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    Nikolay Vazov
    @vazovn
    Ok found it - this is actually the latest
    Helena Rasche
    @hexylena:matrix.org
    [m]
    for what it's worth: it existed as a separate role largely because of the zergling setup we did, there's a strong chance we'll merge the features from that into the main galaxy role at some point in the near future.
    1 reply
    Nikolay Vazov
    @vazovn
    Hi, I forgot I was running an old role for galaxyproject - 0.9.7. Now I updated it and I am configuring it step by step. There are changes which are exactly the changes I needed - enabling me to unstall systemd galaxy as galaxy user. We are having a slightly different setup now - instead of mounting partitions from the cluster, we have setup a directory in our IBM Elastic Storage System (ESS) which will be used to host the data from Galaxy, like job dirs, file dirs ect. We are mounting it a root_squash and I have some issues adapting the roles to this setup. But I am working on it.
    Helena Rasche
    @hexylena:matrix.org
    [m]
    sounds fun!
    Nikolay Vazov
    @vazovn
    Will let you know :)
    Nikolay Vazov
    @vazovn
    Hi, I am running the latest ansible-playbook and installing version 21.09. The systemd would fail throwing three errors about the location of three files: 
    File "/galaxy/srv/galaxy/server/lib/galaxy/config/schema.py", line 48, in _read_schema
    with open(path) as f:
FileNotFoundError: [Errno 2] No such file or directory: '/galaxy/srv/galaxy/server/lib/galaxy/config/../config_schema.yml'

 File "/galaxy/srv/galaxy/server/lib/galaxy/util/yaml_util.py", line 25, in include
    with open(filename) as f:
FileNotFoundError: [Errno 2] No such file or directory: '/galaxy/srv/galaxy/server/lib/galaxy/config/../uwsgi_schema.yml'

  File "/galaxy/srv/galaxy/server/lib/galaxy/util/yaml_util.py", line 25, in include
    with open(filename) as f:
FileNotFoundError: [Errno 2] No such file or directory: '/galaxy/srv/galaxy/server/lib/galaxy/config/../job_config_schema.yml'
    I copied them manually :
    cp /galaxy/srv/galaxy/server/lib/galaxy/webapps/galaxy/config_schema.yml /galaxy/srv/galaxy/server/lib/galaxy/ cp /galaxy/srv/galaxy/server/lib/galaxy/webapps/galaxy/uwsgi_schema.yml /galaxy/srv/galaxy/server/lib/galaxy/ cp /galaxy/srv/galaxy/server/lib/galaxy/webapps/galaxy/job_config_schema.yml /galaxy/srv/galaxy/server/lib/galaxy/
    Helena Rasche
    @hexylena:matrix.org
    [m]
    those are part of the galaxy repository, odd that they'd be missing
    Nikolay Vazov
    @vazovn
    And now it seems to be working. Is it something I am doing wrong?
    The were misplaced
    Look where I copied them from ...
    /galaxy/srv/galaxy/server/lib/galaxy/webapps/galaxy/
    Helena Rasche
    @hexylena:matrix.org
    [m]
    hmm
    galaxy_commit_id?
    Nikolay Vazov
    @vazovn
    galaxy_commit_id: release_21.09
    But I guess you need the exact commit?
    Helena Rasche
    @hexylena:matrix.org
    [m]
    no, no that's fine
    just wondered if you were on a weird branch or so
    Nikolay Vazov
    @vazovn
    He, you are asking too much from me :)
    If this can help : 
    changed: [galaxy01.educloud.no] => {
    "msg": "Galaxy version changed from '' to '60ab1d5b7ae4385ca31307b0c23c52c979e337eb'"
}
    Morten Johansen
    @morj-uio
    :point_up: March 27, 2020 2:58 PM
    failed to download http://cvmfs0-psu0.galaxyproject.org/cvmfs/singularity.galaxyproject.org/data/6b/81f0681da21040ce0b4a31c3602255a19c5032P (9 - host returned HTTP error) unexpected HTTP error code 200 - please check the stratum 0 health
    Still getting this same error when trying to replicate stratum 0 singularity repo. Was it not rebuilt? Or has the stratum 0 URL changed? The data repo is replicating successfully. Thanks for any pointers.
    Nikolay Vazov
    @vazovn
    Hi, in the previous versions of the ansible playbook the systemd configuration contained the following variables : galaxy_systemd_zergling_envand galaxy_zergpool_listen_addr. In the latest version where mule is the only systemd mode, there is only galaxy_systemd_envvariable. I am using it but the DRMAA_LIBRARY_PATH=.... variable which I set there is now missing in the galaxy.service file. Is this correct?
    Helena Rasche
    @hexylena:matrix.org
    [m]
    zerg* shouldn't need to be set
    Nikolay Vazov
    @vazovn
    No, I commented it :
    Helena Rasche
    @hexylena:matrix.org
    [m]
    DRMAA should show up if you set it
    Nikolay Vazov
    @vazovn
    # systemd
galaxy_systemd_mode: mule
__galaxy_systemd_memory_limit_merged: 
    mule: 32
galaxy_systemd_env: "DRMAA_LIBRARY_PATH=/galaxy/srv/drmaa/lib/libdrmaa.so.1"
#galaxy_zergpool_listen_addr: 127.0.0.1:8080
galaxy_restart_handler_name: "Restart Galaxy"
#galaxy_systemd_zergling_env: "DRMAA_LIBRARY_PATH=/srv/drmaa/lib/libdrmaa.so.1"
    Helena Rasche
    @hexylena:matrix.org
    [m]
    https://training.galaxyproject.org/training-material/topics/admin/tutorials/connect-to-compute-cluster/tutorial.html#galaxy-and-slurm like so, ja?
    Nikolay Vazov
    @vazovn
    A, sorry, missing []around .
    Helena Rasche
    @hexylena:matrix.org
    [m]
    the tutorial makes it look like it should be an array
    Nikolay Vazov
    @vazovn
    All right, will change. I have an entire novel to write about setting Galaxy up on a root_squash dir. Will send it to you ... when ready :)
    1 reply
    Seems to be working
    Nate Coraor
    @natefoo:matrix.org
    [m]
    I have in my queue a major refactoring of the galaxy role to better support root squash installs.
    Nikolay Vazov
    @vazovn
    Ah, Nate, can you share the link?
    Nate Coraor
    @natefoo:matrix.org
    [m]
    Not much progress yet, I got bogged down in sorting out paths that should be in one root vs. another: https://github.com/galaxyproject/ansible-collection-galaxy
    mzhuangsdsc
    @mzhuangsdsc
    @natefoo:matrix.org Hi Nate. The new version of Galaxy doesn't have a menu item "Interactive Environment" under "Visualize". Is there any way to make the choice "Interactive Environment" appear under "Visualize"? Thanks a lot!
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    @mzhuangsdsc: Look at "Active InteractiveTools" in the User menu.
    mzhuangsdsc
    @mzhuangsdsc
    @nsoranzo:matrix.org Thanks for the info! But there is nothing there. What I meant is: "Interactive Environment", not "Interactive Tools"
    Nicola Soranzo
    @nsoranzo:matrix.org
    [m]
    Those have been deprecated as far as I know.
    mzhuangsdsc
    @mzhuangsdsc
    Really? We developed some tools based on the "Interactive Environment". Now we cannot use them. Is there any way for me to bring up the "Galaxy Interactive Environment Launcher"? Thanks.
    bgruening
    @bgruening:matrix.org
    [m]
    @mzhuangsdsc: the way how you start your containers has changed and is way simpler. So the old IEs have been replaced by "Interactive Tools". Which are way easier to maintain and develop.
    cat-bro
    @cat-bro

    Hello all. I've been experimenting with using mamba instead of conda on pulsar and running tool tests (not in parallel) to get environments to install. It has been great and fast but at one point there was an error:

             LockError:
         LOCKERROR: It looks like conda is already doing something.
         The lock ['/mnt/pulsar/deps/_conda/pkgs/cache.pid1069995.conda_lock'] was found. Wait for it to finish before continuing.

    As far as I could see there were no conda processes running, and as soon as I deleted the lock file things worked again but in the meantime several of my test jobs failed because their environments had not installed. I'm wondering if it's safe to use mamba as the conda exec.

    Björn Grüning
    @bgruening
    It should be safe @cat-bro.
    And we will use that probably also in bioconda more in the near future.
    However, I guess for us it might be actually better to invest the time to migrate to containers.
    Do you have any plans in this regard?
    cat-bro
    @cat-bro
    @bgruening that's a good point
    Ajit Singh
    @AjitPS

    Hi admins, I am trying to update our galaxy at rothamsted from v20.09 to new v21.09.

    1) Have taken snapshot of old galaxy + backup of postgresDB and verified we use python 3.6.8 on our galaxy VM's + hpc/slurm here,
    2) got the new release_21.09 code/branch from github,
    3) reviewed and amended configs: galxy.yml (added our logging setup), job_conf.xml (for our Slurm setup, auth_conf.xml (for python-pam, our institute AD login), tool_conf.xml, datatypes_conf.xml, etc.,
    4) also updated python-pam, drmaa, daemonize in our galaxy .venv,

    5) I tried to run: @nsoranzo:matrix.org @hexylena:matrix.org
    -bash-4.2$ sh manage_db.sh upgrade

    but this fails s:

    Activating virtualenv at .venv
    Traceback (most recent call last):
    File "./scripts/manage_db.py", line 12, in <module>
    from galaxy.model.orm.scripts import get_config
    File "/home/usern/galaxy/galaxy/lib/galaxy/model/init.py", line 72, in <module>
    from sqlalchemy.orm import (
    ImportError: cannot import name 'registry'

    should I start galaxy and see if the postgres version update happens automatically?
    unsure why this upgrade .sh is failing. thoughts? thanks!