It's just a warning, so I thought that won't be necessary
No, definitely not necessary to backport, I didn't know it was on dev.
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
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.
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/
those are part of the galaxy repository, odd that they'd be missing
The were misplaced
Look where I copied them from ...
/galaxy/srv/galaxy/server/lib/galaxy/webapps/galaxy/
galaxy_commit_id?
But I guess you need the exact commit?
just wondered if you were on a weird branch or so
If this can help :
changed: [galaxy01.educloud.no] => {
"msg": "Galaxy version changed from '' to '60ab1d5b7ae4385ca31307b0c23c52c979e337eb'"
}
:point_up: March 27, 2020 2:58 PM
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.
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 healthStill 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.
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?
# 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"
Seems to be working
I have in my queue a major refactoring of the galaxy role to better support root squash installs.
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: Look at "Active InteractiveTools" in the User menu.
@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.
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.
And we will use that probably also in bioconda more in the near future.