Anytime! 

Thank you for the feedback! 

Cheers, 
Nicola 

---- David Trudgian ha scritto ----

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>
>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>; David Trudgian 
><david.trudg...@utsouthwestern.edu>; 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> 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
> 
>
>________________________________________
>UT Southwestern
>Medical Center
>
>The future of medicine, today.
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