaxy you need to manually update Conda (conda update conda) and explicitly set the current channel order in your galaxy.ini file, this should be conda_ensure_channels = iuc,conda-forge,bioconda,defaults With these set you can remove the exisiting conda

Re: [galaxy-dev] java options

Hi Matthias, if a tool prints something to the stderr that is indeed considered to indicate a failure, and it's the default mostly because we don't want to break legacy tools that make this assumption. If you include a profile version in your tool or change your command section to this will more

Re: [galaxy-dev] Unable to install tools from toolshed/mercurial issue in release_18.05 instance

Hi Peter, Recent galaxy releases are using the `hg` command that should be automatically installed along with other galaxy dependencies. If you're running galaxy in a virtualenv then that virtualenv should have the `hg` script in the bin folder. Depending on how you start galaxy you may need to

Re: [galaxy-dev] pbs/torque jobs

settings to the default > deployment but I just switched to uWSGI + Mules and that has fixed my > problem. > > > > Thanks! > > -Sheldon > > > > *From:* Marius van den Beek [mailto:m.vandenb...@gmail.com] > *Sent:* Thursday, June 14, 2018 2

Re: [galaxy-dev] pbs/torque jobs

> directory that is twice as large as the file I changed and it doesn’t look > at all like the current pbs.py. > > > Probably the wrong pbs.py is being called. I’ll need to check the docs on > venv setup again. > > > Thanks, > > -Sheldon > > > > *

Re: [galaxy-dev] pbs/torque jobs

gData/galaxy/galaxy-dist/database/pbs/16117.sh > > galaxy.jobs.runners.pbs DEBUG 2018-06-14 11:12:23,214 [p:63562,w:2,m:0] > [PBSRunner.work_thread-1] (16117) queued in default queue as 1434.locahost > > galaxy.jobs DEBUG 2018-06-14 11:12:23,214 [p:63562,w:2,m:0] > [PBSRunner.work_t

Re: [galaxy-dev] pbs/torque jobs

@canada.ca> wrote: > >> Hi Marius, >> >> >> >> The PBS runner and the user is the galaxy user. I do not use the run as >> real user option. I haven’t been using drmaa_external_runjob_script. >> This setup worked for my old 17.05 and previous versions o

Re: [galaxy-dev] pbs/torque jobs

y user. I do not use the run as > real user option. I haven’t been using drmaa_external_runjob_script. > This setup worked for my old 17.05 and previous versions of galaxy. > > > > Thanks, > > -Sheldon > > > > *From:* Marius van den Beek [mailto:m.vandenb

Re: [galaxy-dev] pbs/torque jobs

Hi Sheldon, is there anything particular about your job configuration, e.g. are you you using the run as real user option or are you using the drmaa_external_runjob_script option ? Are you using the drmaa or the PBS runner ? Best, Marius On 13 June 2018 at 21:13, Briand, Sheldon (NRC/CNRC) <

Re: [galaxy-dev] Samtools running on submit-node and as a slurm job

Hi Christopher, If your galaxy is configured to set metadata externally then you shouldn't see samtools index being run on the node that runs galaxy (On a side-note galaxy will use pysam starting from release 18.01). One possibility is that the metadata setting failed, and it has been tried again

Re: [galaxy-dev] Problems installing Galaxy 18.01

Hi Peter, does the tool show up in the tool panel (Looks like you've installed it into "Get Data")? What commit are you on ? There 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.

Re: [galaxy-dev] Ensuring Python 2.7 when resolving conda dependencies for tool

this case you're asking for an older Biopython > which has to date not been packaged in conda-forge or > bioconda, so I presume in Marius example it comes from > PyPI via pip? > > > Peter > > On Mon, Mar 5, 2018 at 4:46 PM, Marius van den Beek > <m.vandenb...@gmail.com

Re: [galaxy-dev] Ensuring Python 2.7 when resolving conda dependencies for tool

This should actually work properly if you install the dependencies via the Manage dependencies page in the admin menu or if you install the tool via the tool shed. This translates more or less to the following conda command: ``` $ conda create -n mulled-v1 python=2.7 biopython=1.65 -c iuc

Re: [galaxy-dev] Text file busy and conda

Hi John, when you say tool autoinstalled via conda do you mean that the dependencies were automatically installed during the repository installation process, or that you have `conda_auto_install = True` in your galaxy.ini ? The latter is not working reliably while the dependencies have not

Re: [galaxy-dev] Error at the end of a BWA job

Hi Frederic, samtools couldn't be found, which is required for creating the bam index files during the metadata setting. You can install it globally or in the admin panel -> Manage tool dependencies -> Find the "Set External Metadata" tool and hit "Install checked dependencies via Conda". Best,

Re: [galaxy-dev] tool publishing

Hi Matthias, Glad it works. I guess a few characters are blacklisted, but generally you can choose freely. You can see your public name (which is what should be used in the `name` field) by logging in to the toolshed, User -> Preferences -> Manage your Information. Marius On 18 December 2017 at

Re: [galaxy-dev] tool publishing

Hi Matthias, this really looks like it should have worked. The repository has been created, but the revision is not installable. Often times this is because of missing tool data table / loc file references, but I see that your tool is not making use of any of these so they are not necessary. My

Re: [galaxy-dev] Fwd: Job Script Integrity with GalaxyKickStart (galaxy-dev Digest, Vol 137, Issue 5)

Hi John and Christophe, What the job script integrity script does is checking that the script is ready to be executed, by setting the environment variable `ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ` to 1 and then executing the tool_script.sh script that contains the following check: ``` if [ -n

Re: [galaxy-dev] Metadata setting python dependencies

hengs/hpc_storage/home/galaxy_hpc/galaxy-dist/.venv/b > in:/this/is/a/test > > Any idea where that came from? > > Thanks > Ulf > > On 25/10/17 16:05, Marius van den Beek wrote: > >> Hi Ulf, >> >> you can set a virtualenv to be used in your job_

Re: [galaxy-dev] Metadata setting python dependencies

Hi Ulf, you can set a virtualenv to be used in your job_conf.xml file. The following line would go into the `` tag: `` Best, Marius On 25 October 2017 at 16:56, Ulf Schaefer wrote: > Hi again > > Update, sorry for spamming: > > It is not ALL jobs that fail. Only the

Re: [galaxy-dev] error despite success

Hi Matthias, any chance https://github.com/galaxyproject/galaxy/pull/4644 would fix this for you ? Best, Marius On 16 October 2017 at 20:12, Matthias Bernt wrote: > Dear list, > > today I got an erroneous result (red) despite the output of the tool to be > seems fine.

Re: [galaxy-dev] Show history structure : Error 'Undefined' object is not callable

Hi Julie, thanks for reporting this, this is indeed broken. I hope https://github.com/galaxyproject/galaxy/pull/4794 is going to fix this. Best, Marius On 12 October 2017 at 14:53, julie dubois wrote: > Hi all, > I'm on 17.05 galaxy version and display it on firefox. > I'm

Re: [galaxy-dev] Worklist failing on collection with AttributeError: 'object' object has no attribute 'collection'

ype of this input step to "Paired", and hopefully your workflow should run successfully. Let me know if that works for you, Marius On 4 October 2017 at 15:02, Marius van den Beek <m.vandenb...@gmail.com> wrote: > Hi Tony, > > could you include the traceback that leads up to this e

Re: [galaxy-dev] Toolshed partial installation ? deeptools error

, Marius van den Beek <m.vandenb...@gmail.com> wrote: > Hi Julie, > > any chance you are setting PYTHONPATH before starting galaxy's job > handlers (a common place would the supervisor config, in case you're using > that)? > This will interfere with all python modules that

Re: [galaxy-dev] Toolshed partial installation ? deeptools error

Hi Julie, any chance you are setting PYTHONPATH before starting galaxy's job handlers (a common place would the supervisor config, in case you're using that)? This will interfere with all python modules that are installed via conda. Best, Marius On 3 October 2017 at 09:13, julie dubois

Re: [galaxy-dev] Bug in "View all histories", history "disappears"

Hello Christopher, this is a longstanding bug that we recently fixed (initial description https://github.com/galaxyproject/galaxy/issues/3519, fix https://github.com/galaxyproject/galaxy/pull/4610 ), This will be included in galaxy release 17.09, but the fix has also been backported to relaese

Re: [galaxy-dev] Galaxy server requires a restart to activate tools

Hi, Can you check the commit of galaxy that you are using and post the logs that you see when you install a tool that doesn't work ? Does this happen for all tools that you install ? Best, Marius On 19 September 2017 at 15:40, RMSe17 wrote: > Hi Bjoern, > > I upgraded to

Re: [galaxy-dev] installation/conda problems

Hi Matthias, Adding to Bjoern's suggestion you can also check in the admin section under "Manage Tool Dependencies" into which path the dependency has been installed (it may be mulled-), and from there you can also uninstall the dependency. You can also trigger uninstall of the conda dependency

Re: [galaxy-dev] Watching the tools directory and dynamic reloading

Hi Keith, Galaxy has been able to load tools after installation for quite some time, however that did not work for production setups that are using multiple job handler threads. We did indeed refine the tool loading to work for production servers starting with release 16.10 (it's mentioned in

Re: [galaxy-dev] Galaxy Conda resolver install Issue

Hello Evan, this looks suspiciously like a bug that Matthias Bernt has fixed on the development branch a while back. I have backported this to Galaxy release 17.01 and release 17.05. If you update your galaxy branch to the latest commit it should work (or you should receive a more instructive

Re: [galaxy-dev] htseq-count/deseq2 conda dependency issues

Hi Peter, indeed the defaults channel should now be the lowest priority of all conda channels. This recommended setting in galaxy.ini is now conda_ensure_channels = iuc,bioconda,conda-forge,defaults,r Unfortunately these changes appear as changes are made within bioconda, which usually do not

Re: [galaxy-dev] Galaxy Job Error

quot;, line 283, in close self.flush() File "/cm/shared/apps/galaxy/requirements/python/lib/python2.7/socket.py", line 307, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe Marius van den Beek <m.vandenb...@gmail.com>

Re: [galaxy-dev] Galaxy Job Error

Hi Evan, If this is something that you rarely see and your filesystem is on a network drive, you could try setting `retry_job_output_collection` to 10 in the galaxy.ini file. This will let galaxy try to collection the output files 10 times, which should help if there is some delay for the

Re: [galaxy-dev] conda installation fails

That's a little weird, I don't think relying on the system's LD_LIBRARY_PATH is good practice. Maybe you could try what was suggested in the last answer here: https://serverfault.com/questions/372987/centos-usr-local-lib-system-wide-ld-library-path . On 19 April 2017 at 17:57, Matthias Bernt

Re: [galaxy-dev] SSL certificate errors

Hi Matthias, this looks like your python installation does not know how to verify SSL certificates. Redhat have a nice section on troubleshooting that here: https://access.redhat.com/articles/2039753 I can get your error by specifying a nonexsting cert:

Re: [galaxy-dev] drmaa on univa grid engine

Hi Matthias, in addition to the link you posted there is also this here that looks similar: http://dev.list.galaxyproject.org/DRMAA-options-for-SGE-td4140931.html Perhaps qsub is filling in a default queue, and drmaa is not doing that? You could try adding a queue to the nativeSpecification.

Re: [galaxy-dev] SLURM configuration problem

tist > Department of Human Genetics > CHU de Liège | Domaine Universitaire du Sart-Tilman > 4000 Liège | BELGIQUE > Tél: +32-4-366.91.41 > Fax: +32-4-366.72.61 > e-mail: lpalme...@chu.ulg.ac.be > > On 02/20/2017 03:57 PM, Marius van den Beek wrote: > > It doesn't hurt to try this, bu

Re: [galaxy-dev] Dataset Generation Errors

> Sensitive > Local > -- > David Lapointe Ph.D. > Sr. Bioinformatics Specialist > Research Technology (RT) > Tufts Technology Services (TTS) > 16 Dearborn Road > Somerville MA 02144 > > Phone: 617-627-5319 > Fax: 617-627-3667 > http://it.tufts.edu >

Re: [galaxy-dev] Dataset Generation Errors

Hi David, this typically happens on older Galaxy versions (< 17.01) after installing new or updated tools. A galaxy restart should help. Best, Marius On 23 March 2017 at 15:57, Lapointe, David wrote: > I have installed the metaphlan tool ( dannon e951f9d38339) which

Re: [galaxy-dev] startup bug in lib/galaxy/tools/toolbox/base.py

Hi Matthias, so typically what's happening there is that there is no tool_shed_respository entry in the database for this tool. I see this in my development instance when I setup a new database, but keep my old shed_tool_conf.xml. If you want to get rid of these errors you can uninstall the

Re: [galaxy-dev] Problem with installing tools using Conda

e > startsecs = 20 > user= galaxy > environment = PATH=$GALAXY_PATH/.venv/bin:/u > sr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin, > *PYTHONHOME=$GALAXY_PATH/.venv*,DRMAA_LIBRARY_PATH=/usr/local/l > ib/libdrmaa.so > startretries= 1

Re: [galaxy-dev] Problem with installing tools using Conda

Hi Ashok, You should not set the PYTHONPATH in supervisor. That is indeed going to conflict with conda. If you are using uwsgi you can use something like this: [program:galaxy_web] command = /bioinfo/guests/mvandenb/galaxy/.venv/bin/uwsgi --virtualenv

Re: [galaxy-dev] SLURM configuration problem

rtment of Human Genetics > CHU de Liège | Domaine Universitaire du Sart-Tilman > 4000 Liège | BELGIQUE > Tél: +32-4-366.91.41 > Fax: +32-4-366.72.61 > e-mail: lpalme...@chu.ulg.ac.be > > On 02/20/2017 03:13 PM, Marius van den Beek wrote: > > Hi Leonor, > >

Re: [galaxy-dev] installing tool dependencies

Hello Jochen, what version of galaxy are you running? When you are doing this you should have a traceback in your logs, this would be helpful to understand what is going on. When you say "I installed a bunch of tools at the same time", did you really trigger multiple installations at the same

Re: [galaxy-dev] Pulsar: issue configuring to use shared filesystem rather than staging data

I hope John can give some more input on this, but if you're really short on time you could try the ssh runner directly from galaxy without pulsar. I'm very happy with this driving a Torque 4 cluster. The relevant part of my job_conf.xml looks like this: ```

Re: [galaxy-dev] Running unit tests on [dev]

Hi Max, that's './run_tests.sh -unit' (from the root of the clone). You can also go directly through nose (pip install nose) and running nosetests test/unit/ Best, Marius 2016-11-24 17:42 GMT+01:00 Maximilian Friedersdorff : > > >

Re: [galaxy-dev] Installing ToolShed Tools into Galaxy via Browser Interface Exception Thrown

Hello Miuki, this looks like your integrated_tool_panel.xml file has some problems. Can you try to move this file to a different location and try the installation again? It should be located in your galaxy directory. Best, Marius On 11/03/2016 03:16 PM, Yip, Miu ki wrote: Hi all, While

Re: [galaxy-dev] user email info

Hi Mohamed, “$__user_email__” is filled in by galaxy when generating the command line, so you can directly refer to this in your command line. See https://github.com/galaxyproject/tools-iuc/blob/master/tools/tool_factory_2/rgToolFactory2.xml#L12

Re: [galaxy-dev] Changing Tool Shed URL

ll tools from a toolshed on > a Galaxy. > > We will try the second solution and as we already tried to manipulate the > database, we stongly agree that it is not THE solution. > > Cheers, > > - > > Fabien and Olivia and Youssef > > > > Le 20/10/2016 à 10:29, Marius va

Re: [galaxy-dev] Changing Tool Shed URL

Hi Youssef, the tool shed url is also stored in the database, that's why just changing the shed_tool_conf.xml is not working. I think you have a bunch of options here: 1: You can make a list of tools from that toolshed and re-install them from the new toolshed.

Re: [galaxy-dev] Conda: confused dependencies with multiple R versions and rpy

Hi Steve, The scatterplot tool is relatively old and has not had its dependencies updated to be conda compatible. https://github.com/galaxyproject/tools-devteam/blob/master/tools/scatterplot/scatterplot.xml The relevant lines are these: numpy rpy wrote: > Hi, > trying to get my

Re: [galaxy-dev] Conda: confused dependencies with multiple R versions and rpy

Forgot to paste the link: https://github.com/galaxyproject/tools-devteam/issues/385 On 1 September 2016 at 11:08, Marius van den Beek <m.vandenb...@gmail.com> wrote: > Hi Steve, > > The scatterplot tool is relatively old and has not had its dependencies > updated to be conda c

Re: [galaxy-dev] my.galaxy/toolshed bioblend or install_tool_shed_tools swallows toolshed

subdir: > >'http://server/subdir/' > > > >and I use ephemeris > > > >thank you very much, > >ido > > > >> On 30 Aug 2016, at 17:55, Marius van den Beek <m.vandenb...@gmail.com> > wrote: > >> > >> Hi Ido, > >> > >&g

Re: [galaxy-dev] Putting it all together - toolshed tool + conda dependency

Hi Steve, Looks like you're running an older version of galaxy in the docker container, since newer galaxy will build the metadata environment in a separate environment called 'conda-metadata-env', and we have also changed the way that the handlers receive their Python environment (that's why

Re: [galaxy-dev] Python tool wrapper with multiple input and output files

mman > line, becasue "python" is called only at the first iteration of the for > cycle. > > Is there a way to prevent this behaviour or some "best practices" ? > > Thanks a lot, > Marco. > > 2016-06-07 14:05 GMT+02:00 Marius van den Beek <m.vandenb..

Re: [galaxy-dev] Python tool wrapper with multiple input and output files

Hi Marco, you've got an interesting use-case there. You may want to use either a dataset list (if you only supply rna_n.bam), or a paired dataset list (rna_n.bam and dna_n.bam). I would probably implement a conditional, where the user selects either a dataset list or a paired dataset list. The

Re: [galaxy-dev] not sure what I can do about this...

Hi Edgar, it’s a good idea to use python2.7 for galaxy, since 16.01 is the last release supporting python 2.6. In general you can create a new virrtualenv with a a specific python interpreter like this: virtualenv -p If you create a new new virtualenv .venv in your galaxy source folder,

[galaxy-dev] Fwd: Error when uploading files (using Pulsar)

Ah, and if you want to figure out the ID of a tool, you can click the small info button of a dataset produced by the tool, so in the case of the upload tool it reads: Galaxy Tool ID: upload1 On 9 May 2016 at 12:25, Marius van den Beek <m.vandenb...@gmail.com> wrote: > Puhh, you

Re: [galaxy-dev] Error when uploading files (using Pulsar)

Hi Tiziano, I think you are correct in your assumption. If you do not need to have uploads run on pulsar, you should be able to specify a local destination for uploads (the upload tool id is upload1) in your job_conf.xml. There are some examples described here:

Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

loaded end of March, following the link given on the > Galaxy tool installation guide. > > Manual installation of the tools one-by-one from the Admin web page works. > The tools installed show up on the web page. > > > > Thanks, > > Bill > > *From:* Marius va

Re: [galaxy-dev] init scripts version 16.01

t; > On 8 April 2016 at 16:15, Eric Kuyt <eric.ku...@wur.nl> wrote: > >> ​Thanks, works like a charm!​ Clean easy fix, Now why I couldn't come up >> with this myself. >> >> On 2 April 2016 at 11:49, Marius van den Beek <m.vandenb...@gmail.com> >> wrote: &

Re: [galaxy-dev] perl version 5.18.1 repository error

Hi Philipp, I believe you have run into a rather complicated problem with perl's dependencies. We (the IUC) have changed from coreutils-8.22 to coreutils-8.25 for exactly the reason you are reporting (`...generated no output for the defined timeout period of 3600.0 seconds`). So you should update

Re: [galaxy-dev] Trackster in 16.01 broken

been solved, you can switch back to release_16.01 by doing `git checkout release_16.01`. Thanks for reporting the error, Marius On 15 March 2016 at 19:25, Marius van den Beek <m.vandenb...@gmail.com> wrote: > Yes, `git checkout release_16.01` should do it, but wait a second, ther

Re: [galaxy-dev] Trackster in 16.01 broken

Hello Lubos, this should be fixed with https://github.com/galaxyproject/galaxy/pull/1897. If you pull in the latest changes (`git pull`) on the release_16.01 branch things should work again. Cheers, Marius On 15 March 2016 at 18:59, Marius van den Beek <m.vandenb...@gmail.com> wrote: &

Re: [galaxy-dev] Trackster in 16.01 broken

Hello Lubos, this should be fixed with https://github.com/galaxyproject/galaxy/pull/1897. If you pull in the latest changes (git pull) on the release_16.01 branch things should work again. Cheers, Marius On 15 March 2016 at 18:54, Lubos Klucar wrote: > Hi, > > after

Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

, including the dependencies. PS. please keep all traffic on the mailing list On 4 March 2016 at 19:59, Marius van den Beek <m.vandenb...@gmail.com> wrote: > There is no real step by step guide, but the script itself has a help text: > > $ python install_tool_shed_tools.py -h > > Al

Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

s to be in place and what options to use. Is there a > step-by-step guide for using this script somewhere? > > > Best regards, > Bill > > -- > *From:* Marius van den Beek <m.vandenb...@gmail.com> > *Sent:* Friday, March 4, 2016 7:25 AM &

Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

Hi Bill, I think you're trying to use the ansible-galaxy-tools role as a playbook: This won't work, you can only include the role in your playbook, or use this playbook https://github.com/afgane/galaxy-tools-playbook You can also directly use the python script in

Re: [galaxy-dev] Docker tools

Hello Abdulrahman, I believe you can control the docker host in the job_conf.xml. https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L227 I haven't' tried this yet, but it seems that it should work. Cheers, Marius On 2 March 2016 at 09:55, Abdulrahman Azab

Re: [galaxy-dev] Difficulty uploading BAM files

Hello Scott, you do need a samtools binary on GALAXY's PATH. This is not samtools installed from the toolshed. Best, Marius On 26 February 2016 at 18:49, Scott Szakonyi wrote: > Hi, > > I'm having trouble uploading BAM files in our development environment. > Other

Re: [galaxy-dev] Collapse tool panel and history panel

Hi Makis, if you change the javascript in client/ ... you need to run grunt. The instructions are in https://github.com/galaxyproject/galaxy/blob/dev/client/README.md. Cheers, Marius On 25 February 2016 at 10:57, Makis Ladoukakis wrote: > Just an update/bump of the

Re: [galaxy-dev] Docker and alpine linux

Just my 2 cents about this: I feel your pain, our connection to the docker hub is horrible, it takes an hour to pull the GIE images ... . (While it only takes seconds from the cloud ...). The galaxy docker images are pretty fat, because we use them VM-style, in principle nothing wrong about that.

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

I have occasionally seen this. GNU-coreutils hangs while compiling on ubuntu 14.04 ... there is a `nanosleep` in the configure step, which is never returning. "checking for working nanosleep..." https://bugs.launchpad.net/ubuntu/+source/coreutils/+bug/1079889 Just kill the process (this will

Re: [galaxy-dev] Importing workflows via command-line/Docker script

Hi Cam, this would be possible using bioblend ( https://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html?highlight=workflow#module-bioblend.galaxy.workflows). Take a look at the `import_workflow_from_local_path` function. You'll need to have galaxy running for this (same as for

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

Hello Hans, I'm not sure if it would help to use the pre-compiled binaries, as you would still need some of the underlying libraries for building R packages. We're not far from having this fixed ... there is a newer revision of R on the main toolshed, that nevertheless will (probably) fail

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