2021-04-01 16:12:14 +00:00
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# StarLIMS Data Pull
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2021-04-13 19:55:29 +00:00
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Pulls positive SC2 sample IDs and relevant dates from StarLIMS.
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2021-04-01 16:12:14 +00:00
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2021-04-13 19:55:29 +00:00
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**NOTE:** These scripts are encrypted, but are generally intended for use on
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Windows machines. Decrypt them on a Linux/Mac machine using the [entire repo
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2021-04-29 01:27:56 +00:00
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instructions](https://github.com/MillironX/sc2-sequencing/blob/master/README.md),
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2021-04-13 19:55:29 +00:00
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then copy over using a secure flash drive or similar method.
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2021-04-01 16:12:14 +00:00
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## Usage
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Double-click `refresh-lims-data.bat` in any location.
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## Installation
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2021-04-13 19:55:29 +00:00
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This script requires
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[Miniconda](https://conda.io/en/master/miniconda.html#windows-installers).
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2021-04-01 16:12:14 +00:00
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1. Download and install Miniconda
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1. Select "Just Me" when asked who to install for
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2. All other default options will work
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2. Press `Win+R`, type `%USERPROFILE%` and press Enter
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3. Create a new folder called `limsdatapull`
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2021-04-01 16:23:31 +00:00
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4. Copy all of the decrypted files to `limsdatapull`
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5. Open Anaconda console (not PowerShell) from the Start Menu
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6. Run `conda create -n limsdatapull -f
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%USERPROFILE%\limsdatapull\limsdatapull.yaml`
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2021-04-01 16:23:31 +00:00
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7. Answer `y` to all the prompts
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8. Close the console
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9. (Optional) Copy `refresh-lims-data.bat` to the Desktop
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10. (Optional) Set up a scheduled task to run `refresh-lims-data.bat` regularly
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2021-04-13 19:55:29 +00:00
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When `refresh-lims-data.bat` is run, a new file called `SequenceDatabase.xlsx`
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will be added to `limsdatapull`. This file can be referenced by other
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spreadsheets for efficient and timely lookup data from StarLIMS.
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