parameter_dependencies.in

# starIndex: provide the full path to the STAR index directory
# NetSeqPipeline will:
#	  1) create a large index files for the selected reference genome
#   2) if index has been previously created: make sure it is available in the given starIndex location 
#     in a subdirectory with name of the reference
#     example: for a reference genome e.g. GRCh38, make sure the file is located in /pathToStarIndex/GRCh38/
# IMPORTANT: make sure you have write permission
# example: starIndex=/pathToStarIndex
starIndex=

# parametersSTAR: provide the full path to the STAR parameter directory + name of the parameter file
# example: parametersSTAR=/pathToParameters/parameter_STAR.in
parametersSTAR=

# starApp: provide the full path to the STAR application directory + name of the application executable
# example: starApp=/pathToStarApp/STAR
starApp=

# samtools: provide the full path to the samtools application directory + name of the application executable
# example: samtools=/PathToSamtools/samtools
samtools=

# bedtools: provide the full path to the bedtools application directory + name of the application executable
# example: bedtools=/PathToBedtools/bedtools
bedtools=