Nicola,

Just a note that the resolver setup worked nicely to have manual tool-deps for 
those that concern infosec – and can now use the tools we need.

Thanks again for the pointer to that!

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: David Trudgian
Sent: Wednesday, April 13, 2016 11:12 AM
To: 'Nicola Soranzo' <nsora...@tiscali.it>; Martin Čech <mar...@bx.psu.edu>; 
galaxy-dev@lists.galaxyproject.org
Subject: RE: [galaxy-dev] Tool shed tools, manual dep installation

Nicola,

Thanks! I completely missed that. That’s very useful to know.

Martin – yes a PR is on the to-do list, but unfortunately it’s a low-ish 
priority as the wish is to be using system / module deps. Have an impending 
vacation, so am having to get through a lot of stuff right now. Hopefully 
eventually we can get back to tool shed deps.

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: Nicola Soranzo [mailto:nicola.sora...@gmail.com] On Behalf Of Nicola 
Soranzo
Sent: Wednesday, April 13, 2016 11:03 AM
To: Martin Čech <mar...@bx.psu.edu<mailto:mar...@bx.psu.edu>>; David Trudgian 
<david.trudg...@utsouthwestern.edu<mailto:david.trudg...@utsouthwestern.edu>>; 
galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>
Subject: Re: [galaxy-dev] Tool shed tools, manual dep installation

Hi David,
in the server I am administering I don't use the Tool Shed dependency resolver 
and is not much work if you are used to environment modules. For more 
information, see:

https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html

Cheers,
Nicola
On 13/04/16 16:42, Martin Čech wrote:
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<mailto: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<mailto:mar...@bx.psu.edu>]
Sent: Wednesday, April 13, 2016 8:47 AM
To: David Trudgian 
<david.trudg...@utsouthwestern.edu><mailto:david.trudg...@utsouthwestern.edu>; 
galaxy-dev@lists.galaxyproject.org<mailto: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<mailto: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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