Hi Bjoern,

Yes, we can reach stuff in the cargo-port. Unfortunately doing that isn’t a 
solution as the package that concerns our infosec is the same older version 
there in cargo-port as it has been trying to pull from SourceForge. Galaxy 
might be able to get it then, but I’m not permitted to install that package.

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: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com]
Sent: Wednesday, April 13, 2016 8:46 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,

which sites are blocked?
Can you access tools that take it's binaries from 
https://github.com/galaxyproject/cargo-port?

If so Eric has ported all URLs over to cargo-port sometime ago. So we just need 
to update the packages for you.
This only holds true for IUC packages and we probably need to update the 
toolshed repos for a few packages.

An other solution would be to get a similar setup as your cluster running 
elsewhere install all tools on this computer and just move your installations 
over. This should work as well.

Cheers,
Bjoern
On 12.04.2016 23:42, David Trudgian 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tool-dep package that is quite out of date (details sent off list previously).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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