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Wetlab settings

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[email protected] edited this page Mar 4, 2019 · 16 revisions

A configuration file has been created to define the settings without the needs to modify the code. To customize iSkyLIMS wetlab to your organization you need to edit the file wetlab_config.py to define your settings.

Config file has many settings that you do not need to modify. They are in the file to avoid the hardcode settings inside the code and having in mind that if illumina changes the format of the files, can be modified without changing the code. Our recommendation is to modify only, the dummy values (user/password) and folders location that you have to follow in your organization. Then the changes that yo have to do are:

  • Samba Configuration Settings
  • Email Settings
  • User Settings
  • Log Settings

Samba Configuration Settings

When Sequencer finish the process the output files will be sent to external storage where all these files will be for a long period of time. iSkyLIMS Wetlab needs to fetch some of these files to process them and show the processed information.

Samba connection will be used to fetch them. See picture below.

Samba Connection Data Settings

################### SAMBA SETTINGS  ##########################
## SAMBA settings for connecting quibitka server to fetch the run files
SAMBA_USER_ID = 'your_samba_user'
SAMBA_USER_PASSWORD = 'your_password'
SAMBA_SHARED_FOLDER_NAME = 'your_shared_folder'
#   Write the subfolder name in case that run folder are not under the
#   shared folder directory. Leave empty in other case
SAMBA_APPLICATION_FOLDER_NAME = ''
SAMBA_REMOTE_SERVER_NAME = 'server_name'
SAMBA_NTLM_USED = True
SAMBA_IP_SERVER = 'your_ip_address'
SAMBA_PORT_SERVER = '445'
## SAMBA_DOMAIN MUST be empty if domain value is not used for samba connection
SAMBA_DOMAIN='your_domain'

Folder used to store the files fetched

############## FOLDER SETTINGS ###############################
## Directory settings for processing the run data files ######
## Relative path from settings.BASE_DIR
LOG_DIRECTORY = 'logs/'
## Relative path from settings.MEDIA_ROOT
RUN_TEMP_DIRECTORY_RECORDED = 'wetlab/tmp/recorded/'
RUN_TEMP_DIRECTORY = 'wetlab/tmp'
RUN_TEMP_DIRECTORY_PROCESSING = 'wetlab/tmp/processing'
RUN_IMAGES_DIRECTORY = 'wetlab/images_plot'
RUN_SAMPLE_SHEET_DIRECTORY = 'wetlab/SampleSheets/'

##############################################################

inconnect to a Samba resource where all New tables to load values for :
Errors, state

Samba connection settings to remote server

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