[Bio-Linux] GALAXY version and failure to install a tool from the toolshed

[Ian Donaldson]

Dear Tim,

Thanks for your detailed reply!  

The essence of the problem is that our MACS2 tool has a few dependencies that need to be installed in order, which is something the Bio-Linux version cannot do and newer versions can.  My aim is to give a set of ChIP-seq tutorials and allow people to run the analyses themselves using Galaxy in Bio-Linux.  Bio-Linux Galaxy is great as it works out of the box, however several tweaks are needed already, so I don't think getting people to reinstall Galaxy is an option. 

The MACS2 tool installs MACS2.1.0 including numpy.  Pre-installing MACS2.1.0 seems to be an option, as even if the installation fails MACS2 would still be available.  However I do not know how this effects the distribution of the VM.  

Regards,
Ian

________________________________________
From: Tim Booth [tbooth at ceh.ac.uk]
Sent: 22 April 2015 11:01
To: Bio-Linux help and discussion
Cc: Peter Briggs
Subject: Re: [Bio-Linux] GALAXY version and failure to install a tool from the toolshed

Hi Ian,

I'm wary of upgrading the Galaxy package, because unless it gets a whole
load of testing it tends to break people's exiting configurations and
workflows.  I'll do it at some point, but not soon.

Certainly some stuff from the Tool Shed is still installing fine, so I'm
wondering if it might be possible to persuade this package to install
and just add it in to the galaxy-tools-bl package.  All Tool Shed
installation actually does, despite the big song-and-dance you see in
the web interface, is to copy a few files into a directory.  This would
be much easier for me to do than upgrading Galaxy.  Do you think it
would solve your problem?

How are you installing the actual macs21 tool?  Bio-Linux still has only
macs20 just now but I could upgrade it.

If the version of Galaxy on Bio-Linux is giving you trouble and you are
happy with your BitBucket installation then you could always try
removing galaxy-server from the VM image and cloning the configuration
you have working.  On Bio-Linux I tried to make Galaxy set-up "smart"
and "foolproof" but the downside of that is that if something goes
wrong, or needs manual updating, it can be very confusing, so if my
version is doing more harm than good you don't have to use it.

Cheers,

TIM

On Tue, 2015-04-21 at 11:18 +0100, Ian Donaldson wrote:
> Hi,
>
> We have been trying to prepare a suite of tools to use on our
> production GALAXY instance and on a Bio-Linux 8 VM instance (for the
> purpose of running tutorials).  The tool in the link below installs
> correctly on our GALAXY (a clone of galaxy-dist from bitbucket,
> changeset 16062:a7ae7afffa8f ), but does not install correctly in
> Bio-Linux.
>
> https://testtoolshed.g2.bx.psu.edu/view/pjbriggs/macs21/9f6d5cae9181
>
> All we can say at the moment is that the older version handles the
> installation differently...  Is it possible to update the version of
> GALAXY in Bio-Linux, or there some other work around to get the tool
> installed?
>
> Thank you,
> Ian
>
>

--
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB

http://environmentalomics.org/bio-linux
+44 1491 69 2297

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