The following installation instructions were kindly provided by Christoph Hahn
==============================================================================

Took me also a while to get CEGMA running on Ubuntu. I am using 10.04 /
64 bit also.

the genewise problem I overcame by using apt-get to install wise and
wise-doc. Then I also downloaded the genewise tarball in order to set
the environmental variable to the wiseconfig directory there. It worked
for me!

Thanks again to Keith for his help!

cheers,
Christoph

Here´s what I did in detail:

## FAlite.pm dowloaded into perl directory
cd /etc/perl
sudo wget http://homepage.mac.com/iankorf/FAlite.pm

##install genewise
sudo apt-get install wise
sudo apt-get install wise-doc
wget http://korflab.ucdavis.edu/Datasets/cegma/wise2.2.3-rc7.tar.gz
tar xvfz wise2.2.3-rc7.tar.gz
cd wise2.2.3-rc7/
cd wisecfg/
pwd
##set environmental variable WISECONFIGDIR in ~/.bashrc
nano ~/.basrc
export WISECONFIGDIR=/home/derhazel/src/wise2.2.3-rc7/wisecfg/
. ~/.bashrc ## source .bashrc

##install geneid
wget
ftp://genome.crg.es/pub/software/geneid/geneid_v1.4.4.Jan_13_2011.tar.gz
tar xvfz geneid_v1.4.4.Jan_13_2011.tar.gz
cd geneid/
make
##stdout
mkdir ./bin;
mkdir ./objects;
gcc -c -I./include -Wall -O3 ./src/geneid.c -o ./objects/geneid.o
gcc -c -I./include -Wall -O3 ./src/BackupGenes.c -o ./objects/BackupGenes.o
gcc -c -I./include -Wall -O3 ./src/PeakEdgeScore.c -o
./objects/PeakEdgeScore.o
gcc -c -I./include -Wall -O3 ./src/GetTranscriptTermini-usingslopes.c -o
./objects/GetTranscriptTermini-usingslopes.o
gcc -c -I./include -Wall -O3 ./src/BuildAcceptors.c -o
./objects/BuildAcceptors.o
gcc -c -I./include -Wall -O3 ./src/BuildU12Acceptors.c -o
./objects/BuildU12Acceptors.o
gcc -c -I./include -Wall -O3 ./src/BuildDonors.c -o ./objects/BuildDonors.o
gcc -c -I./include -Wall -O3 ./src/BuildInitialExons.c -o
./objects/BuildInitialExons.o
gcc -c -I./include -Wall -O3 ./src/BuildInternalExons.c -o
./objects/BuildInternalExons.o
gcc -c -I./include -Wall -O3 ./src/BuildZeroLengthExons.c -o
./objects/BuildZeroLengthExons.o
gcc -c -I./include -Wall -O3 ./src/BuildUTRExons.c -o
./objects/BuildUTRExons.o
gcc -c -I./include -Wall -O3 ./src/BuildORFs.c -o ./objects/BuildORFs.o
gcc -c -I./include -Wall -O3 ./src/BuildSingles.c -o
./objects/BuildSingles.o
gcc -c -I./include -Wall -O3 ./src/BuildSort.c -o ./objects/BuildSort.o
gcc -c -I./include -Wall -O3 ./src/BuildTerminalExons.c -o
./objects/BuildTerminalExons.o
gcc -c -I./include -Wall -O3 ./src/ComputeStopInfo.c -o
./objects/ComputeStopInfo.o
gcc -c -I./include -Wall -O3 ./src/CookingGenes.c -o
./objects/CookingGenes.o
gcc -c -I./include -Wall -O3 ./src/CorrectExon.c -o ./objects/CorrectExon.o
gcc -c -I./include -Wall -O3 ./src/Dictionary.c -o ./objects/Dictionary.o
gcc -c -I./include -Wall -O3 ./src/DumpHash.c -o ./objects/DumpHash.o
gcc -c -I./include -Wall -O3 ./src/FetchSequence.c -o
./objects/FetchSequence.o
gcc -c -I./include -Wall -O3 ./src/GetSitesWithProfile.c -o
./objects/GetSitesWithProfile.o
gcc -c -I./include -Wall -O3 ./src/GetStopCodons.c -o
./objects/GetStopCodons.o
gcc -c -I./include -Wall -O3 ./src/Output.c -o ./objects/Output.o
gcc -c -I./include -Wall -O3 ./src/PrintExons.c -o ./objects/PrintExons.o
gcc -c -I./include -Wall -O3 ./src/PrintSites.c -o ./objects/PrintSites.o
gcc -c -I./include -Wall -O3 ./src/ReadExonsGFF.c -o
./objects/ReadExonsGFF.o
gcc -c -I./include -Wall -O3 ./src/ReadGeneModel.c -o
./objects/ReadGeneModel.o
gcc -c -I./include -Wall -O3 ./src/ReadSequence.c -o
./objects/ReadSequence.o
gcc -c -I./include -Wall -O3 ./src/ReadHSP.c -o ./objects/ReadHSP.o
gcc -c -I./include -Wall -O3 ./src/RecomputePositions.c -o
./objects/RecomputePositions.o
gcc -c -I./include -Wall -O3 ./src/RequestMemory.c -o
./objects/RequestMemory.o
gcc -c -I./include -Wall -O3 ./src/ProcessHSPs.c -o ./objects/ProcessHSPs.o
gcc -c -I./include -Wall -O3 ./src/ScoreExons.c -o ./objects/ScoreExons.o
gcc -c -I./include -Wall -O3 ./src/SearchEvidenceExons.c -o
./objects/SearchEvidenceExons.o
gcc -c -I./include -Wall -O3 ./src/SetRatios.c -o ./objects/SetRatios.o
gcc -c -I./include -Wall -O3 ./src/SortExons.c -o ./objects/SortExons.o
gcc -c -I./include -Wall -O3 ./src/SortSites.c -o ./objects/SortSites.o
gcc -c -I./include -Wall -O3 ./src/SortHSPs.c -o ./objects/SortHSPs.o
gcc -c -I./include -Wall -O3 ./src/SwitchFrames.c -o
./objects/SwitchFrames.o
gcc -c -I./include -Wall -O3 ./src/SwitchPositions.c -o
./objects/SwitchPositions.o
gcc -c -I./include -Wall -O3 ./src/Translate.c -o ./objects/Translate.o
gcc -c -I./include -Wall -O3 ./src/account.c -o ./objects/account.o
gcc -c -I./include -Wall -O3 ./src/beggar.c -o ./objects/beggar.o
gcc -c -I./include -Wall -O3 ./src/genamic.c -o ./objects/genamic.o
gcc -c -I./include -Wall -O3 ./src/manager.c -o ./objects/manager.o
gcc -c -I./include -Wall -O3 ./src/readparam.c -o ./objects/readparam.o
gcc -c -I./include -Wall -O3 ./src/readargv.c -o ./objects/readargv.o
./src/readargv.c: In function ‘printHelp’:
./src/readargv.c:54: warning: format not a string literal and no format
arguments
gcc -I./include -Wall -O3 -o ./bin/geneid ./objects/geneid.o
./objects/BackupGenes.o ./objects/PeakEdgeScore.o
./objects/GetTranscriptTermini-usingslopes.o ./objects/BuildAcceptors.o
./objects/BuildU12Acceptors.o ./objects/BuildDonors.o
./objects/BuildInitialExons.o ./objects/BuildInternalExons.o
./objects/BuildZeroLengthExons.o ./objects/BuildUTRExons.o
./objects/BuildORFs.o ./objects/BuildSingles.o ./objects/BuildSort.o
./objects/BuildTerminalExons.o ./objects/ComputeStopInfo.o
./objects/CookingGenes.o ./objects/CorrectExon.o ./objects/Dictionary.o
./objects/DumpHash.o ./objects/FetchSequence.o
./objects/GetSitesWithProfile.o ./objects/GetStopCodons.o
./objects/Output.o ./objects/PrintExons.o ./objects/PrintSites.o
./objects/ReadExonsGFF.o ./objects/ReadGeneModel.o
./objects/ReadSequence.o ./objects/ReadHSP.o
./objects/RecomputePositions.o ./objects/RequestMemory.o
./objects/ProcessHSPs.o ./objects/ScoreExons.o
./objects/SearchEvidenceExons.o ./objects/SetRatios.o
./objects/SortExons.o ./objects/SortSites.o ./objects/SortHSPs.o
./objects/SwitchFrames.o ./objects/SwitchPositions.o
./objects/Translate.o ./objects/account.o ./objects/beggar.o
./objects/genamic.o ./objects/manager.o ./objects/readparam.o
./objects/readargv.o -lm

cd bin/
./geneid -h ## test geneid
sudo cp geneid /usr/bin
## put ~/src/geneid/bin/./ into path
nano ~/.profile
PATH=$PATH:~/src/geneid/bin/./
export PATH
. ~/.profile ## source .profile


##install blast2.2.25+
wget
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.25+-x64-linux.tar.gz
tar xvfz ncbi-blast-2.2.25+-x64-linux.tar.gz
cd ncbi-blast-2.2.25+/
cd bin/
## put ~/src/ncbi-blast-2.2.25+/bin/./ into PATH
nano ~/.profile
PATH=$PATH:~/src/ncbi-blast-2.2.25+/bin/./
export PATH
. ~/.profile ##sourse profile

##install hmmer 3.0
wget ftp://selab.janelia.org/pub/software/hmmer3/3.0/
tar xvfz hmmer-3.0.tar.gz
cd hmmer-3.0.tar
./configure
make
make check
sudo make install
##set path to hmmer in .profile

##install cegma
wget http://korflab.ucdavis.edu/Datasets/cegma/cegma_v2.4.010312.tar.gz
tar xvfz cegma_v2.4.010312.tar.gz
cd cegma_v2.4.010312/
make
##stdout
###
### RUNNING MAKEFILE
###
### Mon Jan 16 13:34:36 CET 2012 -- derhazel
###
mkdir ./bin;
### Finishing PERL script from "src/cegma.pl" -> "bin/cegma"
### Finishing PERL script from "src/genome_map.pl" -> "bin/genome_map"
### Finishing PERL script from "src/local_map.pl" -> "bin/local_map"
### Finishing PERL script from "src/parsewise.pl" -> "bin/parsewise"
### Finishing PERL script from "src/hmm_select.pl" -> "bin/hmm_select"
### Finishing PERL script from "src/completeness.pl" -> "bin/completeness"
### Finishing PERL script from "src/geneid-train.pl" -> "bin/geneid-train"
### Finishing PERL script from "src/make_paramfile.pl" ->
"bin/make_paramfile"
###
### MAKEFILE DONE...
###

cd bin
./cegma -h ## test cegma
## put ~/src/cegma_v2.4.010312/bin/./ into PATH
nano ~/.profile
PATH=$PATH:~/src/cegma_v2.4.010312/bin/./
export PATH
. ~/.profile ## source .profile
## set environmental variable CEGMA and PERL5LIB in ~/.bashrc
nano ~/.basrc
export CEGMA=/home/derhazel/src/cegma_v2.4.010312/
export PERL5LIB=/home/derhazel/src/cegma_v2.4.010312/lib/
. ~/.bashrc ## source .bashrc