setup.py

import os
import subprocess
import sys

programDirectory = os.path.dirname(os.path.abspath(__file__))
with open(os.path.join(programDirectory,"config_template/FindSV.config"), 'r') as myfile:
    template=myfile.read()

valid_response=["1","2"]
while True:
    print ("print 1 for local executor, or 2 for slurm")
    selection=input()
    if not selection in valid_response:
        print ("invalid option, print 1 for local  executor (i.e you run the jobs locally, on the cores available to you), or 2 for slurm (i.e nextflow will submit jobs via slurm)")
    else:

        if selection == "1":
            selection = "local"
        else:   
            selection = "slurm"
        break
        
template=template.replace("{executor}", "\'{}\'".format(selection) )
if selection == "slurm":
    print ("enter slurm account, or press enter")
    selection=input()
    
template=template.replace("{account}", "{}".format(selection) )

print ("enter the standard output directory")
selection=input()
template=template.replace("{working_dir}", "\'{}\'".format(selection) )

print ("Set the path to the reference genome(needs to be indexed using bwa and samtools 0.19)")
selection=input()
template=template.replace("{genome}", "\'{}\'".format(selection) )

print ("add the path of the directory containing reference files (i.e the directory should contain one fasta file per contig)")
selection=input()
template=template.replace("{CNVnator_reference_dir_path}", "\'{}\'".format(selection) )

print ("setting up internal pipeline scripts")
template=template.replace("{contig_sort_path}", "\'{}\'".format( os.path.join(programDirectory,"internal_scripts/contigSort.py") ) )
template=template.replace("{clear_vep_path}", "\'{}\'".format( os.path.join(programDirectory,"internal_scripts/clear_vep.py") ) )
template=template.replace("{cleanVCF_path}", "\'{}\'".format( os.path.join(programDirectory,"internal_scripts/cleanVCF.py") ) )
template=template.replace("{the_annotator_path}", "\'{}\'".format( os.path.join(programDirectory,"internal_scripts/the_annotator.py") ) )
template=template.replace("{gene_keys_dir_path}", "\'{}\'".format( os.path.join(programDirectory,"gene_keys") ) )
template=template.replace("{frequency_filter_path}", "\'{}\'".format( os.path.join(programDirectory,"internal_scripts/frequency_filter.py") ) )
template=template.replace("{FindSV_home_path}", "\'{}\'".format( os.path.join(programDirectory) ) )
template=template.replace("{run_fermikit_path}", "\'{}\'".format( os.path.join(programDirectory,"internal_scripts/run_fermikit.py") ) )

print ("add the variant_effect_predictor.pl script path, the path is set to vep if left blank")
print ("remember to download the VEP cache file! more info is found on the VEP ENSMBLE website")

selection=input()
if selection == "":
    selection = "vep"
template=template.replace("{VEP_path}", "\'{}\'".format(selection) )

print ("add the path of an SVDB exported database file/sv vcf database(or leave blank to skip the frequency db)")
selection=input()
if selection == "":
    selection = "\"\""
template=template.replace("{SVDB_path}", "\'{}\'".format(selection) )

print ("add the genmod ini file path, if left blank, the default genmod_SV.txt file will be used")
selection=input()
if selection == "":
    selection = os.path.join(programDirectory,"genmod_SV.txt")
template=template.replace("{genmod_rank_model_path}", "\'{}\'".format(selection) )

print ("enter the filename of the new config file(or leave blank to set the config file to FindSV.conf)")
selection=input()
if selection == "":
    selection = "FindSV.conf"
f= open(selection, "w")
f.write(template)
f.close()

print ("creating FindSV environment script")
print ("modules: print uppmax if you are using uppmax. Otherwise, print a line of each module to use, or leave empty to skip modules")
print ("example: bioinfo-tools vep, to load the modules bioinfo-tools and vep")
selection=input()
if selection == "UPPMAX" or selection ==  "uppmax":
    selection = "bioinfo-tools vep manta vcftools Nextflow"

FindSV_env=""
if selection != "":
    FindSV_env += "module load {}\n".format(selection)

FindSV_env+="\nexport NXF_LAUNCHER={}/nextflow_tmp".format(programDirectory)
FindSV_env+="\nexport NXF_TEMP={}/nextflow_tmp".format(programDirectory)

os.system("mkdir -p {}/nextflow_tmp".format(programDirectory))
f= open("FindSV_env.sh", "w")
f.write(FindSV_env)
f.close()

os.system("chmod +x FindSV_env.sh")