defs.py.sample 2.75 KB
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###
### Vidjil server, main configuration file
### This file must be named 'modules/defs.py' to be taken into account
###

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### Email notifications for server errors
SMTP_SERVER = 'localhost'
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SMTP_CREDENTIALS = 'vidjil:XXXXXX' # set to None if no auth required
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# SMTP_SERVER = 'logging' # no mail
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FROM_EMAIL = 'root@vidjil.org'
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ADMIN_EMAILS = ['notifications@vidjil.org']
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EMAIL_SUBJECT_START = '[Vidjil]' # Customize the start of the email subject
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### Server healthcare compliance
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### Please see <http://www.vidjil.org/doc/server#healthcare>
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HEALTHCARE_COMPLIANCE = False

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### Specific accounts
LIMITED_ACCOUNTS = [ ]

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### address for the sql database
###
DB_ADDRESS = 'sqlite://storage.sqlite'
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DB_ADDRESS = 'mysql://vidjil:XXXXXXXX@localhost/vidjil'

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DB_POOL_SIZE = 4

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### Backup file
DB_BACKUP_FILE = 'backup.csv'
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### 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/'

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### Temporary directory to store vidjil results, and basename of files in this directory
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### Formatted with 'data_id' in models/task.py
DIR_OUT_VIDJIL_ID = '/mnt/result/tmp/out-%06d/'
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DIR_PRE_VIDJIL_ID = '/mnt/result/tmp/pre/out-%06d/'
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BASENAME_OUT_VIDJIL_ID = '%06d'
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### Directory for program used in task.py
### relative path start from server/web2py
DIR_VIDJIL = '../../'
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DIR_VIDJIL_NEXT = '../../'
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DIR_FUSE = '../../tools'
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DIR_MIXCR = '../../'
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DIR_IGREC = '../../'
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DIR_PEAR = '../../'
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DIR_FLASH2 = '../../'
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DIR_CLONEDB = '../../../clonedb'
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### Directory that store the germlines used by Vidjil
DIR_GERMLINE = DIR_VIDJIL + 'germline/'
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DIR_GERMLINE_NEXT = DIR_VIDJIL_NEXT + 'germline/'
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### Port on which to run the fuse server
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### Used in models/task.py and in /server/fuse_server.py
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FUSE_SERVER = 'localhost'
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PORT_FUSE_SERVER = 12789
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### Log files
DIR_LOG = '/var/vidjil/'
LOG_INFO = DIR_LOG + 'vidjil.log'
LOG_DEBUG = DIR_LOG + 'vidjil-debug.log'

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

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### Reverse IP file
REVERSE_IP = '/home/vidjil/ips.txt'
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### Locus (should be parsed from germlines.data)
LOCUS = ['TRA', 'TRA+D', 'TRB', 'TRG', 'TRD', 'TRD+',
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         'IGH', 'IGH+', 'IGK', 'IGK+', 'IGL']

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### Sample sets types
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### Tables are defined with these names:
### do not change these values once the server is set
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SET_TYPE_GENERIC = 'generic'
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SET_TYPE_PATIENT = 'patient'
SET_TYPE_RUN = 'run'



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# Preventu upload and run when 1% space is left in target disk
FS_LOCK_THRESHHOLD = 1
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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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REQUIRE_HTTPS = True
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BROWSER_PATH='browser/index.html'