cmd.go

   1 package main
   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 )
  12
  13 var (
  14         handler = cmd.Multi(map[string]cmd.Handler{
  15                 "version":   cmd.Version,
  16                 "-version":  cmd.Version,
  17                 "--version": cmd.Version,
  18
  19                 "vcf2fasta":          &vcf2fasta{},
  20                 "import":             &importer{},
  21                 "export-numpy":       &exportNumpy{},
  22                 "filter":             &filterer{},
  23                 "build-docker-image": &buildDockerImage{},
  24                 "pca":                &pythonPCA{},
  25                 "plot":               &pythonPlot{},
  26         })
  27 )
  28
  29 func main() {
  30         os.Exit(handler.RunCommand(os.Args[0], os.Args[1:], os.Stdin, os.Stdout, os.Stderr))
  31 }
  32
  33 type buildDockerImage struct{}
  34
  35 func (cmd *buildDockerImage) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  36         tmpdir, err := ioutil.TempDir("", "")
  37         if err != nil {
  38                 fmt.Fprint(stderr, err)
  39                 return 1
  40         }
  41         defer os.RemoveAll(tmpdir)
  42         err = ioutil.WriteFile(tmpdir+"/Dockerfile", []byte(`FROM debian:10
  43 RUN DEBIAN_FRONTEND=noninteractive \
  44   apt-get update && \
  45   apt-get dist-upgrade -y && \
  46   apt-get install -y --no-install-recommends bcftools samtools python3-sklearn python3-matplotlib && \
  47   apt-get clean
  48 `), 0644)
  49         if err != nil {
  50                 fmt.Fprint(stderr, err)
  51                 return 1
  52         }
  53         docker := exec.Command("docker", "build", "--tag=lightning-runtime", tmpdir)
  54         docker.Stdout = stdout
  55         docker.Stderr = stderr
  56         err = docker.Run()
  57         if err != nil {
  58                 return 1
  59         }
  60         fmt.Fprintf(stderr, "built and tagged new docker image, lightning-runtime\n")
  61         return 0
  62 }