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-hgvs":        &exportHGVS{},
  23                 "export-numpy":       &exportNumpy{},
  24                 "filter":             &filterer{},
  25                 "build-docker-image": &buildDockerImage{},
  26                 "pca-go":             &goPCA{},
  27                 "pca-py":             &pythonPCA{},
  28                 "plot":               &pythonPlot{},
  29                 "diff-fasta":         &diffFasta{},
  30                 "stats":              &stats{},
  31         })
  32 )
  33
  34 func main() {
  35         os.Exit(handler.RunCommand(os.Args[0], os.Args[1:], os.Stdin, os.Stdout, os.Stderr))
  36 }
  37
  38 type buildDockerImage struct{}
  39
  40 func (cmd *buildDockerImage) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  41         tmpdir, err := ioutil.TempDir("", "")
  42         if err != nil {
  43                 fmt.Fprint(stderr, err)
  44                 return 1
  45         }
  46         defer os.RemoveAll(tmpdir)
  47         err = ioutil.WriteFile(tmpdir+"/Dockerfile", []byte(`FROM debian:10
  48 RUN DEBIAN_FRONTEND=noninteractive \
  49   apt-get update && \
  50   apt-get dist-upgrade -y && \
  51   apt-get install -y --no-install-recommends bcftools bedtools samtools python2 python3-sklearn python3-matplotlib && \
  52   apt-get clean
  53 `), 0644)
  54         if err != nil {
  55                 fmt.Fprint(stderr, err)
  56                 return 1
  57         }
  58         docker := exec.Command("docker", "build", "--tag=lightning-runtime", tmpdir)
  59         docker.Stdout = stdout
  60         docker.Stderr = stderr
  61         err = docker.Run()
  62         if err != nil {
  63                 return 1
  64         }
  65         fmt.Fprintf(stderr, "built and tagged new docker image, lightning-runtime\n")
  66         return 0
  67 }