#!/usr/bin/env python
import os
import sys
import multiprocessing
import subprocess

if __name__ == '__main__':
    print 'Please do not run me! Use run_pconsc.py'
    print '\n\tYours sincerely,\n\n\t', sys.argv[0]
    sys.exit(0)

# Directory where PconsC in the distributable package is located
#root = os.path.dirname(os.path.abspath(sys.argv[0])) + '/'
root = '/scratch/arne/PconsC2//'
print root

########################################################
### Please adjust the following paths to your system ###
########################################################

### Jackhmmer executable ###
#jackhmmer = root + 'dependencies/hmmer-3.0/src/jackhmmer'
jackhmmer = '/scratch/arne/PconsC2-extra/hmmer-3.1b1-linux-intel-x86_64/binaries/jackhmmer'
uniref = '/scratch/data/uniref90.fasta'

### HHblits executable ###
#hhblits = root + 'dependencies/hhsuite-2.0.16/bin/hhblits'
hhblits = '/usr/local/bin/hhblits'
hhdatabase = '/scratch/data/hhsuite/hhsuite_dbs/nr20_12Aug11'

### PSICOV executable ###
#psicov = root + 'dependencies/psicov-1.11/psicov'
psicov = '/usr/local/bin/psicov'

### NetSurfP executable ###
#netsurf = root + 'dependencies/netsurfp-1.0/netsurfp'
netsurf = '/usr/local/bin/netsurfp'

### PSIPRED executable ###
#psipred = root + 'dependencies/psipred/runpsipred'
psipred = '/scratch/arne/PconsC2-extra/psipred/runpsipred'

### MATLAB executable ###
# Please set this variable to None if you don't have access to matlab. 
# PconsFold will then try to use the compiled version. 
#matlab = '/sw/apps/matlab/x86_64/8.1/bin/matlab'
#matlab = None
matlab= '/pdc/vol/matlab/r2012a/bin/matlab'

### Path to MATLAB compiler ###
# Only needed if matlab is not available.
matlabdir = '' 

# Directory to PconsC3 scripts (i.e. this one)
PconsC3 = '/scratch/arne/PconsC3/'


########################################################
###  Please do not change anything below this line   ###
########################################################

# Paths to included scripts
trim2jones = root + 'scripts/a3mToJones.py'
trim2trimmed = root + 'scripts/a3mToTrimmed.py'
#trim = root + 'scripts/trim.py'
#trim2 = root + 'scripts/trimToFasta.py'

# Reformat script scavenged from HHsuite. Please cite the HHblits paper!
reformat = root + 'scripts/reformat.pl'

# Maximum amount of cores to use per default
n_cores = multiprocessing.cpu_count()

# Enable work-around for PSICOV not handling low complexity alignments
psicovfail = True

# Adjust plmdca path to either standalone or compiled, 
# depending on presence of matlab.
if matlab:
    plmdca = None # matlab licence present: do not use compiled version
#    plmdcapath = root + 'dependencies/plmDCA_symmetric_v2'
    plmdcapath = '/scratch/arne/PconsC2-extra/plmDCA_asymmetric_v2'
else:
    plmdca = root + 'dependencies/plmdca_standalone/2012/build01/bin/plmdca'
    plmdcapath = None

