Run "filter" and "export" in arvados containers.

[lightning.git] / filter.go

diff --git a/filter.go b/filter.go
index a2bf12d7296cbd994ce560ec3a988d310ef2bb13..87d94ef62c9b0817af27e729aa6018ef3384ca20 100644 (file)
--- a/filter.go
+++ b/filter.go
@@ -3,12 +3,17 @@ package main
 import (
        "bufio"
        "encoding/gob"
+       "errors"
        "flag"
        "fmt"
        "io"
+       "io/ioutil"
        "log"
        "net/http"
        _ "net/http/pprof"
+       "os"
+
+       "git.arvados.org/arvados.git/sdk/go/arvados"
 )
 
 type filterer struct {
@@ -25,6 +30,10 @@ func (cmd *filterer) RunCommand(prog string, args []string, stdin io.Reader, std
        flags := flag.NewFlagSet("", flag.ContinueOnError)
        flags.SetOutput(stderr)
        pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
+       runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
+       projectUUID := flags.String("project", "", "project `UUID` for output data")
+       inputFilename := flags.String("i", "", "input `file`")
+       outputFilename := flags.String("o", "", "output `file`")
        maxvariants := flags.Int("max-variants", -1, "drop tiles with more than `N` variants")
        mincoverage := flags.Float64("min-coverage", 1, "drop tiles with coverage less than `P` across all haplotypes (0 < P ≤ 1)")
        maxtag := flags.Int("max-tag", -1, "drop tiles with tag ID > `N`")
@@ -43,8 +52,52 @@ func (cmd *filterer) RunCommand(prog string, args []string, stdin io.Reader, std
                }()
        }
 
+       if !*runlocal {
+               if *outputFilename != "" {
+                       err = errors.New("cannot specify output file in container mode: not implemented")
+                       return 1
+               }
+               runner := arvadosContainerRunner{
+                       Name:        "lightning filter",
+                       Client:      arvados.NewClientFromEnv(),
+                       ProjectUUID: *projectUUID,
+                       RAM:         64000000000,
+                       VCPUs:       2,
+               }
+               err = runner.TranslatePaths(inputFilename)
+               if err != nil {
+                       return 1
+               }
+               runner.Args = []string{"filter", "-local=true",
+                       "-i", *inputFilename,
+                       "-o", "/mnt/output/library.gob",
+                       "-max-variants", fmt.Sprintf("%d", *maxvariants),
+                       "-min-coverage", fmt.Sprintf("%f", *mincoverage),
+                       "-max-tag", fmt.Sprintf("%d", *maxtag),
+               }
+               err = runner.Run()
+               if err != nil {
+                       return 1
+               }
+               return 0
+       }
+
+       var infile io.ReadCloser
+       if *inputFilename == "" {
+               infile = ioutil.NopCloser(stdin)
+       } else {
+               infile, err = os.Open(*inputFilename)
+               if err != nil {
+                       return 1
+               }
+               defer infile.Close()
+       }
        log.Print("reading")
-       cgs, err := ReadCompactGenomes(stdin)
+       cgs, err := ReadCompactGenomes(infile)
+       if err != nil {
+               return 1
+       }
+       err = infile.Close()
        if err != nil {
                return 1
        }
@@ -105,7 +158,17 @@ func (cmd *filterer) RunCommand(prog string, args []string, stdin io.Reader, std
 
        log.Print("filtering done")
 
-       w := bufio.NewWriter(cmd.output)
+       var outfile io.WriteCloser
+       if *outputFilename == "" {
+               outfile = nopCloser{cmd.output}
+       } else {
+               outfile, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0777)
+               if err != nil {
+                       return 1
+               }
+               defer outfile.Close()
+       }
+       w := bufio.NewWriter(outfile)
        enc := gob.NewEncoder(w)
        log.Print("writing")
        err = enc.Encode(LibraryEntry{
@@ -119,5 +182,9 @@ func (cmd *filterer) RunCommand(prog string, args []string, stdin io.Reader, std
        if err != nil {
                return 1
        }
+       err = outfile.Close()
+       if err != nil {
+               return 1
+       }
        return 0
 }