cmd.go

   1 package lightning
   2
   3 import (
   4         "fmt"
   5         "io"
   6         "io/ioutil"
   7         "os"
   8         "os/exec"
   9
  10         "git.arvados.org/arvados.git/lib/cmd"
  11         "github.com/mattn/go-isatty"
  12         "github.com/sirupsen/logrus"
  13 )
  14
  15 var (
  16         handler = cmd.Multi(map[string]cmd.Handler{
  17                 "version":   cmd.Version,
  18                 "-version":  cmd.Version,
  19                 "--version": cmd.Version,
  20
  21                 "ref2genome":         &ref2genome{},
  22                 "vcf2fasta":          &vcf2fasta{},
  23                 "import":             &importer{},
  24                 "annotate":           &annotatecmd{},
  25                 "export":             &exporter{},
  26                 "export-numpy":       &exportNumpy{},
  27                 "numpy-comvar":       &numpyComVar{},
  28                 "filter":             &filtercmd{},
  29                 "build-docker-image": &buildDockerImage{},
  30                 "pca-go":             &goPCA{},
  31                 "pca-py":             &pythonPCA{},
  32                 "plot":               &pythonPlot{},
  33                 "diff-fasta":         &diffFasta{},
  34                 "stats":              &statscmd{},
  35                 "merge":              &merger{},
  36                 "dumpgob":            &dumpGob{},
  37         })
  38 )
  39
  40 func Main() {
  41         if !isatty.IsTerminal(os.Stderr.Fd()) {
  42                 logrus.StandardLogger().Formatter = &logrus.TextFormatter{DisableTimestamp: true}
  43         }
  44         os.Exit(handler.RunCommand(os.Args[0], os.Args[1:], os.Stdin, os.Stdout, os.Stderr))
  45 }
  46
  47 type buildDockerImage struct{}
  48
  49 func (cmd *buildDockerImage) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  50         tmpdir, err := ioutil.TempDir("", "")
  51         if err != nil {
  52                 fmt.Fprint(stderr, err)
  53                 return 1
  54         }
  55         defer os.RemoveAll(tmpdir)
  56         err = ioutil.WriteFile(tmpdir+"/Dockerfile", []byte(`FROM debian:bullseye
  57 RUN DEBIAN_FRONTEND=noninteractive \
  58   apt-get update && \
  59   apt-get dist-upgrade -y && \
  60   apt-get install -y --no-install-recommends bcftools bedtools samtools python2 python3-sklearn python3-matplotlib ca-certificates && \
  61   apt-get clean
  62 `), 0644)
  63         if err != nil {
  64                 fmt.Fprint(stderr, err)
  65                 return 1
  66         }
  67         docker := exec.Command("docker", "build", "--tag=lightning-runtime", tmpdir)
  68         docker.Stdout = stdout
  69         docker.Stderr = stderr
  70         err = docker.Run()
  71         if err != nil {
  72                 return 1
  73         }
  74         fmt.Fprintf(stderr, "built and tagged new docker image, lightning-runtime\n")
  75         return 0
  76 }