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hallamlab / metapathways2

MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds
http://hallam.microbiology.ubc.ca/MetaPathways/
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template_config not recognizing operating system #13

Closed keithmewis closed 9 years ago

keithmewis commented 10 years ago

Thought that Mac was Unix:

Qt is not detecting the operating system and updating the template_config.txt file

# MetaPathways v2.0
# Kishori M. Konwar, Niels W. Hanson
# Configuration File
# Please run: source MetaPathwaysrc before continuing

# Paths for the Python, Perl and Pathway Tools
PYTHON_EXECUTABLE '/usr/bin/python'
PGDB_FOLDER '/Users/kmewis/ptools-local/pgdbs/user'
METAPATHWAYS_PATH '/Users/kmewis/metapathways2-master'

# Replace with your current
PATHOLOGIC_EXECUTABLE '/Users/kmewis/pathway-tools/pathway-tools'

REFDBS '/Users/kmewis/MetaPathways_2/MetaPathways_DBs'

# Executables: replace 'mac' to your platform linux, mac, win
# Bit type - bit32 or bit64 
FORMATDB_EXECUTABLE  'makeblastdb'
BLASTP_EXECUTABLE  'blastp'
BLASTN_EXECUTABLE  'blastn'
EXECUTABLES_DIR  'executables/Unix'
LASTDB_EXECUTABLE  'lastdb'
LAST_EXECUTABLE  'lastal'
PRODIGAL_EXECUTABLE 'prodigal' 
RESOURCES_DIR           'resources/'
SCAN_tRNA_EXECUTABLE      'trnascan-1.4' 

# This is the folder where the scripts folder of the MetaPathways  pipeline 
# # is installed

GBK_TO_FNA_FAA_GFF   'libs/python_scripts/MetaPathways_parse_genbank.py'
GFF_TO_FNA_FAA_GFF   'libs/python_scripts/MetaPathways_input_gff.py'
PREPROCESS_INPUT          'libs/python_scripts/MetaPathways_filter_input.py'
ORF_PREDICTION          'libs/python_scripts/MetaPathways_orf_prediction.py'
ORF_TO_AMINO 'libs/python_scripts/MetaPathways_create_amino_sequences.py'
COMPUTE_REFSCORES 'libs/python_scripts/MetaPathways_refscore.py' 
FUNC_SEARCH 'libs/python_scripts/MetaPathways_func_search.py'
PARSE_FUNC_SEARCH 'libs/python_scripts/MetaPathways_parse_blast.py'
ANNOTATE_ORFS 'libs/python_scripts/MetaPathways_annotate_fast.py'
GENBANK_FILE 'libs/python_scripts/MetaPathways_create_genbank_ptinput_sequin.py'  
CREATE_ANNOT_REPORTS 'libs/python_scripts/MetaPathways_create_reports_fast.py' 
RUN_PATHOLOGIC 'libs/python_scripts/MetaPathways_run_pathologic.py' 
SCAN_rRNA 'libs/python_scripts/MetaPathways_rRNA_stats_calculator.py'
SCAN_tRNA 'libs/python_scripts/MetaPathways_tRNA_scan.py'
MLTREEMAP_CALCULATION 'libs/python_scripts/MetaPathways_mltreemap.py' 
RPKM_CALCULATION 'libs/python_scripts/MetaPathways_rpkm.py' 
RPKM_CALCULATION 'libs/python_scripts/MetaPathways_rpkm.py'