I followed the steps here https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/ to install bwa (aln) to my local galaxy instance but it gives an error status. /home/galaxy/galaxy/Makefile shows RELEASE_CURR:=16.01 so I guess my galaxy version is 16.01
What I tried:
Log in as admin on the web ;
Click on "Search Tool Shed" under "Tools and Tool Shed" ;
Click on "Galaxy Main Tool Shed" ;
Type in "bwa" ;
Click on "bwa_0_7_5" ;
Click on "preview and install" ;
Click on "install to galaxy" ;
Check the box that "When available, install externally managed dependencies (e.g. conda)? Beta" ;
Select existing tool panel section ;
Click on "install" ;
Upgrade to the latest release 17_05 then try again. The way dependencies are managed has changed significantly since the release you are using. Both Galaxy and the newest tools have changed.
Release notes: https://docs.galaxyproject.org/en/master/releases/17.05_announce.html
Thanks, Jen, Galaxy team
Hi Jen, thank you very much. I followed this post https://galaxyproject.org/admin/get-galaxy/ to upgrade galaxy.
However, I see from the Makefile that it's still "RELEASE_CURR:=16.01".
What I did:
git checkout release_17.05 && git pull --ff-only origin release_17.05
sh manage_db.sh upgrade
Anyway it seems to be upgrading but after that when I run "sh run.sh", I still can't install bwa - same error status.