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Wetlab settings

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Sarai Varona edited this page Jun 25, 2019 · 16 revisions

Create the following directories:

Create these folder to store the sample sheet files and the tmp folder for saving temporary the sample sheet that will be copy on the remote samba server.

cd /srv/iSkyLIMS
mkdir -p documents/wetlab/BaseSpaceMigrationFiles
mkdir -p documents/wetlab/tmp/recorded

Config file for Wetlab

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.

vim /srv/iSkyLIMS/iSkyLIMS_wetlab/wetlab_config.py

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 Settings have been group in three blocks:

  • SAMBA SETTINGS
  • FOLDER SETTINGS
  • RUN METRIC FOLDERS AND FILES

SAMBA SETTINGS

To be able to connect to the remote server, where they are the run folder, containing the sequencer output files, you need to define:

"server name", "samba port", "user name" , "user password" and "shared folder"

SAMBA_APPLICATION_FOLDER_NAME has been create to solve the situation that run folders are not just under the shared folder , but a dedicated sub-folder.

Set the SAMBA_DOMAIN, only if for connecting to the storage cabinet you need to specify a domain to log in.

Note.- Server name is used now instead of IP address, because the new Storage Cabinet are configured used multi-IP Address to balance traffic.

################### SAMBA SETTINGS  ##########################
## SAMBA settings for connecting remote 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 SETTINGS

When fetching the files from storage cabinet, the files has to be copied on your local iSkyLIMS to read and process these files.

You can keep the proposed setting or change them according to your organization rules.

############## 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/'

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

RUN METRIC FOLDERS AND FILES

On the run metric settings it is important to check that INTEROP_PATH value matches with the folder you install interop

############ RUN METRIC FOLDERS AND FILES ####################
INTEROP_PATH = '/opt/interop/bin/'
RUN_METRIC_FOLDER = 'InterOp'
PLOT_EXTENSION = '.png'
##############################################################

Email Settings

iSkyLIMS wetlab can be configured to send an email, in case of error when processing the crontab activities.

The variables to set are:

  • SENT_EMAIL_ON_ERROR. Used to define if an email is sent in case of error
  • TO_EMAIL_ADDRESS and FROM_EMAIL_ADDRESS. Note that TO_EMAIL_ADDRESS is a list, so you can send the email to several people. Example : ['email_2@your_domain', 'email_2@your_domain']
################### EMAIL SETTINGS  ##########################
SENT_EMAIL_ON_ERROR = False
TO_EMAIL_ADDRESS = ['your_email@your_domain']
FROM_EMAIL_ADDRESS = 'iSkyLIMS@your_domain'
##############################################################

User Settings

Under user settings we define the name of the group used for Wetlab Manager.

################# USER SETTINGS ##############################
## Wetlab manager
WETLAB_MANAGER = 'WetlabManager'
##############################################################

Log Settings

To get more information when crontab process is running we are dumping information to a log file. Inside the wetlab_config.py file we will define the name of the file which contains the logging configuration settings.

######### CONFIG FILE LOG NAME ###############################
LOGGING_CONFIG_FILE = 'logging_config.ini'
##############################################################

Fill in Errors and Run State tables

Error codes and run states are stored in database. You can fetch the json files inside conf folder or used the following links:

Then use the django utility to load the json file to iSkyLIMS database

cd /srv/iSkyLIMS
source virtualenv/bin/activate
./manage.py loaddata <your_saved_file_location>/dump_errors.json
./manage.py loaddata <your_saved_file_location>/dump_runstates.json
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