Packages

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Overview

Name Upstream Package repository Stable tar.gz Description Home page, license
tar.gz Debian file-system FTP*
blimps http://blocks.fhcrc.org/blocks/uploads/blimps/blimps-3.9.tar.gz svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/blimps/trunk svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/debpacks/blimps/trunk /mnt/project/blimps/blimps-stable.tar.gz ftp://rostlab.informatik.tu-muenchen.de/blimps/blimps-stable.tar.gz blimps [1][2] [3]
coiledcoils http://www.russell.embl-heidelberg.de/coils/coils.tar.gz and in house repo svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/coiledcoils/trunk svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/debpacks/coiledcoils/trunk /mnt/project/coiledcoils/coiledcoils-stable.tar.gz ftp://rostlab.informatik.tu-muenchen.de/coiledcoils/coiledcoils-stable.tar.gz Coiled-coil prediction [4], [5]
disulfinder no public package svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/disulfinder/trunk svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/debpacks/disulfinder/trunk /mnt/project/metaldetector/disulfinder-stable.tar.gz - DISULFIND - Cysteines Disulfide Bonding State and Connectivity Predictor [6][7]
NHGRI::Blastall [8] none svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/debpacks/libnhgri-blastall-perl/trunk [9] - Perl extension for running and parsing NCBI’s BLAST 2.x
norsnet profnet (in house neural-net) svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/norsnet svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/debpacks/norsnet/trunk /mnt/project/profbval/norsnet-stable.tar.gz ftp://rostlab.informatik.tu-muenchen.de/profbval/norsnet-stable.tar.gz norsnet - [NEED TO GET A DESCRIPTION AND REFERENCE FROM AVNER SCHLESSINGER] TODO ( this is from the past five years so it will be non-free)
profbval profnet (in house neural-net) svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/PROFBval svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/debpacks/profbval/trunk /mnt/project/profbval/profbval-stable.tar.gz ftp://rostlab.informatik.tu-muenchen.de/profbval/profbval-stable.tar.gz PROFBval - predicts bvalue rigid and flexible residues [10][11] TODO ( this is from the past five years so it will be non-free)


profnet none svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/profnet svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/debpacks/profnet/trunk /mnt/project/profnet/profnet-stable.tar.gz ftp://rostlab.informatik.tu-muenchen.de/profnet/profnet-stable.tar.gz profnet - neural network from the rostlab GPL



profphd in house (old) svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/PROFphd.svn_repo/trunk svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/debpacks/profphd/trunk /mnt/project/prof/profphd-stable.tar.gz ftp://rostlab.informatik.tu-muenchen.de/profphd/profphd-stable.tar.gz PROFphd - Secondary structure and Solvent Accessibility Predictor [12][13]
sift http://sift.jcvi.org/www/sift3.0.tar svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/sift/trunk svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/debpacks/sift/trunk ? - SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. [14][15] [16]
snpsnap SIFT, BLAST, hmmer, CLUSTAL svn+ssh://rostlab.informatik.tu-muenchen.de/mnt/project/subversion/SNAP.svn_repo/branches/lkajan not assigned ? - SNAP is a method for evaluating effects of single amino acid substitutions on protein function [17][18]

disulfinder

If you prepare a test file res_id_41483.blastPsiMatTmb and a directory results you can do:

<ROOT>/usr/bin/disulfinder -r <ROOT>/usr/share/disulfinder -a 1 -p res_id_41483.blastPsiMatTmb -o results

and it does the Right Thing(tm).

TODO

  • Introduce a 'prefix' make option to act as a global prefix for installation. Do not confuse this with DESTDIR. That serves a different purpose.

sift

Depends: blimps
  • The upstream tar package contains a binary 'fastaseqs' with no source released. The purpose of this binary seems to be to convert from various formats to FASTA format. Since there is no source the fate of this binary is uncertain. Fortunately it does not seem essential or irreplaceable.

snpsnap (SNAP)

Known packaged dependencies:

  1. SIFT 2.1
  2. PSIC (binary with no source)
  3. profnet (used to be called NetRun) rostlab Neural Network (FORTRAN)
  4. PROFBval


Packaged dependencies

  1. BLAST
  2. CLUSTAL
  3. PROFphd
  4. hmmer


PROFBval

Known dependencies:

  1. profnet (used to be called NetRun) - fortran neural net. I (guy) have seen many versions of that binary and cannot determine which one is the most recent and if there were any changes, I will make some investigation. We then need to package this component first since it's central to many programs. Including SNAP.


Notes on FTP

Package distributables (.tar.gz) are copied into the FTP area (rostlab:/mnt/home/ftp) from the project directory by a cron job of user ftp on rostlab. Edit this crontab as root: crontab -u ftp -e.

Packaging HOWTO

Packaging is a nontrivial, fragile and extremely detailed oriented process. That said, please look at these recipes on how to package.