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defs.py 2.12 KB
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###
### Vidjil server, main configuration file
### This file must be named 'modules/defs.py' to be taken into account
###

### Email notifications for server errors
SMTP_SERVER = 'localhost'
# SMTP_SERVER = 'logging' # no mail
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FROM_EMAIL = 'notifications@vidjil.org'
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ADMIN_EMAILS = ['notifications@vidjil.org']

### address for the sql database
###
DB_ADDRESS = 'sqlite://storage.sqlite'
DB_ADDRESS = 'mysql://vidjil:rootpass@mysql/vidjil'
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DB_POOL_SIZE = 4
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### Backup file
DB_BACKUP_FILE = 'backup.csv'

### Upload directory for .fasta/.fastq.
### Old sequences files could be thrown away.
### No regular backup.

DIR_SEQUENCES = '/mnt/upload/uploads/'

### Upload directory for .vidjil/.fused/.analysis
### Regularly backuped

DIR_RESULTS = '/mnt/result/results/'

### Temporary directory to store vidjil results, and basename of files in this directory
### Formatted with 'data_id' in models/task.py
DIR_OUT_VIDJIL_ID = '/mnt/result/tmp/out-%06d/'
DIR_PRE_VIDJIL_ID = '/mnt/result/tmp/pre/out-%06d/'
BASENAME_OUT_VIDJIL_ID = '%06d'

### Directory for program used in task.py
### relative path start from server/web2py
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DIR_VIDJIL = '/usr/share/vidjil/'
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DIR_FUSE = '../../tools'
DIR_MIXCR = '/usr/bin'
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DIR_IGREC = '/usr/local/bin/'
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DIR_GERMLINE = '/usr/share/vidjil/germline'
### Port on which to run the fuse server
### Used in models/task.py and in /server/fuse_server.py
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FUSE_SERVER = 'fuse'
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PORT_FUSE_SERVER = 12789

### Log files
DIR_LOG = '/var/vidjil/'
LOG_INFO = DIR_LOG + 'vidjil.log'
LOG_DEBUG = DIR_LOG + 'vidjil-debug.log'

### Timeouts
# Delay in seconds before a task is considered in timeout
TASK_TIMEOUT = 2 * 60 * 60

### Reverse IP file
REVERSE_IP = '/home/vidjil/ips.txt'

### Locus (should be parsed from germlines.data)
LOCUS = ['TRA', 'TRA+D', 'TRB', 'TRG', 'TRD', 'TRD+',
         'IGH', 'IGH+', 'IGK', 'IGK+', 'IGL']
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# Preventu upload and run when 1% space is left in target disk
FS_LOCK_THRESHHOLD = 1

SCHEDULER_HEARTBEAT = 5
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# Directory to search for files
FILE_SOURCE = '/mnt/data/src'
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FILE_TYPES = ['fasta', 'fastq', 'fastq.gz', 'fa']
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SET_TYPE_PATIENT = 'patient'
SET_TYPE_RUN= 'run'
SET_TYPE_GENERIC = 'generic'
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REQUIRE_HTTPS = True