cmd.go

   1 // Copyright (C) The Lightning Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package lightning
   6
   7 import (
   8         "fmt"
   9         "io"
  10         "io/ioutil"
  11         "os"
  12         "os/exec"
  13         "strings"
  14
  15         "git.arvados.org/arvados.git/lib/cmd"
  16         "github.com/mattn/go-isatty"
  17         "github.com/sirupsen/logrus"
  18 )
  19
  20 var (
  21         handler = cmd.Multi(map[string]cmd.Handler{
  22                 "version":   cmd.Version,
  23                 "-version":  cmd.Version,
  24                 "--version": cmd.Version,
  25
  26                 "ref2genome":         &ref2genome{},
  27                 "vcf2fasta":          &vcf2fasta{},
  28                 "import":             &importer{},
  29                 "annotate":           &annotatecmd{},
  30                 "export":             &exporter{},
  31                 "export-numpy":       &exportNumpy{},
  32                 "flake":              &flakecmd{},
  33                 "slice":              &slicecmd{},
  34                 "slice-numpy":        &sliceNumpy{},
  35                 "numpy-comvar":       &numpyComVar{},
  36                 "filter":             &filtercmd{},
  37                 "build-docker-image": &buildDockerImage{},
  38                 "pca-go":             &goPCA{},
  39                 "pca-py":             &pythonPCA{},
  40                 "plot":               &pythonPlot{},
  41                 "diff-fasta":         &diffFasta{},
  42                 "stats":              &statscmd{},
  43                 "merge":              &merger{},
  44                 "dumpgob":            &dumpGob{},
  45         })
  46 )
  47
  48 func Main() {
  49         if !isatty.IsTerminal(os.Stderr.Fd()) {
  50                 logrus.StandardLogger().Formatter = &logrus.TextFormatter{DisableTimestamp: true}
  51         }
  52         if len(os.Args) >= 2 && !strings.HasSuffix(os.Args[1], "version") {
  53                 cmd.Version.RunCommand("lightning", nil, nil, os.Stderr, os.Stderr)
  54         }
  55         os.Exit(handler.RunCommand(os.Args[0], os.Args[1:], os.Stdin, os.Stdout, os.Stderr))
  56 }
  57
  58 type buildDockerImage struct{}
  59
  60 func (cmd *buildDockerImage) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  61         tmpdir, err := ioutil.TempDir("", "")
  62         if err != nil {
  63                 fmt.Fprint(stderr, err)
  64                 return 1
  65         }
  66         defer os.RemoveAll(tmpdir)
  67         err = ioutil.WriteFile(tmpdir+"/Dockerfile", []byte(`FROM debian:bullseye
  68 RUN DEBIAN_FRONTEND=noninteractive \
  69   apt-get update && \
  70   apt-get dist-upgrade -y && \
  71   apt-get install -y --no-install-recommends bcftools bedtools samtools python2 python3-sklearn python3-matplotlib ca-certificates && \
  72   apt-get clean
  73 `), 0644)
  74         if err != nil {
  75                 fmt.Fprint(stderr, err)
  76                 return 1
  77         }
  78         docker := exec.Command("docker", "build", "--tag=lightning-runtime", tmpdir)
  79         docker.Stdout = stdout
  80         docker.Stderr = stderr
  81         err = docker.Run()
  82         if err != nil {
  83                 return 1
  84         }
  85         fmt.Fprintf(stderr, "built and tagged new docker image, lightning-runtime\n")
  86         return 0
  87 }