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         "runtime/debug"
  14         "strings"
  15
  16         "git.arvados.org/arvados.git/lib/cmd"
  17         "github.com/mattn/go-isatty"
  18         "github.com/sirupsen/logrus"
  19 )
  20
  21 var (
  22         handler = cmd.Multi(map[string]cmd.Handler{
  23                 "version":   cmd.Version,
  24                 "-version":  cmd.Version,
  25                 "--version": cmd.Version,
  26
  27                 "ref2genome":         &ref2genome{},
  28                 "vcf2fasta":          &vcf2fasta{},
  29                 "import":             &importer{},
  30                 "annotate":           &annotatecmd{},
  31                 "export":             &exporter{},
  32                 "export-numpy":       &exportNumpy{},
  33                 "flake":              &flakecmd{},
  34                 "slice":              &slicecmd{},
  35                 "slice-numpy":        &sliceNumpy{},
  36                 "tiling-stats":       &tilingStats{},
  37                 "anno2vcf":           &anno2vcf{},
  38                 "numpy-comvar":       &numpyComVar{},
  39                 "filter":             &filtercmd{},
  40                 "build-docker-image": &buildDockerImage{},
  41                 "plot":               &pythonPlot{},
  42                 "pca-plot":           &pythonPlot{},
  43                 "manhattan-plot":     &manhattanPlot{},
  44                 "diff-fasta":         &diffFasta{},
  45                 "stats":              &statscmd{},
  46                 "merge":              &merger{},
  47                 "dump":               &dump{},
  48                 "dumpgob":            &dumpGob{},
  49                 "choose-samples":     &chooseSamples{},
  50         })
  51 )
  52
  53 func init() {
  54         if os.Getenv("GOGC") == "" {
  55                 debug.SetGCPercent(30)
  56         }
  57 }
  58
  59 func Main() {
  60         if !isatty.IsTerminal(os.Stderr.Fd()) {
  61                 logrus.StandardLogger().Formatter = &logrus.TextFormatter{DisableTimestamp: true}
  62         }
  63         if len(os.Args) >= 2 && !strings.HasSuffix(os.Args[1], "version") {
  64                 // print version (then run subcommand)
  65                 cmd.Version.RunCommand("lightning", nil, nil, os.Stderr, os.Stderr)
  66         }
  67         os.Exit(handler.RunCommand(os.Args[0], os.Args[1:], os.Stdin, os.Stdout, os.Stderr))
  68 }
  69
  70 type buildDockerImage struct{}
  71
  72 func (cmd *buildDockerImage) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  73         tmpdir, err := ioutil.TempDir("", "")
  74         if err != nil {
  75                 fmt.Fprint(stderr, err)
  76                 return 1
  77         }
  78         defer os.RemoveAll(tmpdir)
  79         err = ioutil.WriteFile(tmpdir+"/Dockerfile", []byte(`FROM debian:bullseye
  80 RUN DEBIAN_FRONTEND=noninteractive \
  81   apt-get update && \
  82   apt-get dist-upgrade -y && \
  83   apt-get install -y --no-install-recommends bcftools bedtools samtools python2 python3-sklearn python3-matplotlib python3-pip ca-certificates && \
  84   apt-get clean && \
  85   pip3 install qmplot
  86 `), 0644)
  87         if err != nil {
  88                 fmt.Fprint(stderr, err)
  89                 return 1
  90         }
  91         docker := exec.Command("docker", "build", "--tag=lightning-runtime", tmpdir)
  92         docker.Stdout = stdout
  93         docker.Stderr = stderr
  94         err = docker.Run()
  95         if err != nil {
  96                 return 1
  97         }
  98         fmt.Fprintf(stderr, "built and tagged new docker image, lightning-runtime\n")
  99         return 0
 100 }