10 "git.arvados.org/arvados.git/lib/cmd"
14 handler = cmd.Multi(map[string]cmd.Handler{
15 "version": cmd.Version,
16 "-version": cmd.Version,
17 "--version": cmd.Version,
19 "ref2genome": &ref2genome{},
20 "vcf2fasta": &vcf2fasta{},
21 "import": &importer{},
22 "export-numpy": &exportNumpy{},
23 "filter": &filterer{},
24 "build-docker-image": &buildDockerImage{},
26 "pca-py": &pythonPCA{},
27 "plot": &pythonPlot{},
28 "diff-fasta": &diffFasta{},
34 os.Exit(handler.RunCommand(os.Args[0], os.Args[1:], os.Stdin, os.Stdout, os.Stderr))
37 type buildDockerImage struct{}
39 func (cmd *buildDockerImage) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
40 tmpdir, err := ioutil.TempDir("", "")
42 fmt.Fprint(stderr, err)
45 defer os.RemoveAll(tmpdir)
46 err = ioutil.WriteFile(tmpdir+"/Dockerfile", []byte(`FROM debian:10
47 RUN DEBIAN_FRONTEND=noninteractive \
49 apt-get dist-upgrade -y && \
50 apt-get install -y --no-install-recommends bcftools bedtools samtools python2 python3-sklearn python3-matplotlib && \
54 fmt.Fprint(stderr, err)
57 docker := exec.Command("docker", "build", "--tag=lightning-runtime", tmpdir)
58 docker.Stdout = stdout
59 docker.Stderr = stderr
64 fmt.Fprintf(stderr, "built and tagged new docker image, lightning-runtime\n")