create_conf.pl

Configuration example

Generation of a config script

When you run protTrace for the first time, it is advisable to run the create_conf.pl script, which will then check all dependencies and will create a config file

$ bin/create_conf.pl -name=prog.config
Testing for linsi
Testing for hmmscan
Testing for hmmfetch
Testing for makeblastdb
Testing for blastp
Testing for iqtree
Testing for Rscript
Testing for python
Testing for perl
Testing for java
Dependency successfully established: /usr/local/bin/linsi
Dependency successfully established: /Users/ingo/anaconda/envs/py27/bin/hmmscan
Dependency successfully established: /Users/ingo/anaconda/envs/py27/bin/hmmfetch
Dependency successfully established: /Users/ingo/anaconda/envs/py27/bin/makeblastdb
Dependency successfully established: /Users/ingo/anaconda/envs/py27/bin/blastp
Dependency successfully established: /Users/ingo/anaconda/envs/py27/bin/iqtree
Dependency successfully established: /usr/local/bin/Rscript
Dependency successfully established: /Users/ingo/anaconda/envs/py27/bin/python
Dependency successfully established: /opt/local/bin/perl
Dependency successfully established: /usr/bin/java

Please select from the list the groups you whish to update or enter q to quit. To use defaults, just hit enter:
[0] - General Options
[1] - Preprocessing Settings
[2] - Advanced Preprocessing Settings
[3] - Scaling factors
[4] - Indel parameter
[5] - Traceability calculation
[6] - Program paths
[7] - Paths to files
If you select more than one group, separate them by a comma or give a range. Leave blank to initialize with default values: 
nothing to update

Re-configuring protTrace

Once you have successfully created a config file, you can later update it with the help of the create_conf.pl script. During the update procedure, the dependency check is omitted. This simplifies the procedure in cases where executables are not accessible via a path that is represented in the environment variable $PATH.

$ bin/create_conf.pl -name=prog.config -update

Please select from the list the groups you whish to update or enter q to quit. To use defaults, just hit enter:
[0] - General Options
[1] - Preprocessing Settings
[2] - Advanced Preprocessing Settings
[3] - Scaling factors
[4] - Indel parameter
[5] - Traceability calculation
[6] - Program paths
[7] - Paths to files
If you select more than one group, separate them by a comma or give a range. Leave blank to initialize with default values: 0-1
General Options
        [0] - species
        [1] - nr_of_processors
        [2] - delete_temporary_files
        [3] - reuse_cache
        [4] - path_work_dir
        [5] - path_cache

Select the entries for updating or type q to quit: 0
Preprocessing Settings
        [6] - preprocessing
        [7] - orthologs_prediction
        [8] - search_oma_database

Select the entries for updating or type q to quit: 8
0 - species
        Current value: YEAST
        Enter new value or type k to keep old [OMA 5 letter Species Identifier: e.g. HUMAN]: HUMAN
1 - search_oma_database
        Current value: YES
        Enter new value or type k to keep old [YES|NO]: k
Nothing to update, keeping old