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Commit d867af58 authored by Davide Lagoa's avatar Davide Lagoa
Browse files

new jar version

parent 20aad4da
#### CONFIGURATION FILE ####
#This file contains the configurations in which TranSyT depends.
#All configurations are editable, just place the value or array of values desired next to the "=" sign after the keyWord
#### CONFIGURATION FILE ####
#This file contains the configurations in which TranSyT depends.
#All configurations are editable, just place the value or array of values desired next to the "=" sign after the keyWord
# 1 - E-value threshold to automatically accept result (use the format xE-x where x represents numbers).
EvalueAccept=1E-50
# 2 - Similarity score blast TCDB
similarity=0.3
# 3 - Path to blastp executable or system alias (ex: '/usr/local/ncbi/blast/bin/blastp' or 'blastp')
blastpAlias=blastp
# 4 - Relative path to the temp directory (used to save temporary files)
#temp=transyt-scraper/temp/
# 5 - Relative path to the TCDB_queries_Backup directory (used to debug purposes only)
#queriesBackupPath=temp=triage/Files/TCDB_queries_Backup/
# 6 - Relative path to the TCDB_queries_Backup directory (used to debug purposes only)
#queriesBackupPath=temp=transyt-scraper/Files/TCDB_queries_Backup/
# 7 - E-value threshold for blast against TCDB sequences file (use the format xE-x where x represents numbers).
Evalue=1
# 8 - Blast query coverage threshold.
coverage=0.8
# 9 - Blast bit score threshold.
bitScore=50
# 10 - Select the IDs to generate the reactions. Select 'ModelSEED', 'BiGG', 'MetaCyc', or 'KEGG'.
IDsDatabase=KEGG
EvalueAccept=0
#EvalueAccept=1E-50
# 2 - Similarity score blast TCDB
similarity=0.3
# 3 - Path to blastp executable or system alias (ex: '/usr/local/ncbi/blast/bin/blastp' or 'blastp')
blastpAlias=blastp
# 4 - Alpha value for reactions annotation
alpha=0.75
# 5 - Penalty of reactions that are associated to a low number of homologous genes (used in taxonomy score)
beta=0.3
# 6 - Minimum hits to avoid penalty in taxonomy score calculations
minHits=2
# 7 - E-value threshold for blast against TCDB sequences file (use the format xE-x where x represents numbers).
Evalue=1E-20
# 8 - Blast query coverage threshold.
coverage=0.8
# 9 - Blast bit score threshold.
bitScore=50
# 10 - Select the IDs to generate the reactions. Select 'ModelSEED', 'BiGG', 'MetaCyc', or 'KEGG'.
IDsDatabase=ModelSEED
# 11 - Allowed difference between compartments (set a value between 0% and 50%).
difference=30
# 12 - Minimum alpha helices.
helices=1
# 13 - Minimum beta strands for barrels identification.
strands=8
# 14 - URI for bolt connection to TranSyT's internal database.
uri=bolt://localhost:7687
# 15 - Database username
username=neo4j
# 16 - Database password
password=password
# 11 - Allowed difference between compartments (set a value between 0% and 50%).
difference=30
# 17 - Score above which a reaction is accepted
annotationScore=0.75
# 12 - Minimum alpha helices.
helices=1
# 18 - Paramenter used to balance the weight between frenquency and similarity scores
alphaFamilies=0.4
# 13 - Minimum beta strands for barrels identification.
strands=8
# 19 - Override common ontologies filter (true or false)
overrideCommonOnt=false
# 14 - URI for bolt connection to TranSyT's internal database.
uri=bolt://localhost:7687
# 20 - URI for bolt connection to Reference TranSyT's internal database.
ref_uri=bolt://localhost:7687
# 21 - Reference Database username
ref_username=neo4j
# 22 - Reference Database password
ref_password=password
# 15 - Database username
username=neo4j
# 23 - Percentage of blast the top blast results that should be accepted for each entry.
percent_accept=10
# 16 - Database password
password=password
# 24 - Threshold for config#23 acceptance
limit_evalue_accept=1E-50
# 25 - Ignore method 1
ignore_m1=false
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