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Cleanup limsdatapull README

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This commit is contained in:
Thomas A. Christensen II 2021-04-13 13:55:29 -06:00
parent 4cbe3aa529
commit ab3f468564
Signed by: millironx
GPG key ID: 139C07724802BC5D
2 changed files with 14 additions and 5 deletions
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2
.vscode/settings.json vendored
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@ -1,11 +1,13 @@
{
"cSpell.words": [
"LIMS",
"Nanopore",
"chmod",
"cygpath",
"demux",
"fasta",
"fastas",
"limsdatapull",
"miseq",
"mkdir",
"wphl"

17
limsdatapull/README.md
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@ -1,8 +1,11 @@
# StarLIMS Data Pull
Pulls positive SC2 sample IDs and relavant dates from StarLIMS.
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](https://github.com/MillironX/wphl-bioinformatics/blob/master/README.md), then copy over using a secure flash drive or similar method.
**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](https://github.com/MillironX/wphl-bioinformatics/blob/master/README.md),
then copy over using a secure flash drive or similar method.
## Usage
@ -10,7 +13,8 @@ Double-click `refresh-lims-data.bat` in any location.
## Installation
This script requires [Miniconda](https://conda.io/en/master/miniconda.html#windows-installers).
This script requires
[Miniconda](https://conda.io/en/master/miniconda.html#windows-installers).
1. Download and install Miniconda
1. Select "Just Me" when asked who to install for
@ -19,10 +23,13 @@ This script requires [Miniconda](https://conda.io/en/master/miniconda.html#windo
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`
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 `SeqenceDatabase.xlsx` will be added to `limsdatapull`. This file can be referenced by other spreadsheets for efficient and timely lookup data from StarLIMS.
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.