SSH Transport Implemented #34
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added 2 commits
October 16, 2014 13:54
Provides the file action "remote_rsync_transfer". This currently
*requires* you to use a `file_action_config` on the Galaxy side, as
extra configuration is required.
Galaxy job_conf.xml:
<destination ...>
<param id="file_action_config">file_actions.yaml</param>
Galaxy file_actions.yaml:
paths:
- path: /home/vagrant/
action: remote_rsync_transfer
ssh_user: vagrant
ssh_host: my.fqdn
ssh_port: 2222
ssh_key: |
-----BEGIN RSA PRIVATE KEY-----
MIIEowIBAAKCAQEAwWYGEOhiJgbWv8eBV2LJp0MCSgrAPeX9FbsGn1I+UC110PPW
This passes configuration information in every message to Pulsar. While
suboptimal in terms of message size (ssh key is ~3x the size of a normal
message), it opens the door to multiple galaxies connecting to a single pulsar,
still using rsync. Additionally it lets the Galaxy admin reconfigure the SSH
parameters without any interaction on the Pulsar admin's part (with the
exception of `ssh_key`, as of now). This will be very beneficial if the two
groups do not have a close working relationship.
|
Tested in a live Galaxy instance, works there. |
added 3 commits
October 16, 2014 14:52
Galaxy file_actions.yaml:
paths:
- path: /home/vagrant/
action: remote_scp_transfer
Behaves identically to rsync
|
@jmchilton (sorry for all the messages), just wanted to add, since I switched to not using the persistent data directory, all SSH parameters are reconfigurable at any time by the admin. Want to cycle SSH keys/ports/username? Just update config and restart galaxy process. |
|
Super cool! |
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Provides the file actions:
This currently requires you to use a
file_action_configon the Galaxy side, as extra configuration is required.Galaxy job_conf.xml:
Galaxy file_actions.yaml:
This passes configuration information in every message to Pulsar. The ssh_key is treated separately, pending a framework for passing transport-metadata. This lets the Galaxy admin reconfigure the SSH
parameters (user/host/port/key) without any interaction on the Pulsar admin's part. This will be very beneficial if the two groups do not have a close working relationship.
Future Work
meta), which are handled much more generically than the current hardcoding ofssh_keyeverywhere.