let default_toolkit
~run_program
~host ~install_tools_path
?(mutect_jar_location = default_tool_location "Mutect")
?(gatk_jar_location = default_tool_location "GATK")
?(netmhc_tool_locations = default_netmhc_locations)
() =
let install installable =
Installable_tool.render ~host installable ~install_tools_path ~run_program
in
let install_git installable =
Git_installable_tool.render ~host installable ~install_tools_path ~run_program
in
Machine.Tool.Kit.concat [
Machine.Tool.Kit.of_list [
mutect_tool ~run_program ~host ~install_tools_path (mutect_jar_location ());
gatk_tool ~run_program ~host ~install_tools_path (gatk_jar_location ());
install bwa;
install samtools;
install bedtools;
install vcftools;
install strelka;
install picard;
install somaticsniper;
install sambamba;
install varscan;
install muse;
install virmid;
install star;
install stringtie;
install cufflinks;
install @@ hisat Machine.Tool.Default.hisat;
install @@ hisat Machine.Tool.Default.hisat2;
install mosaik;
install kallisto;
install fastqc;
install samblaster;
install_git freebayes;
];
Biopam.default ~run_program ~host
~install_path:(install_tools_path // "biopam-kit") ();
Python_package.default ~run_program ~host
~install_path: (install_tools_path // "python-tools") ();
Netmhc.default ~run_program ~host
~install_path: (install_tools_path // "netmhc-tools")
~files:(netmhc_tool_locations ()) ();
]