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Drylab settings

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Sarai Varona edited this page Jun 25, 2019 · 12 revisions

Drylab requires that you define some settings that are used later. The main ones are:

  • Define Services.
  • Define file extensions.
  • Define platforms.
  • Define Sequencer Machines.
  • Define Samba connection.

Define Services

Before starting using Drylab you need to define the three main type of services:

  • SERVICE REQUEST
  • COUNSELING REQUEST
  • INFRASTRUCTURE REQUEST

Note.- Use the Django admin utility to create the new services

Creating "SERVICE REQUEST" services

Write "http://localhost/admin/iSkyLIMS_drylab/" in your web browser, and click "Add" on AvailableServices.

In the text field form write "Genomic Data Analysis", and save it.

Once it is create you can define your own sub-services that depends on this by selecting it in the "Parent" choice field.

Creating "COUNSELING REQUEST" services

In the text field form write "Bioinformatics consulting and training", and save it.

Once it is create you can define your own sub-services that depends on this by selecting it in the "Parent" choice field.

Creating "INFRASTRUCTURE REQUEST" services

In the text field form write "User support", and save it.

Once it is create you can define your own sub-services that depends on this by selecting it in the "Parent" choice field.

**IMPORTANT **. The three main services "Genomic Data Analysis", "Bioinformatics consulting and training" and "User support", must named exactly as they are.

Define file extensions

Write "http://localhost/admin/iSkyLIMS_drylab/fileext/" in your web browser, and click on the ADD button. For example ".fastq"

Define as many file extension you believe will be used in your organization

Define Platforms

Write "http://localhost/admin/iSkyLIMS_drylab/platform/" in your web browser, and click on the ADD button

Define as many different sequencer platforms you believe will be used in your organization

Define Sequencer machines

Write "http://localhost/admin/iSkyLIMS_drylab/machines/" in your web browser, and click on the ADD button

Select from the choice menu the platform that the sequencer uses. Define the name of machine and the number of lanes.

Rest of fields in the form are optional, but could be nice to fill them if you know them.

Define as many different sequencer platforms you believe will be used in your organization

IMPORTANT.

When a sequencer is installed in the lab, it is defined with a name. This name is dumped into the some output files generated during the sequencing process.

When later, on wetlab, the crontab process, fetch these files, the machine value found will be matched with the one defined on this table.

If there is not match an error will be generated.

For that reason the name of the machine (in the form) must be the same as it is defined in the sequencer.

Define Samba connection

Drylab need to connect to an external server where Bioinformatic keep the analysis information done because of the requested services.

To configure Samba for Drylab, similar settings as defined for Wetlab are defined in the "drylab_config.py" file.

## SAMBA settings for connect to external server to create the folder request services
SAMBA_USER_ID = 'samba_user'
SAMBA_USER_PASSWORD = 'samba_password'
SAMBA_SHARED_FOLDER_NAME = 'shared_folder_name'
SAMBA_REMOTE_SERVER_NAME = 'server_name'
SAMBA_NTLM_USED = True
SAMBA_DOMAIN = 'your_domain'
SAMBA_IP_SERVER = 'ip_address'
SAMBA_PORT_SERVER = '445'
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