• Share
  • Email
  • Embed
  • Like
  • Save
  • Private Content
visagie_freebsd
 

visagie_freebsd

on

  • 774 views

 

Statistics

Views

Total Views
774
Views on SlideShare
774
Embed Views
0

Actions

Likes
0
Downloads
1
Comments
0

0 Embeds 0

No embeds

Accessibility

Categories

Upload Details

Uploaded via as Microsoft PowerPoint

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

    visagie_freebsd visagie_freebsd Presentation Transcript

    • FreeBSD-bio porting project Johann Visagie <johann@egenetics.com> / <wjv@FreeBSD.org>
    • The FreeBSD operating system
      • Direct descendent of Berkeley 4.4BSD-Lite
        • 25+ year history
        • Legendary stability and network performance
        • The reference implementation of TCP/IP stack in Unix
      • Geared towards the server room
        • Tools for large scale system administration, automation
        • Easy to configure and optimise for high-throughput serving
        • Secure default install
      • Free (under extraordinarily permissive licence)
        • Largest community-maintained software project?
    • (Open Source) Bioinformatics apps
      • Can be a real pain to install
        • Archaic, obscure, or simply broken build mechanisms
        • Hard-to-port C/C++ code
        • Messy installs leaving files all over the place
        • Tons of dependencies (*mumble* Bioperl *grumble*)
      • … and then you have to keep them up to date!
      • Not every scientist has a sysadmin at hand
      • In an open source world, duplicating all this effort seems just wrong
    • FreeBSD ports
      • Set of 7000+ &quot;build skeletons&quot; for 3 rd party apps
        • Download, patch, build and install an application
        • Automatically handle dependencies
        • May be cleanly uninstalled
        • Flexible and streamlined update, automation mechanisms
        • Can be built to a binary package (for CD/DVD distribution)
      • Integrated with operating system's CVS tree
      • Tool for &quot;industrial strength&quot; system administration
        • Open Source principles applied to system administration?
      • root@industrial:~# cd /usr/ports/biology/emboss
      • root@industrial:/usr/ports/biology/emboss# make install
      • >> Attempting to fetch from ftp://ftp.uk.embnet.org/pub/EMBOSS/.
      • Receiving EMBOSS-2.4.1.tar.gz (9079913 bytes): 100%
      • ===> Extracting for emboss-2.4.1
      • >> Checksum OK for emboss/EMBOSS-2.4.1.tar.gz.
      • ===> emboss-2.4.1 depends on executable: gmake - found
      • ===> emboss-2.4.1 depends on shared library: gd.2 - not found
      • ===> Verifying install for gd.2 in /usr/ports/graphics/gd
      • ===> Extracting for gd-1.8.4_6
      • >> Checksum OK for gd-1.8.4.tar.gz.
      • ===> gd-1.8.4_6 depends on shared library: jpeg - found
      • ===> gd-1.8.4_6 depends on shared library: png - found
      • ===> gd-1.8.4_6 depends on shared library: freetype - found
      • ===> Patching for gd-1.8.4_6
      • ===> Applying FreeBSD patches for gd-1.8.4_6
      • ===> Configuring for gd-1.8.4_6
      • ===> Building for gd-1.8.4_6
      • ===> Installing for gd-1.8.4_6
      • ===> Generating temporary packing list
      • ===> Running ldconfig
      • ===> Registering installation for gd-1.8.4_6
      • ===> Returning to build of emboss-2.4.1
      ===> emboss-2.4.1 depends on shared library: Xm.2 - found ===> emboss-2.4.1 depends on shared library: X11.6 - found ===> Patching for emboss-2.4.1 ===> Applying FreeBSD patches for emboss-2.4.1 ===> Configuring for emboss-2.4.1 ===> Building for emboss-2.4.1 ===> Installing for emboss-2.4.1 ===> emboss-2.4.1 depends on shared library: gd.2 - found ===> emboss-2.4.1 depends on shared library: Xm.2 - found ===> emboss-2.4.1 depends on shared library: X11.6 - found ===> Generating temporary packing list ===> Running ldconfig ===> Registering installation for emboss-2.4.1 root@industrial:/usr/ports/biology/emboss#
    • The bio-porters
      • Mission: Get as many Bioinformatics applications as possible into the FreeBSD ports tree
        • Create an out-of-the-box Bioinformatics server
      • Collaborate via a mailing list
        • Friendly, supportive environment for porting newbies
      • Communally maintain certain ports via list
      • Note: Anyone can submit and maintain a port
    • Successes and challenges
      • Successfully ported many major Bioinformatics apps:
        • Bioperl, Biopython, Biojava, Bioruby, Clustal W, EMBOSS, HMMER, NCBI toolkit, Phylip, etc., etc.
      • And for our next trick… Bioinformatics databases?
    • How can we infect others?
      • OpenBSD has ports; NetBSD pkg-src
        • Both originally based on FreeBSD's ports
      • Ports for Darwin (MacOS X) are being jump-started from FreeBSD
      • Linux distros:
        • Redhat's RPM
        • Debian's apt-get
        • Gentoo's portage
        • etc.
    • Acknowledgements
      • Electric Genetics
        • for giving me the time
      • The FreeBSD Project
        • for giving me the OS
      • The members of the FreeBSD-bio list
        • for sharing the work
    • Links
      • FreeBSD:
        • http://www.FreeBSD.org/
        • http://www.FreeBSD.org/doc/en/books/porters-handbook/
      • FreeBSD ports: &quot;biology&quot; category:
        • http://www.FreeBSD.org/ports/biology.html
        • http://cvsweb.FreeBSD.org/ports/biology/
      • FreeBSD-bio porters mailing list:
        • http://www.PLiG.net/mailman/listinfo/freebsd-bio/