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
<[email protected]
<mailto:[email protected]>> 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:[email protected]
<mailto:[email protected]>]
Sent: Wednesday, April 13, 2016 8:47 AM
To: David Trudgian <[email protected]>;
[email protected]
<mailto:[email protected]>
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
<[email protected]
<mailto:[email protected]>> 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.
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
