README

To install the geneid_training from Bitbucket

What is the status

Latest commit works (80% training, 20% for eveluation mode)

• Quick summary
• Version
• Learn Markdown

How do I get set up?

• install required Perl modules easiest is to use cpanm to get modules located in:

$HOME/perl5/lib/perl5/

cpanm Modern::Perl

cpanm Carp

cpanm Carp::Always

cpanm Carp::Assert

cpanm Data::Dumper

cpanm Cwd

cpanm Getopt::Long

cpanm File::Path

cpanm File::Basename

cpanm File::Temp

cpanm IPC::System::Simple

cpanm Readonly

set the PERL5LIBS: i.e. in fish shell set -gx PERL5LIB $HOME/perl5/lib/perl5/ $PERL5LIB

run pmarinus totalseqs4training

``./run_test_train.sh`

clean up all training results

clean_test_train_results.sh

• C programs

cd src/c/evaluation
mkdir ./bin
mkdir ./objects
make
cp -i ./bin/* ../../../bin/
cd ../../../

cd src/c/ssgff
make
cp -i ./bin/* ../../../bin/
cd ../../../

cd src/c/pictogram
make
cp -i pictogram ../../../bin/
cd ../../../

compile geneid (not included in this distribution)

How do I run the test

./run_test_train.sh

clean up all training results

clean_test_train_results.sh

Bitbucket code access etc.

For an easy "git clone" etc. one needs to create a personal ssh key on a workstation/server of interest and make it known to Bitbucket.