From Rost Lab Open
Revision as of 18:36, 18 November 2013 by Goldberg (talk | contribs) (Package overview)

I want to install a package onto my Ubuntu/Debian system

  • Our packages are listed in the Packages Section below. Review that list to find your desired predictor.
  • Debian/Ubuntu repository - detailed instructions on how to install packages from our debian repository

I want to install a package onto my RHEL/SUSE/CentOS

Please check out the page on our RPM package repository for RHEL/SUSE/CentOS.


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Package overview

Package name Build depends Depends Resources Project directory Package repository Description Home page, license rpm available
Upstream Debian
blast2 svn+ssh:// n.a.

The purpose of this package is to provide the working blast2 that we have in Debian Lenny for CentOS


blimps /mnt/project/blimps Debian Med svn+ssh:// blimps [1][2] FHCRC NONCOMMERCIAL LICENSE *

cd-hit /mnt/project/software/free See Debian p.r. svn+ssh:// Cluster Database at High Identity with Tolerance cd-hit [3]

chhblits hhblits See Debian p.r. file:///mnt/project/aliqeval/hhblits/repos/chhblits Cached hhblits - results are cached for faster response. GPL

chopperdb no repo, files seem to be in /mnt/project/chop/chopper-db ? ? database required for profchop CHOP, GPL

coils Debian Med svn+ssh:// Coiled-coil prediction GPL [4]

disulfinder libboost, libboost-graph, libf2c2 /mnt/project/metaldetector no upstream from orig authors, in-house: svn+ssh:// Debian Med svn+ssh:// DISULFIND - Cysteines Disulfide Bonding State and Connectivity Predictor GPL [5][6]

dssp Debian Med svn+ssh:// Standardized secondary structure assignment. [7] Boost-1.0 (free)

fastprofkernel /mnt/project/fastprofkernel svn+ssh:// A protein classification system using protein profiles and the original profile kernel Academic free

ffindex Debian Med svn+ssh:// simple index/database for huge amounts of small files CC-BY-SA-3.0, GPL-2.0+

freecontact ssh:// Debian Med ssh:// Free software for protein contact prediction. GPL-3+

libfreecontact-perl ssh:// Debian Med svn+ssh:// Free software for protein contact prediction - Perl module. Artistic or GPL-3+

hhsuite ffindex Debian Med svn+ssh:// sensitive protein sequence searching based on HMM-HMM alignment GPL-2.0+, GPL-3.0+

hmmer2 hmmer version 2 - no longer developed, the current version is 3; This package is the debian stable version with the package and the executables renamed so it can coexist with the version 3 hmmer package *
idmapper perl svn+ssh:// maps IDs between over 20 different databases GPL

libai-fann-perl Debian Med svn+ssh:// Perl wrapper for the FANN library Perl Artistic License

libnhgri-blastall-perl none NHGRI-Blastall-[0-9.]+.tar.gz Debian Med git:// Perl extension for running and parsing NCBI’s BLAST 2.x PUBLIC DOMAIN

librg-dudek-bundle-perl svn+ssh:// Perl wrapper for blastpgp written by Dariusz Przybylski. 2000, 2001 Przybylski, Rost, 'like Perl' license (Artistic or GPLv1+) *

librg-blast-parser-perl svn+ssh:// Very fast blast(all|pgp) output (default, -m 0) parser - perl module (binding for the C/C++ library). Perl Artistic License

librostlab svn+ssh:// Debian Med svn+ssh:// C++ library from the Rost Lab [8] LGPL

librostlab-blast svn+ssh:// Debian Med svn+ssh:// Very fast C++ NCBI BLAST parser library [9] LGPL

librg-data-perl perl, liblog-log4perl-perl, libwww-perl, wget, tar, rsync, ncftp, blast2, cd-hit /mnt/project/rost_db svn+ssh:// Rostlab-data commonly used perl libraries GPL

librg-exception-perl perl svn+ssh:// Debian Med svn+ssh:// RG::Exception perl module Perl Artistic

librg-liu-bundle-perl libxml-dom-perl svn+ssh:// Perl modules written by Jinfeng Liu Same as Perl *

librg-pp-bundle-perl svn+ssh:// PP perl modules and tools including result conversion to XML Same as Perl

librg-pp-queuemgr-perl pp-cache-mgr svn+ssh:// PredictProtein queue manager perl module GPL

librg-utils-perl profphd-utils svn+ssh:// Debian Med svn+ssh:// Set of wrappers and conversion utilities for bioinformatics databases GPL *

libzerg Debian Med svn+ssh:// fast blast parser in C GPL

libzerg-perl libzerg Debian Med svn+ssh:// fast blast parser perl module GPL

ligscan Math::Vector::Real::kdTree /mnt/project/ligscan svn+ssh:// none This program analyzes structural features from the PDB structures and extracts binding affinities from them Perl Artistic License

loctree hmmer2, librg-utils-perl, loctree-data, predictnls, ps-scan, signalp, svm-light 5.00(!) CBlast80, Pfamls2, PrositeDat, SwissDocKeyIdxL, SwissBlast /mnt/project/loctree svn+ssh:// loctree - prediction of sub-cellular localization of proteins 2005 Nair and Rost, GPL

loctree-data rsync /mnt/project/loctree svn+ssh:// svn+ssh:// data files for loctree [10] 2005 Nair and Rost, GPL

loctree2 CBlast80 /mnt/project/loctree2 svn+ssh:// LocTree2 - Prediction of sub-cellular localization for all proteins in all domains of life GPL

loctree3 CBlast80 /mnt/project/loctree3 svn+ssh:// LocTree3 - Improved prediction of protein localization in all domains of life GPL

lowcompseg /mnt/project/seg svn+ssh:// segment sequence(s) by local complexity PUBLIC DOMAIN *

metadisorder perl, profnet-md, tcsh svn+ssh:// svn+ssh:// alias MD (C) 2009 Avner Schlessinger, Non-free
metastudent blast2, java, perl, python2.6 /mnt/project/metastudent svn+ssh:// svn+ssh:// MetaStudent predicts GO terms for a protein with a homology search. Download source via FTP GPL-2+

metastudent-data blast2, rsync /mnt/project/metastudent svn+ssh:// svn+ssh:// MetaStudent predicts GO terms for a protein with a homology search. This package provides architecture independent data files. GPL-2+

metastudent-data-2 rsync /mnt/project/metastudent svn+ssh:// svn+ssh:// MetaStudent predicts GO terms for a protein with a homology search. This package provides more architecture independent data files. GPL-2+

mprof ssh:// reprof replacement, mutationscan GPL

nlprot debhelper (>= 7), autotools-dev, po-debconf blast2, svm-light5, nlprot-data /mnt/project/nlprot/ svn+ssh:// Non-free, restricted-distribution

nlprot-data /mnt/project/nlprot/ svn+ssh:// Non-free, restricted-distribution

norsnet /mnt/project/norsnet svn+ssh:// Debian Med svn+ssh:// NORSnet - identifies unstructured loops from sequence 2007 Schlessinger, Liu and Rost, GPL

norsp /mnt/project/norsp svn+ssh:// Debian Med svn+ssh:// norsp - predictor of non-regular secondary structure Copyright 2003 Liu and Rost, GPL *

pp2features svn+ssh:// converts PredictProtein results to machine learning features - the converters also support conversion to BioXSD GPL

pp2html svn+ssh:// converts PredictProtein results for WWW presentation GPL

pp-cache-mgr libboost-filesystem, libboost-program-options, libboost-regex, libc6, libgcc1, libmysql++, libstdc++ svn+ssh:// PredictProtein results cache Non-free

pp-popularity-contest svn+ssh:// Debian Med svn+ssh:// PredictProtein popularity contest GPL *

pp-queue-mgr librg-pp-queuemgr-perl svn+ssh:// PredictProtein queue manager Non-free

ppmi /mnt/project/predictprotein/vm_image/ svn+ssh:// PredictProtein Machine Image maintenance scripts PredictProtein Image License

ppsudo libboost-program-options, libc6, libgcc1, libstdc++6 svn+ssh:// execute command as PredictProtein user GPL

predcellcycle (pcc) blast2 CBlast svn+ssh:// Determine estimates for involvement in the cell cycle process or search CellCycleDB for predicted cell cycle proteins among six eukaryotic proteomes [11], [12] Non-free

predictnls File::Temp, perl /mnt/project/predictnls svn+ssh:// Debian Med svn+ssh:// predictnls - prediction and analysis of nuclear localization signals [13] 2000 Cokol, Nair and Rost, GPL
Reimplementation available from the Galaxy Tool Shed

predictprotein blast2, bioperl, ncoils, disulfinder, libnhgri-blastall-perl, libnhgri-blastall-perl, librg-liu-bundle-perl, librg-utils-perl, loctree, lowcompseg, metadisorder, norsnet, profasp, profbval, profchop, profcon, profdisis, profglobe, profisis, profphd, proftmb CBlast, CBlast80, ProDomBlast, PrositeConvDat, SwissBlast /mnt/project/predictprotein svn+ssh:// Debian Med svn+ssh:// PredictProtein pipeline 2004 Rost, Yachdav and Liu, GPL

predictprotein-nonfree signalp, svm-light5, loctree, profasp, metadisorder, psic, rost-runpsic, tmhmm /mnt/project/predictprotein svn+ssh:// Meta package that depends on the optional non-free or contrib components of PredictProtein. Optional components of PredictProtein are Suggests and do not get installed automatically. This package is to aid the administrator at the Rost Lab (as only the Rost Lab has these dependencies, since they are non-redistributable). GPL
ppweb debconf (>= 0.5), debhelper (>= 7), autotools-dev, po-debconf, dbconfig-common php5-cgi | php5, php5-mysql | php5-mysqli, apache2, mysql-server, pp2html, pp-queue-manager, ppsudo, librg-pp-bundle-perl, libjs-jquery, libjs-jquery-ui svn+ssh:// PredictProtein web interface GPL

predictprotein-xsd svn+ssh:// PredictProtein XML schema definition GPL

profbval profnet, Recommends: librg-utils-perl /mnt/project/profbval svn+ssh:// Debian Med svn+ssh:// PROFBval - predicts bvalue rigid and flexible residues 2006 Schlessinger, Yachdav and Rost, GPL *

profchop hmmer2, profphd, profnet-chop, librg-dudek-bundle-perl, librg-liu-bundle-perl, librg-utils-perl svn+ssh:// Method for dissecting proteins into domain-like fragments based on sequence homology [14] CHOP, GPL

profcon File::Temp, perl, blast2,lowcompseg, profnet_profcon, librg-utils-perl, librg-dudek-bundle-perl, profphd /mnt/project/profbval svn+ssh:// svn+ssh:// Prediction of protein inter-residue contacts 2005 Punta, Rost, GPL *

profdisis Config::IniFiles, perl (>= 5.10.0), svm-light5 svn+ssh:// DISIS (packaged as profdisis) - DNA binding sites prediction 2007 Ofran, Mysore and Rost, GPL

profglobe perl /mnt/project/globe svn+ssh:// profglobe - predicts the globularity of a protein 1999 Rost, GPL

profisis Config::IniFiles, perl, profnet svn+ssh:// Debian Med svn+ssh:// ISIS (packaged as profisis) - protein binding sites prediction [15] 2007 Ofran and Rost, GPL

profnet /mnt/project/profnet svn+ssh:// Debian Med svn+ssh:// profnet - neural network from the rostlab: both 'phd' and 'prof' kinds GPL

profphd profnet, profphd-utils, librg-utils-perl /mnt/project/prof svn+ssh:// Debian Med svn+ssh:// PROFphd - Secondary structure and Solvent Accessibility Predictor [16][17] GPL *

profphd-utils /mnt/project/prof svn+ssh:// Debian Med svn+ssh:// PROFphd utilities: convert_seq, filter_hssp GPL *

proftmb libgsl0, libopt /mnt/project/proftmb svn+ssh:// Debian Med svn+ssh:// Per-residue prediction of bacterial transmembrane beta barrels [18] 2004 Bigelow, Petrey, Liu, Przybylski and Rost, GPL *

ps-scan svn+ssh:// ps_scan is a program used to scan patterns, rules and/or profiles from PROSITE against protein sequences [19] GPL *

pssh2 hhblits uniprot20, pdb_full /mnt/project/pssh/pssh2_project/ git /mnt/project/pssh/pssh2_project/ pssh2 can be used to generate the pssh2 database of alignments of sequences against pdb structures, more specifically generate_pssh2 maps one sequence onto related pdb structures GPL *

rate4site /mnt/project/consurf/package/rate4site/ file:///mnt/project/subversion/rate4site/trunk file:///mnt/project/subversion/rate4site/trunk/debian detects conserved amino-acid sites by computing the relative evolutionary rate for each site in the multiple sequence alignment (MSA). GPL

reprof libai-fann-perl, libfann2 /mnt/project/reprof/ svn+ssh:// Debian Med svn+ssh:// reprof is a protein secondary structure and accessibility predictor by Peter Hoenigschmid GPL

reprof.c libfann2 reprof.c is Peter Hoenigschmid's protein secondary structure and accessibility predictor, optimized and implemented in C by Martin Steinegger GPL?

rost-runpsic psic svn+ssh:// Provides GPL *

rost-utils libssl-dev svn+ssh:// Rost Lab utilities without their own packages GPL

rostlab-data librg-data-perl, hmmer, dssp /mnt/project/rost_db svn+ssh:// Bioinformatics database synchronization and post-processing solution GPL

rostlab-share-scripts /mnt/project/subversion/rostlab_share_scripts.git ssh:// Useful reusable scripts to share among rostlab members Non-free by default (subject to each script's author)

sepia /mnt/project/? svn+ssh:// Christian Schaefer's project

shtimelimit svn+ssh:// limited absolute execution time sh GPL

sift blimps-utils, libblimps /mnt/project/sift Debian Med svn+ssh:// SIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. [20][21] [22]FHCRC NONCOMMERCIAL LICENSE *

snap-cache-mgr svn+ssh:// snap results cache GPL

snap2 blast2, libai-fann-perl, libfile-chdir-perl, librg-utils-perl, predictprotein, reprof, run-psic, sift, CBlast80, dbSwiss, SwissBlast, swiss_dat /mnt/project/resnap svn+ssh:// SNAP2 is a method for evaluating effects of single amino acid substitutions on protein function by Maximilian Hecht Academic Software License Agreement

snap2cc snap2 /mnt/project/resnap svn+ssh:// autonomous snap2 for cloud clients Academic Software License Agreement

snapc-ra /mnt/project/resnap svn+ssh:// Snap cache remote access:<tool> Perl Artistic License

snapfun hmmer2, librg-liu-bundle-perl, librg-utils-perl, profbval, profphd, profnet, run-psic, sift CBlast, CBlast80, dbSwiss, Pfamls2, SwissBlast, swiss_dat /mnt/project/snap svn+ssh:// SNAP is a method for evaluating effects of single amino acid substitutions on protein function [23][24] NON COMMERCIAL SOFTWARE LICENSE AGREEMENT *

svm-light5 svn+ssh:// Non-free, non-redistributable, redistributable by Rostlab by special authorization, [25]

squashblast perl svn+ssh:// 'squashblast' can convert -m 0 blast output without loss of information to a format ~33% smaller than the original GPL and LGPL (for libraries)

ucon File::Temp, perl /mnt/project/ucon svn+ssh:// UCON NON COMMERCIAL SOFTWARE LICENSE AGREEMENT *

uniqueprot python, blast2 /mnt/project/uniqueprot svn+ssh:// svn+ssh://[latest_version] UniqueProt 2.0 - Reduce the redundancy in a set of protein sequences; FTP download GPL


  • Repositories accessible via ssh (e.g. svn+ssh, git over ssh) are not public. You will need to get an account on the respective host to access these.

What is packaged? - a list of all packaged files | What provides ... ?

Look in the Contents files of your distribution (most often 'stable') in .

In these lists you find all files packaged for the 'stable' distribution:

Architecture Contents

You can also use apt-file(1) instead of searching the Contents files (apt-file does just that).

Downloading and installing a .tar.gz

Notes on tar.gz

'tar.gz' packages of our software are available for expert users - please e-mail us. The complexity of cross-dependencies among these packages make installation and especially following updates of say 'prof' from tar.gz a nightmare. We recommend that all users use the Debian/Ubuntu packages for installing our prediction methods. This option allows you to install methods with a single click and receive updates automatically. Drink a tea or a coffee instead of trying to find the right Fortran compiler and the correct placement of an updated perl module.

Not convinced? - here is a disclaimer

Disclaimer: if you are unlucky enough to not be able to use our Debian/Ubuntu package repository we provide these steps for you to get the programs install the hard way. Note however that the Debian/Ubuntu packages are the solution to the problem of installing software easily. What you are about to read is already way beyond what you would ever experience on a graphical user interface. Follow the steps very carefully. The slightest change or inaccuracy (such as a spelling mistake or inaccurate copying) is likely to result in a complete failure of the whole procedure.

Proceed at your own risk/time

  1. You downloaded package.tar.gz.
  2. Look up the Depends list of the software in the table above.
  3. Install all dependencies before proceeding. Important: use the same prefix you intend to use when installing this package. $HOME is usually a good prefix.
  4. Proceed when all dependencies are installed.
  5. Execute: cd /tmp
  6. Execute: tar -xvzf package.tar.gz
  7. Note the directory that was created in the above step. cd into that directory
  8. Look for a README file and follow it - it may contain package specific instructions
  9. Decide where you would like the package to install. If there are dependencies install the package with the same prefix you used for the dependencies. A good prefix is $HOME - your home directory. I assume you choose this.
  10. Execute: make prefix=$HOME
    • If this fails get back to us. Your system may be missing a build dependency - look at the Depends column - or is altogether not supported. But it is likely that we can help you. If you yourself know what development library is missing install it and repeat this step until it completes with success.
  11. Execute: make prefix=$HOME install
  12. Add $HOME/usr/bin to your PATH
    • If you use bash execute: export PATH="$HOME/usr/bin:$PATH"
    • If you use bash add this line to your ~/.bashrc:
      export PATH="$HOME/usr/bin:$PATH"
  13. Add $HOME/usr/share/perl5 to the list of directories in which to look for Perl library files
    • If you use bash execute: export PERL5LIB="$HOME/usr/share/perl5:$PERL5LIB"
    • If you use bash add this line to your ~/.bashrc:
      export PERL5LIB="$HOME/usr/share/perl5:$PERL5LIB"
  14. Add $HOME/usr/lib to the shared library lookup path
    • If you use bash execute: export LD_LIBRARY_PATH="$HOME/usr/lib:$LD_LIBRARY_PATH"
    • If you use bash add this line to your ~/.bashrc:
      export LD_LIBRARY_PATH="$HOME/usr/lib:$LD_LIBRARY_PATH"
  15. Add $HOME/usr/share/man to the manual page lookup path
    • If you use bash execute: export MANPATH="$HOME/usr/share/man:$MANPATH"
    • If you use bash add this line to your ~/.bashrc:
      export MANPATH="$HOME/usr/share/man:$MANPATH"
  16. Further files needed for operation may have been installed into $HOME/usr/share/package/. The copyright, license, documentation and examples may have been installed into $HOME/usr/share/doc/package/.
  17. You are done. Ready to run the program you installed.



  • in order to work with the hssp format (use copf, etc.) your protein identifiers must be up to 12 character long and no longer
  • what identifier means is yet to be clarified - TODO - but see examples below
  • identifiers longer than 12 characters cause cryptic, hard to recognize error messages and failures in various programs and scripts
  • An example:
    • Bad line in blast results - copf fails:
    >gnl|swiss|P01730_CD4_HUMAN_458 T-cell surface glycoprotein CD4 OS=Homo sapiens GN=CD4 PE=1 SV=1
    • Good blast result line - will work with copf:
    >gnl|swiss|P01730 T-cell surface glycoprotein CD4 OS=Homo sapiens GN=CD4 PE=1 SV=1

It is important to notice that the blast database you run proteins against has to be made with the right length (<=12) of identifiers. Otherwise blast2saf creates a saf with too long identifiers and then copf (converting saf to hssp) fails.

Resource definitions

comprehensive blast database, e.g. UniProt + PDB
comprehensive blast database - redundancy reduced, e.g. to 80%
SwissProt database flat file ID index generated by dbSwiss(1)
Pfam_ls file compatible with HMMER2.0
blast database formed of ProDom
prosite_convert.dat file. Generated by (local copy). The (6) fields are separated with space. Format example:
N[^P][ST][^P] ASN_GLYCOSYLATION PS00001 PDOC00001 1 "N-glycosylation site"
[RK]{2}.[ST] CAMP_PHOSPHO_SITE PS00004 PDOC00004 1 "cAMP- and cGMP-dependent protein kinase phosphorylation site"
prosite.dat file
SwissProt 'dat' file
blast database formed of SwissProt
swissprot/docs/keyindex.txt file
Swiss-Prot keyindex.txt converted for loctree. Use the perl/ program from the loctree package to generate this file.

Packaging HOWTO

Packaging is a non-trivial, fragile and extremely details oriented process. That said, please look at these recipes on how to package.

Packaging project status

Here is a list that keeps track on the progress of our lab packaging project. In case you are interested in a NON-packaged program and would like to help and package it, please email