Week Six | Docker for netboxr Galaxy tool installation

Tasks

1. Work on Galaxy tool development Status: In progress Branch: None PR: None

2. Study Galaxy tool deployment Status: In progress Branch: None PR: None

3. Meeting with supervisors Status: Thursday Branch: None PR: None

Progress report

Docker commands

docker rm -f galaxy removes instance of container

docker run –name galaxy -it bgruening/galaxy-stable:20.09 bash creates new instance of container bgruening/galaxy-stable:20.09 (container) - name of user, project, version if i wanted to run planemo, i would write planemo instead of bash -it tells if you want interactive session you can type in

docker exec -it galaxy bash creates new connection to existing instance

docker commit FIXME_6fdb2b8de2bb bgruening/galaxy-stable:gsoc docker commit 9c32395cfb39cfdaa2d4e1388f4639ec652151733d4f17850291ff3f6661e4f5 bgruening/galaxy-stable:gsoc

commits existing state (of instance) to container gsoc - instead of rewriting it, we have a new one

docker run -p 9080:80 -p 9021:21 –name galaxy -it bgruening/galaxy-stable:gsoc bash number on the left = local computer, number on the right = virtual machine

docker run -d -p 9080:80 -p 9021:21 –name galaxy bgruening/galaxy-stable:gsoc d - daemon, when you want something to run in the background

docker run -i -t -p 8080:80 bgruening/galaxy-stable:gsoc

127.0.0.1:8080 -internet and web browsers local host (everything before colon) - address of computer

    Is the server running on host "localhost" (127.0.0.1) and accepting
    TCP/IP connections on port 5432? could not connect to server: Cannot assign requested address
    Is the server running on host "localhost" (::1) and accepting
    TCP/IP connections on port 5432?

docker stats what is running and how many resources its taking up

docker rm -f galaxy-planemo; docker run –name galaxy-planemo -v /c/Users/s_ara/Desktop/GSoC:/gsoc bgruening/galaxy-stable:gsoc

docker commit d581ff23cdc986d3be4af370f99e1b8bafbaac14648feee275fb0663c9baa2c0 bgruening/galaxy-stable:gsoc

Changing ‘resolution’ to ‘resolution_parameter’ https://github.com/mil2041/netboxr/commit/b344b4236e7434b7bd5c50a1224299d8266d419d