CALeDNA Anacapa Container for Linux/HPC (modified)

This is a modified version of the CALeDNA Anacapa/CRUX Dat Container (Linux/HPC) published by Maxwell Ogden. The modifications are as follows:

• anacapa-1.5.0.img: this Singularity Container has been modified to enable it to run on a high-performance computing cluster that requires two-step authentication (e.g. Stanford Research Computing Center Sherlock). 
• anacapa.zip: this archive has several changes from the corresponding anacapa.tar.gz from the CALeDNA Anacapa/CRUX Dat Container (Linux/HPC). Several scripts were modified slightly to address errors when running them on Stanford's Sherlock computing cluster. Additionally, the original Anacapa CO1 reference library has been moved to a folder called "CO1_anacapa_old," and the core "CO1" reference library folder contains the MIDORI2 reference database, a quality controlled and updated database built from GenBank release 253 (20 December 2022), including the required Bowtie 2 index library needed to use the reference library with the Anacapa Toolkit (see CRUX for more information on this process). 
• crux_db.tar.gz: this archive is unchanged from the CALeDNA Anacapa/CRUX Dat Container (Linux/HPC)

We have also included the two scripts, run-anacapa-QC-full.sh and run-anacapa-classifier-full.sh, needed to run the two core Anacapa modules via HPC. 

Further Instructions for Use:

More detailed instructions for running the Anacapa Toolkit in a Singularity container can be found here, and a comprehensive overview of the Anacapa Toolkit itself can be found here; if you have not used the Anacapa Toolkit before, these resources are crucial context for implementing this workflow. 

Additional Citation Information:

The original citation for the Anacapa Toolkit is: 

Curd, E.E., Gold, Z., Kandlikar, G.S., Gomer, J., Ogden, M., O’Connell, T., Pipes, L., Schweizer, T.M., Rabichow, L., Lin, M., Shi, B., Barber, P.H., Kraft, N., Wayne, R., Meyer, R.S., 2019. Anacapa Toolkit: An environmental DNA toolkit for processing multilocus metabarcode datasets. Methods in Ecology and Evolution 10, 1469–1475. https://doi.org/10.1111/2041-210X.13214

If you are using this particular modified and containerized version of the Anacapa Toolkit, you are welcome to cite this Zenodo workflow but please ensure you also cite the original Anacapa Toolkit.