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entap_v1.3.0_config.ini
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entap_v1.3.0_config.ini
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#-------------------------------
# [ini_instructions]
#When using this ini file keep the following in mind:
# 1. Do not edit the input keys to the left side of the '=' sign
# 2. Be sure to use the proper value type (either a string, list, or number)
# 3. Do not add unecessary spaces to your input
# 4. When inputting a list, only add a ',' between each entry
#-------------------------------
# [configuration]
#-------------------------------
#Specify whether you would like to generate EnTAP databases locally instead of downloading them. By default, EnTAP will download the databases. This may be used if you are experiencing errors with the default process.
#type:boolean (true/false)
data-generate=false
#Specify which EnTAP database you would like to download/generate or use throughout execution. Only one is required.
# 0. Serialized Database (default)
# 1. SQLITE Database
#It is advised to use the default Serialized Database as this is fastest.
#type:list (integer)
data-type=0,
#-------------------------------
# [entap]
#-------------------------------
#Path to the EnTAP binary database
#type:string
entap-db-bin=/core/labs/Wegrzyn/EnTAP/EnTAP_v0.10.8/EnTAP/databases/entap_database.bin
#Path to the EnTAP SQL database (not needed if you are using the binary database)
#type:string
entap-db-sql=/core/labs/Wegrzyn/EnTAP/EnTAP_v0.10.8/EnTAP/databases/entap_database.db
#Path to the EnTAP graphing script (entap_graphing.py)
#type:string
entap-graph=/core/labs/Wegrzyn/EnTAP/EnTAP_v0.10.8/EnTAP/src/entap_graphing.py
#-------------------------------
# [expression_analysis-rsem]
#-------------------------------
#Execution method of RSEM Calculate Expression.
#Example: rsem-calculate-expression
#type:string
rsem-calculate-expression=/home/FCAM/ahart/EnTAP/entap_software/RSEM-1.3.3/rsem-calculate-expression
#Execution method of RSEM SAM Validate.
#Example: rsem-sam-validator
#type:string
rsem-sam-validator=/home/FCAM/ahart/EnTAP/entap_software/RSEM-1.3.3/rsem-sam-validator
#Execution method of RSEM Prep Reference.
#Example: rsem-prepare-reference
#type:string
rsem-prepare-reference=/home/FCAM/ahart/EnTAP/entap_software/RSEM-1.3.3/rsem-prepare-reference
#Execution method of RSEM Convert SAM
#Example: convert-sam-for-rsem
#type:string
convert-sam-for-rsem=/home/FCAM/ahart/EnTAP/entap_software/RSEM-1.3.3/convert-sam-for-rsem
#-------------------------------
# [frame_selection-transdecoder]
#-------------------------------
#Method to execute TransDecoder.LongOrfs. This may be the path to the executable or simply TransDecoder.LongOrfs
#type:string
transdecoder-long-exe=/home/FCAM/ahart/EnTAP/entap_software/TransDecoder-TransDecoder-v5.7.1/TransDecoder.LongOrfs
#Method to execute TransDecoder.Predict. This may be the path to the executable or simply TransDecoder.Predict
#type:string
transdecoder-predict-exe=/home/FCAM/ahart/EnTAP/entap_software/TransDecoder-TransDecoder-v5.7.1/TransDecoder.Predict
#-------------------------------
# [ontology-eggnog-mapper]
#-------------------------------
#Path to EggNOG-mapper executable. Likely just 'emapper.py'
#type:string
eggnog-map-exe=emapper.py
#Path to directory containing the EggNOG SQL database(s).
#type:string
eggnog-map-data=/home/FCAM/ahart/EnTAP/eggnog_testing/eggnog_mapper/temp_databases
#Path to EggNOG DIAMOND configured database that was generated during the Configuration stage
#type:string
eggnog-map-dmnd=/home/FCAM/ahart/EnTAP/eggnog_testing/eggnog_mapper/temp_databases/eggnog_proteins.dmnd
#-------------------------------
# [ontology-interproscan]
#-------------------------------
#Execution method of InterProScan. This is how InterProScan is generally ran on your system. It could be as simple as 'interproscan.sh' depending on if it is globally installed.
#type:string
interproscan-exe=interproscan.sh
#-------------------------------
# [similarity_search]
#-------------------------------
#Method to execute DIAMOND. This can be a path to the executable or simply 'diamond' if installed globally.
#type:string
diamond-exe=/home/FCAM/ahart/EnTAP/entap_software/diamond-2.1.8/bin/diamond