KhufuEnv is an open-source, Unix-based auxiliary environment consisting of flexible tools for manipulating and analyzing genomic data and other datasets. The KhufuEnv provides a buildable platform for constructing pipelines for several genomic analyses across different species.
Every tool in KhufuEnv is designed to meet the following criteria:
- Single-thread process.
- Does not require significant computational resources.
- Does a simple job.
- Bash-compatible.
- Does not require special dependencies or other third-party computational tools.
-
Additional packages:
- data.table
- tidyr
- plyr
- Download the package.
git clone https://github.com/w-korani/KhufuEnv - Go to the package folder.
cd KhufuEnv_main - Run the installer.
sudo bash ./installer.sh - Add the source for the Bash Shell Environment.
echo "source /etc/KhufuEnv/call.sh" >> ~/.bashrc - Refresh the Bash Shell Environment.
. ~/.bashrc
- Go to the package folder.
cd KhufuEnv_main - Run the uninstaller.
sudo bash ./uninstaller.sh - Remove the source for the Bash Shell Environment.
sed -i "/^source \/etc\/KhufuEnv\/call.sh$/d" ~/.bashrc - Refresh the Bash Shell Environment.
or
. ~/.bashrcexec bash
- To list all tools:
KhufuEnvHelp
- To show the documentation of a specific tool:
KhufuEnvHelp <tool-name>
In order to help users test the functionality of these tools, a directory containing test input files for each section is provided. Each tool is associated with its own documentation, which includes a specific example of how to use it.
- Navigate to the main test directory.
cd KhufuEnv_main/TestingData
- Each section has their own set of test inputs. You will need to navigate to the appropriate subdirectory for the section's tools you want to test, replacing
<section-inputs>with the name of the section's corresponding directory.
cd <section-inputs>
-
Display the documentation for the tool using
KhufuEnvHelp <tool-name>. -
In the tool's documentation, you will find an example command as shown below:
#####################
KhufuEnv.Ver1.0.0: hapmapFilterMissingVariant
Usage: hapmapFilterMissingVariant hapmap missing
Description:
The hapmapFilterMissingVariant function filters the input hapmap to remove sites where the percentage of variants missing is greater than the specified threshold.
Parameters:
hapmap ex: test1.hapmap Hapmap to be processed.
missing ex: 0.75 Missing percentage to be used. Must be in decimal format.
Example:
hapmapFilterMissingVariant test1.hapmap 0.75
#####################
-
For instance, to test the output of the
hapmapFilterMissingVarianttool, type or copy and pastehapmapFilterMissingVariant test1.hapmap 0.75into the terminal and execute it. -
The output will be displayed as shown below:
$ hapmapFilterMissingVariant test1.hapmap 0.75 | column -t
chr pos SM001 SM002 SM003 SM004 SM005 SM006 SM007 SM008 SM009 SM010
TRv2Chr.01 296910 C - - A,C A,C - - - A,C A,C
TRv2Chr.01 9470991 C - - C - - C - - -
TRv2Chr.01 13207367 - - T C C - C C,T C -
TRv2Chr.01 30479088 - - C C - - C - C -
TRv2Chr.01 66933056 G - G A,G G - A,G A,G A,G A,G
TRv2Chr.01 66944054 T T - T T T - T T T
TRv2Chr.01 73021455 C - - - - - - C C -
TRv2Chr.01 95590686 A,G G - A,G G - - - - G
TRv2Chr.01 95593242 - - G C - C - - - -
TRv2Chr.01 95608110 - - - A - A,G - - A -
TRv2Chr.01 112412989 A,G A,G A A,G A - A,G A,G A,G -
TRv2Chr.02 71100 C,T C,T C,T C,T - - C C,T C,T -
TRv2Chr.02 74281 A A A A - A A A A -
TRv2Chr.02 80175 C,T C,T C,T C,T C,T C C,T C,T C,T -
TRv2Chr.02 107994 - G A A - - A,G A,G G -
TRv2Chr.02 119526 - G G G,T - - G,T G G,T -
TRv2Chr.02 27794987 - - - G - - - G A,G -
TRv2Chr.02 67801286 C,T C T C,T C,T - - - C,T C,T
TRv2Chr.02 84715892 - A - A - - - A - -
TRv2Chr.03 31478009 T T - C,T T T C,T T C,T -
TRv2Chr.03 106731401 - A - A - - - - A -
Note: the command column -t has been piped for better display. It is not required.
Wright, Hallie C, Catherine E. M. Davis, Josh Clevenger, and Walid Korani. “KhufuEnv, an Auxiliary Toolkit for Building Computational Pipelines for Plant and Animal Breeding.” bioRxiv, January 1, 2025, 2025.03.28.645917. https://doi.org/10.1101/2025.03.28.645917.