Many thanks for your detailed reply. I like the sound of the second solution
which should be no problem to setup on our systems.
Still hoping it'll be possible to get a proxy exception for our system and
avoid this altogether longer term, but good to know it should be possible for
From: Dave Bouvier [mailto:d...@bx.psu.edu]
Sent: Monday, March 30, 2015 8:03 AM
To: David Trudgian; email@example.com
Subject: Re: [galaxy-dev] Safe / possible to sync toolshed tools and deps from
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
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.
On 03/27/2015 11:36 AM, David Trudgian wrote:
> 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
> 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
> Dave Trudgian
> Medical Center
> The future of medicine, today.
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