User: machinelearner

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Posts by machinelearner

<prev • 15 results • page 1 of 2 • next >
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Moving a Galaxy Docker instance from one server to another
... Hi everyone! Is there a way to move one instance of Docker Galaxy over from one server to another? Here is the general timeline of events we have tried: 0. Pull the stable base image 1. Run the base image to create a container 2. Made changes in the container (such as installing conda in the cont ...
docker galaxy written 5 weeks ago by machinelearner10 • updated 5 weeks ago by Bjoern Gruening4.7k
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Comment: C: Docker Galaxy Job conf file and SLURM
... This worked! Thanks for the quick reply, I appreciate it! ...
written 6 weeks ago by machinelearner10
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Docker Galaxy Job conf file and SLURM
... Hi everyone, Is it possible to run multiple thread processes on Docker Galaxy via SLURM? According to SLURM documentation, using the --cpus-per-task flag allows for multiple CPUs to run. However, running this on Galaxy results in the following error: Unable to run job due to a misconfiguratio ...
galaxy slurm written 6 weeks ago by machinelearner10 • updated 6 weeks ago by Devon Ryan1.6k
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Comment: C: docker galaxy apt-get update & upgrade error
... Solved, temporarily ...
written 10 weeks ago by machinelearner10
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Comment: C: docker galaxy apt-get update & upgrade error
... This has been temporarily fixed on our end. Explanation for anyone who stumbles on this problem in the future: Looks like doing a apt-get upgrade and upgrading all the packages in the container will also upgrade nginx packages. This led to a error log report in /var/log/nginx saying that upload_sto ...
written 10 weeks ago by machinelearner10
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(Closed) docker galaxy apt-get update & upgrade error
... Hi everyone, We have recently pulled down an image of the docker Galaxy and created a container with it. Some of the tools that we want to install require perl modules such as GD::Graph. The only way that we were able to get these modules installed were by updating and upgrading apt-get first. ...
docker galaxy written 10 weeks ago by machinelearner10
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Comment: C: Docker Galaxy submitting jobs to UGE
... Thanks for the reply! We are hesitant to do this because UGE is a license product and we don't want it in the container itself. ...
written 3 months ago by machinelearner10
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Docker Galaxy submitting jobs to UGE
... Hi all, Has anyone been able to submit jobs on a Docker Galaxy instance to SGE or UGE on a centOS7 machine? After referring to https://github.com/bgruening/docker-galaxy-stable#Using-an-external-Grid-Engine-cluster we were still not able to have jobs passed on to UGE. Going into the container, we ...
uge docker galaxy written 3 months ago by machinelearner10
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Answer: C: Cannot copy datasets from one history to another on local Galaxy
... This issue has resolved itself. Not sure how, as there was no restart or any changed made recently on our end. ...
written 5 months ago by machinelearner10
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Cannot copy datasets from one history to another on local Galaxy
... Hi all, We have a local instance of Galaxy installed but it is not able to be copy files from one history to another via the "copy datasets" option on the right tool bar. Is there a setting that has to be set so that this can occur, I have not found anything in the galaxy.ini file, but I could have ...
galaxy written 5 months ago by machinelearner10

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