flake.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         "context"
   9         "flag"
  10         "fmt"
  11         "io"
  12         "net/http"
  13         _ "net/http/pprof"
  14
  15         "git.arvados.org/arvados.git/sdk/go/arvados"
  16         log "github.com/sirupsen/logrus"
  17 )
  18
  19 type flakecmd struct {
  20         filter filter
  21 }
  22
  23 func (cmd *flakecmd) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  24         var err error
  25         defer func() {
  26                 if err != nil {
  27                         fmt.Fprintf(stderr, "%s\n", err)
  28                 }
  29         }()
  30         flags := flag.NewFlagSet("", flag.ContinueOnError)
  31         flags.SetOutput(stderr)
  32         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  33         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  34         projectUUID := flags.String("project", "", "project `UUID` for output data")
  35         priority := flags.Int("priority", 500, "container request priority")
  36         inputDir := flags.String("input-dir", "./in", "input `directory`")
  37         outputDir := flags.String("output-dir", "./out", "output `directory`")
  38         cmd.filter.Flags(flags)
  39         err = flags.Parse(args)
  40         if err == flag.ErrHelp {
  41                 err = nil
  42                 return 0
  43         } else if err != nil {
  44                 return 2
  45         }
  46
  47         if *pprof != "" {
  48                 go func() {
  49                         log.Println(http.ListenAndServe(*pprof, nil))
  50                 }()
  51         }
  52
  53         if !*runlocal {
  54                 runner := arvadosContainerRunner{
  55                         Name:        "lightning flake",
  56                         Client:      arvados.NewClientFromEnv(),
  57                         ProjectUUID: *projectUUID,
  58                         RAM:         700000000000,
  59                         VCPUs:       96,
  60                         Priority:    *priority,
  61                         KeepCache:   2,
  62                         APIAccess:   true,
  63                 }
  64                 err = runner.TranslatePaths(inputDir)
  65                 if err != nil {
  66                         return 1
  67                 }
  68                 runner.Args = []string{"flake", "-local=true",
  69                         "-pprof", ":6060",
  70                         "-input-dir", *inputDir,
  71                         "-output-dir", "/mnt/output",
  72                         "-max-variants", fmt.Sprintf("%d", cmd.filter.MaxVariants),
  73                         "-min-coverage", fmt.Sprintf("%f", cmd.filter.MinCoverage),
  74                         "-max-tag", fmt.Sprintf("%d", cmd.filter.MaxTag),
  75                 }
  76                 var output string
  77                 output, err = runner.Run()
  78                 if err != nil {
  79                         return 1
  80                 }
  81                 fmt.Fprintln(stdout, output)
  82                 return 0
  83         }
  84
  85         tilelib := &tileLibrary{
  86                 retainNoCalls:       true,
  87                 retainTileSequences: true,
  88                 compactGenomes:      map[string][]tileVariantID{},
  89         }
  90         err = tilelib.LoadDir(context.Background(), *inputDir)
  91         if err != nil {
  92                 return 1
  93         }
  94
  95         log.Info("filtering")
  96         cmd.filter.Apply(tilelib)
  97         log.Info("tidying")
  98         tilelib.Tidy()
  99         err = tilelib.WriteDir(*outputDir)
 100         if err != nil {
 101                 return 1
 102         }
 103         return 0
 104 }