David,

You can have multiple versions of tool 'installed' manually (i.e. without
shed).

That said, there is an option of working with the IUC to make the wanted
packages to be up-to-date and secure. i am pretty sure any PRs this
direction will get merged.

M.

On Wed, Apr 13, 2016 at 11:39 AM David Trudgian <
david.trudg...@utsouthwestern.edu> wrote:

> Hi Martin,
>
> Thanks for the input - yes there is going to be maintenance headache
> either way, private tool-shed or not. If we don't go with our own tool-shed
> though, am I right in thinking we lose versioning for tools? I.E.
> installing manually into 'tools' and tool_conf.xml I can't use <version>
> tags like the tool shed stuff does in shed_tool.conf. The infosec concern
> is mainly with libraries which are provided by tool-shed dependency package
> installs, not the main software package the tool wrapper is calling. With a
> tool shed it's feasible then we could keep older versions of tools/wrappers
> for reproducibility, rebuilding them against updated (but compatible)
> libraries when there's a security issue, perhaps?
>
> Glad to know that my idea of the workflow isn't totally wrong though.
>
> Thanks,
>
> DT
>
> --
> David Trudgian Ph.D.
> Computational Scientist, BioHPC
> Lyda Hill Department of Bioinformatics
> UT Southwestern Medical Center
> Dallas, TX 75390-9039
> Tel: (214) 648-4833
>
> From: Martin Čech [mailto:mar...@bx.psu.edu]
> Sent: Wednesday, April 13, 2016 8:47 AM
> To: David Trudgian <david.trudg...@utsouthwestern.edu>;
> galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Tool shed tools, manual dep installation
>
> Hi David,
>
> one thing that you might be missing is that the wrapper for the
> infosec-approved version might not exist yet (you would have to adapt the
> older shed-wrapped version if there were any relevant changes). But this
> largely depends on what software you want to use.
>
> Besides that your flow seems quite accurate. I would probably argue
> against own tool shed, as the maintenance overhead will probably not be
> worth it for you.
>
> Let us know if we can help in any way,
>
> thank you for using Galaxy.
>
> Martin
>
> On Tue, Apr 12, 2016 at 5:42 PM David Trudgian <
> david.trudg...@utsouthwestern.edu> wrote:
> Hi All,
>
> I’m currently caught between the requests of our Galaxy users to install
> things from main tool-shed, and our information security dept’s concerns
> r.e. the automated installation of tool-deps on our systems. Due to
> restrictive web access policies for servers here our galaxy server can’t
> access SourceForge, where many tool-dep downloads are. A request to unblock
> this for a particular tool-dep package led to our infosec justifiably
> raising concerns r.e. a tool-dep package that is quite out of date (details
> sent off list previously). We’re now currently unable to install tool-shed
> tools that users have requested.
>
> The current proposal from our infosec dept is to get all our deps from
> system repos etc. However the way I’m aware of implementing this for
> tool-shed tools, which need to run across our cluster, would be something
> pretty arduous like:
>
> * Clone the tool from the upstream toolshed repo
> * Edit the tool code to remove the package requirements
> * Identify and install all the requirements on the cluster as system pkgs
> / environment modules – with attention to versions so things work as
> expected
> * Edit the tool code so it knows to load the right environment modules /
> set right PATH when it runs
> * Install the tool into our galaxy ‘tools’ dir , not the ‘shed_tools’
> * Manually add the tool to galaxy’s tool_conf.xml.main
> * Schedule downtime to restart galaxy
> * Test things out
>
> …. or we have to host our own tool shed, import tools we want from
> upstream, edit out the package requirements, provide the deps ourselves.
> These have all the headaches of merging things in when upstream shed-tools
> change.
>
> Just wondering if I’m missing anything? I know you can turn off ‘handle
> repository dependencies’ when installing a tool, but the tool still defines
> ‘requirements’ in its XML file and shows ‘Missing repository/tool
> dependencies’ in the Admin.  Has anyone had any experience of dealing with
> this kind of situation?
>
> Many thanks!
>
> --
> David Trudgian Ph.D.
> Computational Scientist, BioHPC
> Lyda Hill Department of Bioinformatics
> UT Southwestern Medical Center
> Dallas, TX 75390-9039
> Tel: (214) 648-4833
>
>
> ________________________________________
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> Medical Center
>
> The future of medicine, today.
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