Hi,

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

This means that I can't update
/opt/galaxy/pkg/cloudbiolinux/config/galaxy_default_biodata.yaml and
run install_data_s3 again to get more genomes. The first time I ran it
I only included phiX (just to test it, and because that's the
default). fab fails the second time whether I edit the yaml file or
not. I found a file called sam_fa_indices.loc under
/mnt/galaxyTools/galaxy-central/tool-data and sure enough it has write
permissions off unless you are user galaxy (not galaxyadmin, which you
are at that point in the instructions).

What am I doing wrong? Is this list the right venue for these questions?

I also noticed a couple of minor things in earlier stages of the instructions:
sudo mount /dev/sdb /mnt/galaxyData
and
sudo mount /dev/sdb /mnt/galaxyIndices
are telling the user to mount the same device on both; sdb is only
illustrative but should probably be sdc or something.

Also those `sudo mount` commands mount galaxyData and galaxyIndices as
root-only, so running fab will fail with permissions errors even the
first time. I changed the permissions on /mnt/galaxyIndices to get
round this, just to try it out, but in general this might have been a
bad thing to do!

Finally: something I don't understand happens if I try to redirect the
stdout and/or stderr from fab into a file. So it's hard to keep
records of what happened each time I ran it. If anyone understands
what's going on there that would be helpful too!

Sorry for what are probably basic questions, I'm new to python fabric.

Thanks,
Clare


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