millironx/sc2-sequencing
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sc2-sequencing/limsdatapull
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Thomas A. Christensen II affa7796ac
Sanitize redacted name
2021-04-28 19:27:56 -06:00
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limsdatapull.yaml Add auto-updating sample database 2021-03-26 14:25:22 -06:00
README.md Sanitize redacted name 2021-04-28 19:27:56 -06:00
refresh-lims-data.bat Add auto-updating sample database 2021-03-26 14:25:22 -06:00
updatedata.py Add auto-updating sample database 2021-03-26 14:25:22 -06:00

README.md

StarLIMS Data Pull

Pulls positive SC2 sample IDs and relevant dates from StarLIMS.

NOTE: These scripts are encrypted, but are generally intended for use on Windows machines. Decrypt them on a Linux/Mac machine using the entire repo instructions, then copy over using a secure flash drive or similar method.

Usage

Double-click refresh-lims-data.bat in any location.

Installation

This script requires Miniconda.

  1. Download and install Miniconda
    1. Select "Just Me" when asked who to install for
    2. All other default options will work
  2. Press Win+R, type %USERPROFILE% and press Enter
  3. Create a new folder called limsdatapull
  4. Copy all of the decrypted files to limsdatapull
  5. Open Anaconda console (not PowerShell) from the Start Menu
  6. Run conda create -n limsdatapull -f %USERPROFILE%\limsdatapull\limsdatapull.yaml
  7. Answer y to all the prompts
  8. Close the console
  9. (Optional) Copy refresh-lims-data.bat to the Desktop
  10. (Optional) Set up a scheduled task to run refresh-lims-data.bat regularly

When refresh-lims-data.bat is run, a new file called SequenceDatabase.xlsx will be added to limsdatapull. This file can be referenced by other spreadsheets for efficient and timely lookup data from StarLIMS.