[Bio-linux-devel] Best method to build a regularly updated bioinformatics platform

[Squires, Richard (NIH/NIAID) [C]]

Hello Luca,

Thank you for the input. That is very helpful to know!


Cheers,

Burke


--
R. Burke Squires
Computational Genomics Specialist
Contractor: Medical Sciences & Computing, Inc.
Bioinformatics and Computational Biosciences Branch (BCBB)
National Institutes of Allergy and Infectious Diseases (NIAID)
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On 10/31/16, 11:11 AM, "Luca Beltrame" <marionegri at heavensinferno.net on behalf of luca.beltrame at marionegri.it> wrote:

    In data lunedì 31 ottobre 2016 14:59:59 CET, Squires, Richard (NIH/NIAID) [C] 
    ha scritto:
    
    Hello,
    
    > 1. I appreciate the use of Ubuntu but am not a fan of the Unity desktop. I
    > find the Elementary OS (https://elementary.io, based on Ubuntu from what I
    
    While not directly involved in Bio-Linux (save as a user of the installs we 
    have here at Mario Negri Institute), I collaborate in my spare time with 
    distributions, and I would strongly recommend a firm base to develop Bio-Linux 
    on. I would not suggest Elementary as it's basically a new Desktop Environment 
    on an Ubuntu LTS base with additional software, which means that problems in 
    the DE fall mostly upon Elementary people's shoulders rather than the larger 
    Ubuntu community. 
    
    > a. Alternatively, we could pick a different flavor of
    > Ubuntu such as kubuntu or lubuntu as the reference
    
    Kubuntu is suffering a lot recently due to developer drain and for other 
    reasons that are off-topic to this, so I would not recommend it at the moment. 
    As for Lubuntu... depends on what DE it uses at the moment.
    
    > I am not treading on difficult ground here.) 2. The idea of creating USB
    > flash drives for people to use their own laptops is an attractive option as
    
    Tony has tried this approach too here when he went to give a talk in our 
    institute. There was at least limited interest in this (but "limited" because 
    90% of the scientists here do wet lab stuff). 
    
    > 4. My initial (hopefully not too naïve) thoughts are to replace the single
    > biolinux distribution with a pipeline that can build custom packages of
    
    I would suggest for this to use established pipelines, and adopt the path of 
    least effort to do so. I'm used to the Open Build System, but likely whatever 
    Ubuntu uses now to build its own distro could be used, if available (note: I 
    don't have a lot of experience in that, as I am from the RPM world). 
    	
    -- 
    Luca Beltrame, Ph.D.
    Translational Genomics Unit, Department of Oncology
    IRCCS Istituto di Ricerche Farmacologiche "Mario Negri"