Create new_project_ch1.sh

create_project_directory/new_project_ch1.sh

@@ -0,0 +1,77 @@
+#!/bin/bash
+
+# Constants
+README_CONTENT="### Few pointers for Project Organization\n- Use GitHub for collaborating, sharing, and version control of your scripts!\n- Add your raw data, backup data, and any large files >50 Mb to .gitignore file.\n- Use a pipeline management tool such as snakemake or nextflow\n- Document each step of the genome assembly and annotation process.\n- Store intermediate files for reproducibility."
+
+# Function to create directory with validation
+create_directory() {
+ if [ ! -d "$1" ]; then
+ mkdir "$1"
+ echo "Created directory: $1"
+ else
+ echo "Directory '$1' already exists. Skipping..."
+ fi
+}
+
+# User input for project name
+read -p "Enter the name of your project (avoid spaces, use underscores): " project_name
+
+# Create project directory
+create_directory "$project_name"
+
+# Create subdirectories
+create_directory "$project_name/data"
+create_directory "$project_name/data/short_reads"
+create_directory "$project_name/data/long_reads"
+
+create_directory "$project_name/assembly"
+create_directory "$project_name/assembly/spades"
+create_directory "$project_name/assembly/rescaffolding"
+create_directory "$project_name/assembly/purging"
+create_directory "$project_name/assembly/polishing"
+
+create_directory "$project_name/annotation"
+create_directory "$project_name/annotation/computational"
+create_directory "$project_name/annotation/denovo_gene_finding"
+
+create_directory "$project_name/docs"
+create_directory "$project_name/docs/protocols"
+create_directory "$project_name/docs/analysis_notes"
+
+create_directory "$project_name/scripts"
+create_directory "$project_name/scripts/assembly_scripts"
+create_directory "$project_name/scripts/annotation_scripts"
+
+create_directory "$project_name/results"
+create_directory "$project_name/results/assembly_results"
+create_directory "$project_name/results/annotation_results"
+
+create_directory "$project_name/tmp"
+create_directory "$project_name/tmp/assembly_tmp"
+create_directory "$project_name/tmp/annotation_tmp"
+
+# Create readme files
+echo "$README_CONTENT" > "$project_name/README.md"
+echo "This directory is for raw short reads." > "$project_name/data/short_reads/readme.md"
+echo "This directory is for raw long reads." > "$project_name/data/long_reads/readme.md"
+
+echo "This directory contains assembly results using SPAdes." > "$project_name/assembly/spades/readme.md"
+echo "This directory contains results from rescaffolding tools." > "$project_name/assembly/rescaffolding/readme.md"
+echo "This directory contains results after purging haplotigs." > "$project_name/assembly/purging/readme.md"
+echo "This directory contains polished genome assembly results." > "$project_name/assembly/polishing/readme.md"
+
+echo "This directory contains computational annotation results." > "$project_name/annotation/computational/readme.md"
+echo "This directory contains de novo gene finding annotation results." > "$project_name/annotation/denovo_gene_finding/readme.md"
+
+echo "This directory contains protocols for various steps." > "$project_name/docs/protocols/readme.md"
+echo "This directory contains analysis notes for each step." > "$project_name/docs/analysis_notes/readme.md"
+
+echo "This directory contains scripts for genome assembly." > "$project_name/scripts/assembly_scripts/readme.md"
+echo "This directory contains scripts for genome annotation." > "$project_name/scripts/annotation_scripts/readme.md"
+
+echo "This directory contains assembly results for each step." > "$project_name/results/assembly_results/readme.md"
+echo "This directory contains annotation results for each step." > "$project_name/results/annotation_results/readme.md"
+
+# Success message
+echo "Project Initialization completed successfully!"
+tree "$project_name"