diff --git a/.vscode/settings.json b/.vscode/settings.json index 8d3b224..415a687 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,11 +1,13 @@ { "cSpell.words": [ + "LIMS", "Nanopore", "chmod", "cygpath", "demux", "fasta", "fastas", + "limsdatapull", "miseq", "mkdir", "wphl" diff --git a/limsdatapull/README.md b/limsdatapull/README.md index 986ca40..2b8f9eb 100644 --- a/limsdatapull/README.md +++ b/limsdatapull/README.md @@ -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.