RE: UTAP

[Refael Kohen <Refael.Kohen@weizmann.ac.il>]

Hello,

I will create tag.
The genomes and other dependencies are must for UTAP. In my installation the user load the docker container with paths to it (according his installation parameters).

Refael.

-----Original Message-----
From: Andreas Tille <andreas@an3as.eu> 
Sent: Tuesday, April 02, 2019 5:09 PM
To: Tony Travis <tony.travis@minke-informatics.co.uk>
Cc: Marilyn Safran <marilyn.safran@weizmann.ac.il>; Dena Leshkowitz <Dena.Leshkowitz@weizmann.ac.il>; Refael Kohen <Refael.Kohen@weizmann.ac.il>; Debian Med Project List <debian-med@lists.debian.org>
Subject: Re: UTAP

Hi,

On Sun, Mar 31, 2019 at 06:17:16PM +0100, Tony Travis wrote:
> On 31/03/2019 12:51, Marilyn Safran wrote:
> > Hi Tony,
> > 
> > Feel free to try out the software without using a docker container, 
> > and prepare and distribute the Debian-Med package.
> > 
> > Please let us know when that package becomes available, and how to 
> > access it.
> > 
> > And please make sure to acknowledge our paper so that others can 
> > contact us if needed.
> 
> Hi, Marilyn.
> 
> The first step is for me to let the Debian-Med team know about UTAP, 
> by CC to the Debian-Med mailing list, and for me to try it without 
> using a Docker container to see what other software dependencies UTAP requires.
> 
> @debian-med list,
> 
> I'm interested in packaging UTAP:
> 
> > https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-
> > 019-2728-2
> 
> ...
>
> The software is available under GPLv3:
> 
> > https://utap.readthedocs.io/en/latest/
> I've contacted the upstream authors Refael Kohen, Dena Leshkowitz, and 
> Marilyn Safran who are willing to let us package and distribute their 
> UTAP software for Debian-Med.

Regarding packaging it would help a lot if somebody could convince upstream to tag a release.  I have not found any tags at

    https://bitbucket.org/bbcu/utap/downloads/?tab=tags

Would you mind contacting upstream about this?

Moreover, I wonder what to do with these large data, that are mentioned here

    https://utap.readthedocs.io/en/latest/rst/installation.html#create-a-directory-for-utap-software-and-its-output

Kind regards

      Andreas. 

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