WormCat Batch

Overview

WormCat Batch is a command line tool that allows you to batch multiple runs of WormCat from a Microsoft Excel File or a directory path with WormCat formatted csv files.

Note: You can also run WormCat Batch as a docker container. Find more information on running WormCat Batch as a Docker container here.

Prerequisites

WormCat Batch requires Python 3.5+ and R 3.4.1+ with a WormCat package installed.

If you are unsure if you have WormCat installed, you can run find.package("wormcat") from an R command prompt.

If WormCat is not installed, you can follow the directions here to install WormCat.

Note: WormCat can be installed as an R package you; do NOT need to checkout the source unless you intend to modify WormCat. The readme file explains how to install WormCat as an R package.

Excel spreadsheet Naming Conventions

Once you have the R package installed, you will create an Excel Spreadsheet with the required data for batch execution.

See the file Example/Murphy_TS.xsl for details on formating the Excel.

Note:

• The Spreadsheet Name should ONLY be composed of Letters, Numbers and Underscores (_) and has an extension .xlsx, .xlt, .xls
• The Sheet Names within the spreadsheet should ONLY be composed of Letters, Numbers, and Underscores (_) other characters may cause the batch process to fail!
• Each sheet requires a column name 'Sequence ID' or 'Wormbase ID' (This column name is case-sensitive)

To Run the Batch Process

To run the batch process, open a terminal window, change the directory to your project directory.

$pip install wormcat_batch
$wormcat_cli --help

After execution, the Output Directory will contain all the WormCat run data and a summary Excel spreadsheet.

Sample Output

Local development /test hints

Setup to test

• conda activate <appropriate_env>
• pip install .

Test

• cd /Users/dan/delme #some working directory
• wormcat_cli --input-excel ${PROJ_HOME}/Example/Murphy_TS.xlsx --output-path ./output
• wormcat_cli --input-csv-path ${PROJ_HOME}/Example/Murphy_TS_CSV--output-path ./output

Deploy

• Advance the version number in setup.py
• conda deactivate # twine is installed in base env
• increment setup.py version
• cd <project directory>
• rm -rf ./dist
• rm -rf ./wormcat_batch.egg-info
• python setup.py sdist
• twine check dist/*
• twine upload --repository pypi dist/*
• git add .
• git commit -m "some comment"
• git push