Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

check installed tools and report issues #389

Merged
merged 1 commit into from
Apr 9, 2024
Merged

check installed tools and report issues #389

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
36 changes: 35 additions & 1 deletion partition-before-pggb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -257,7 +257,41 @@ if [ "$show_help" == true ]; then
echo
echo "Use wfmash, seqwish, smoothxg, odgi, gfaffix, and vg to build, project and display a pangenome graph."
exit
elif [ "$input_fasta" = "false" ] || [ "$output_dir" = "false" ]; then
fi

# Function to check if a tool is in PATH
check_tool_availability() {
local tool_name=$1
local tool_command=$2

if ! command -v $tool_command &> /dev/null; then
# Instead of exiting immediately, add the tool name to the array of missing tools
missing_tools+=("$tool_name")
fi
}

# Check availability of each tool
check_tool_availability "wfmash" "wfmash"
check_tool_availability "seqwish" "seqwish"
check_tool_availability "smoothxg" "smoothxg"
check_tool_availability "odgi" "odgi"
check_tool_availability "gfaffix" "gfaffix"
check_tool_availability "vg" "vg"
check_tool_availability "vcfbub" "vcfbub"
check_tool_availability "vcfwave" "vcfwave"
check_tool_availability "bcftools" "bcftools"
check_tool_availability "MultiQC" "multiqc"

# If there are missing tools, report them and exit
if [ ${#missing_tools[@]} -ne 0 ]; then
echo "[pggb] ERROR: the following tools are not installed or not in the PATH:"
for tool in "${missing_tools[@]}"; do
echo "- $tool"
done
exit 1
fi

if [ "$input_fasta" = "false" ] || [ "$output_dir" = "false" ]; then
>&2 echo "[pggb] ERROR: mandatory argument: -i/--input-fasta and -o/--output-dir"
exit
elif [ ! -f "${input_fasta}.fai" ]; then
Expand Down
36 changes: 35 additions & 1 deletion pggb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -257,7 +257,41 @@ if [ "$show_help" == true ]; then
echo
echo "Use wfmash, seqwish, smoothxg, odgi, gfaffix, and vg to build, project and display a pangenome graph."
exit
elif [ "$input_fasta" = "false" ] || [ "$output_dir" = "false" ]; then
fi

# Function to check if a tool is in PATH
check_tool_availability() {
local tool_name=$1
local tool_command=$2

if ! command -v $tool_command &> /dev/null; then
# Instead of exiting immediately, add the tool name to the array of missing tools
missing_tools+=("$tool_name")
fi
}

# Check availability of each tool
check_tool_availability "wfmash" "wfmash"
check_tool_availability "seqwish" "seqwish"
check_tool_availability "smoothxg" "smoothxg"
check_tool_availability "odgi" "odgi"
check_tool_availability "gfaffix" "gfaffix"
check_tool_availability "vg" "vg"
check_tool_availability "vcfbub" "vcfbub"
check_tool_availability "vcfwave" "vcfwave"
check_tool_availability "bcftools" "bcftools"
check_tool_availability "MultiQC" "multiqc"

# If there are missing tools, report them and exit
if [ ${#missing_tools[@]} -ne 0 ]; then
echo "[pggb] ERROR: the following tools are not installed or not in the PATH:"
for tool in "${missing_tools[@]}"; do
echo "- $tool"
done
exit 1
fi

if [ "$input_fasta" = "false" ] || [ "$output_dir" = "false" ]; then
>&2 echo "[pggb] ERROR: mandatory argument: -i/--input-fasta and -o/--output-dir"
exit
elif [ ! -f "${input_fasta}.fai" ]; then
Expand Down
Loading