Clare;
I am trying to use install_data_s3 (data_fabfile.py) to get data from the cloudbiolinux bucket into a virtualbox VM, as per the instructions at usegalaxy.org/vm .
When I ran fab -f data_fabfile.py -H localhost install_data_s3:config/galaxy_default_biodata.yaml the first time, it worked.
But when I try running it a second time, it dies with [localhost] run: echo 'index phix /mnt/galaxyIndices/genomes/phiX174/phix/seq/phix.fa >> sam_fa_indices.loc [localhost] out: /bin/bash: sam_fa_indices.loc: Permission denied
The fabric script is running standard shell commands, so all of the normal unix permissions will apply. As you mention, if the permissions to /mnt/galaxyTools/galaxy-central/tool-data/sam_fa_indices.loc do not allow access to galaxyadmin you'll need to adjust that from the commandline.
Reading the instructions, the 'galaxyadmin' and 'galaxy' user suggestions are a bit confusing. My suggestion it to run the install_data_s3 command as the 'galaxy' user, and do: 'sudo chmod -R galaxy /directory/name' on any directories with permission issues. Since you later run the server as 'galaxy', this will ensure that user has proper permissions.
Hope this helps, Brad