Software Installation - EGAPx and FCS-GX on Klone

2026
Hyak
Klone
EGAPx
FCS-GX
annotation
Author

Sam White

Published

March 5, 2026

INTRO

Laura asked me to install EGAPx and FCS-GX on Klone (GitHub Issue) so that she can use them for annotation of some existing snow crab RNA-seq data she is working with.

METHODS

[FCS-GX]

The steps below follow those outlined in the FCS-GX documentation.

Get FCS Python script

cd /gscratch/srlab/containers \
&& curl -LO https://github.com/ncbi/fcs/raw/main/dist/fcs.py

Get FCS-GX Singularity image

curl https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/latest/fcs-gx.sif -Lo fcs-gx.sif

Get FCS-GX databases

This downloads ~500GB of data, so be sure you have enough storage space before running this command! Additionally, the download may take a while to complete.

module load coenv/python/3.13.11

cd /gscratch/scrubbed/samwhite/databases

SOURCE_DB_MANIFEST="https://ncbi-fcs-gx.s3.amazonaws.com/gxdb/latest/all.manifest"

python3 /gscratch/srlab/containers/fcs.py \
--image /gscratch/srlab/containers/fcs-gx.sif \
db \
get --mft "$SOURCE_DB_MANIFEST" \
--dir "./gxdb"

Screenshot of completed DB downloads

Screenshot of completed DB downloads

Installation was not tested by running an annotation job, but the above steps were successfully completed without issue.

EGAPx

The steps below follow those outlined in the EGAPx documentation.

Containers and scripts

I created an Apptainer (Singularity) container for EGAPx and a script to execute it.

Container definition file: srlab-NCBI-EGAPx.def (GitHub)

  • This container is based on the EGAPx Dockerfile and includes EGAPx and all dependencies.

  • Primarily written using Claude Sonnet 4.6 (gAI agent) with some manual edits to ensure it would build correctly.

Execution script: run_egapx.sh (GitHub).

  • This script is designed to execute the srlab-NCBI-EGAPx.sif container. It will create a cache directory, set a cache variable, and execute the container.

Both have been added to Klone and can be found in the /mmfs1/gscratch/srlab/containers directory.

Container and script have been added to Klone:

  • /mmfs1/gscratch/srlab/containers/run_egapx.sh: Script to execute srlab-NCBI-EGAPx.sif container. This will create a cache directory, set a cache variable, and bind directories to the container.

    Example usage: bash ./run_egapx.sh \ /opt/egapx/examples/input_D_farinae_small.yaml \ -e singularity \ -w ./work \ -o ./output

    This requires that the srlab-NCBI-EGAPx.sif container is in the same directory as this script. Both can be copied to other directories, if desired.

  • /mmfs1/gscratch/srlab/containers/srlab-NCBI-EGAPx.sif: Apptainer (Singularity) container. Can be executed by itself, but is better to use with the run_egapx.sh to ensure cache directory is set.

    To see additional help examples for using the srlab-NCBI-EGAPx.sif container:

    singularity run-help srlab-NCBI-EGAPx.sif

Test EGAPx container

The built-in test example was used to test the container. The test completed successfully, with all expected output files generated.

Screenshot of EGAPx test output

Screenshot of EGAPx test output

CONCLUSION

EGAPx and FCS-GX have been successfully installed on Klone. Both were tested to ensure they are working correctly, with FCS-GX tested by downloading the databases and EGAPx tested by running the built-in test example.

For info on how to run EGAPx: https://github.com/ncbi/egapx