Dave,
There are a number of things to consider when doing this, but it should
be possible. Things to keep in mind are, in no particular order:
The tool dependency path on the workstation should match what would be
the path on the server. A substantial number of packages link their
libraries with absolute paths, so any change in paths would of course
break the package at runtime.
The operating system, hardware, and installed libraries on the server
should at worst be a superset of those on the workstation, to avoid
compiling packages on the workstation that have dependencies not present
on the server.
I would recommend setting the install_database_connection option in your
config/galaxy.ini file, so that you can export the database of installed
repositories and tool dependencies from the workstation, and import this
to the server without overwriting users, jobs, and so on.
If those hurdles are cleared, it's likely that installing and copying
dependencies from one system to another might work.
Another solution, more complicated to set up but easier to use, would be
to run a single install database that both systems access, and install
the dependencies on the workstation, into a network filesystem that is
mounted in the same path on both systems. You would still need to sync
the shed_tool_conf.xml across machines, but a restart of the server
would then show all the tools and their dependencies with whatever
status they should have.
--Dave B.
On 03/27/2015 11:36 AM, David Trudgian wrote:
Hi,
I was wondering whether it might be possible/safe to install tools and
deps from the toolshed on a VM galaxy installation, and then rsync the
shed_tools and tool dependencies directories to a production galaxy server?
Unfortunately, our institution has web access only through a proxy and
blocks ‘personal web browsing’ from servers. This works on a white list
– so everything is blocked unless there was considered to be a valid
need when the list was originally setup, or an exception request is made
and approved. We have an exception in place for the main toolshed, but
various dependency downloads will fail, blocked by the proxy. Getting
exceptions for each URL we find not to work is painful and slow.
The suggestion I’ve been given is to download things on a workstation
(not subject to the blocking) and transfer them manually to the server,
hence the question about whether tool directories (and XML conf files)
can be synced between installs? Is there anything in the SQL DB that
would prevent this working, or being safe?
Otherwise I’m installing a lot of deps manually L
Thanks,
Dave Trudgian
------------------------------------------------------------------------
UTSouthwestern
Medical Center
The future of medicine, today.
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