1 // Copyright (C) The Lightning Authors. All rights reserved.
3 // SPDX-License-Identifier: AGPL-3.0
15 "git.arvados.org/arvados.git/lib/cmd"
16 "github.com/mattn/go-isatty"
17 "github.com/sirupsen/logrus"
21 handler = cmd.Multi(map[string]cmd.Handler{
22 "version": cmd.Version,
23 "-version": cmd.Version,
24 "--version": cmd.Version,
26 "ref2genome": &ref2genome{},
27 "vcf2fasta": &vcf2fasta{},
28 "import": &importer{},
29 "annotate": &annotatecmd{},
30 "export": &exporter{},
31 "export-numpy": &exportNumpy{},
34 "slice-numpy": &sliceNumpy{},
35 "anno2vcf": &anno2vcf{},
36 "numpy-comvar": &numpyComVar{},
37 "filter": &filtercmd{},
38 "build-docker-image": &buildDockerImage{},
40 "pca-py": &pythonPCA{},
41 "plot": &pythonPlot{},
42 "diff-fasta": &diffFasta{},
45 "dumpgob": &dumpGob{},
50 if !isatty.IsTerminal(os.Stderr.Fd()) {
51 logrus.StandardLogger().Formatter = &logrus.TextFormatter{DisableTimestamp: true}
53 if len(os.Args) >= 2 && !strings.HasSuffix(os.Args[1], "version") {
54 cmd.Version.RunCommand("lightning", nil, nil, os.Stderr, os.Stderr)
56 os.Exit(handler.RunCommand(os.Args[0], os.Args[1:], os.Stdin, os.Stdout, os.Stderr))
59 type buildDockerImage struct{}
61 func (cmd *buildDockerImage) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
62 tmpdir, err := ioutil.TempDir("", "")
64 fmt.Fprint(stderr, err)
67 defer os.RemoveAll(tmpdir)
68 err = ioutil.WriteFile(tmpdir+"/Dockerfile", []byte(`FROM debian:bullseye
69 RUN DEBIAN_FRONTEND=noninteractive \
71 apt-get dist-upgrade -y && \
72 apt-get install -y --no-install-recommends bcftools bedtools samtools python2 python3-sklearn python3-matplotlib ca-certificates && \
76 fmt.Fprint(stderr, err)
79 docker := exec.Command("docker", "build", "--tag=lightning-runtime", tmpdir)
80 docker.Stdout = stdout
81 docker.Stderr = stderr
86 fmt.Fprintf(stderr, "built and tagged new docker image, lightning-runtime\n")