This repository is a fork of robertaboukhalil/ginkgo
The core functionalities added in this fork are:
(1) Support for building any user-specified genome assembly from a FASTA format file in end2end_buildGenome.sh.
(2) Support for multi-processing (with mclapply) in ginkgo_parallel.sh and process_parallel.sh.
${conda} create -y -n ${ginkgo_envname} bioconductor-ctc bioconductor-dnacopy r-devtools r-inline r-gplots r-scales r-plyr r-ggplot2 r-gridExtra r-fastcluster r-heatmap3 \
bwa bowtie parallel wgsim
# bioconda:bwa, bioconda:bowtie, conda-forge:parallel, and bioconda:wgsim are for building genome.
# The GNU parallel greatly speeds up the genome-building process by multi-processing (running multiple jobs at once).Then, run the commands below to build your target genome:
${conda} activate ${ginkgo_envname}
cd "genomes/${GENOME_NAME_1}/original/"
bash -evx ../../../end2end_buildGenome.sh "${GENOME_FASTA_FILE}" "${GENOME_NAME_2}"
# Recommendation: keep ${GENOME_NAME_1} and ${GENOME_NAME_2} identicalOnce the genome build is complete, you can execute Ginkgo via cli/ginkgo.sh or cli/ginkgo_parallel.sh. This implementation follows exactly the same core logic as the original robertaboukhalil/ginkgo repository.