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                 "ref2genome":         &ref2genome{},
  20                 "vcf2fasta":          &vcf2fasta{},
  21                 "import":             &importer{},
  22                 "export-numpy":       &exportNumpy{},
  23                 "filter":             &filterer{},
  24                 "build-docker-image": &buildDockerImage{},
  25                 "pca":                &pythonPCA{},
  26                 "plot":               &pythonPlot{},
  27         })
  28 )
  29
  30 func main() {
  31         os.Exit(handler.RunCommand(os.Args[0], os.Args[1:], os.Stdin, os.Stdout, os.Stderr))
  32 }
  33
  34 type buildDockerImage struct{}
  35
  36 func (cmd *buildDockerImage) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  37         tmpdir, err := ioutil.TempDir("", "")
  38         if err != nil {
  39                 fmt.Fprint(stderr, err)
  40                 return 1
  41         }
  42         defer os.RemoveAll(tmpdir)
  43         err = ioutil.WriteFile(tmpdir+"/Dockerfile", []byte(`FROM debian:10
  44 RUN DEBIAN_FRONTEND=noninteractive \
  45   apt-get update && \
  46   apt-get dist-upgrade -y && \
  47   apt-get install -y --no-install-recommends bcftools bedtools samtools python3-sklearn python3-matplotlib && \
  48   apt-get clean
  49 `), 0644)
  50         if err != nil {
  51                 fmt.Fprint(stderr, err)
  52                 return 1
  53         }
  54         docker := exec.Command("docker", "build", "--tag=lightning-runtime", tmpdir)
  55         docker.Stdout = stdout
  56         docker.Stderr = stderr
  57         err = docker.Run()
  58         if err != nil {
  59                 return 1
  60         }
  61         fmt.Fprintf(stderr, "built and tagged new docker image, lightning-runtime\n")
  62         return 0
  63 }