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

[lightning.git] / import.go

diff --git a/import.go b/import.go
index 0f224670767698fd609b49f62426a0dbaae898df..14b3667ed7fec34df0c75a4ef5504b4dc356d838 100644 (file)
--- a/import.go
+++ b/import.go
@@ -46,7 +46,7 @@ func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, std
        flags.StringVar(&cmd.tagLibraryFile, "tag-library", "", "tag library fasta `file`")
        flags.StringVar(&cmd.refFile, "ref", "", "reference fasta `file`")
        flags.StringVar(&cmd.outputFile, "o", "", "output `file`")
-       flags.StringVar(&cmd.projectUUID, "project", "", "project `UUID` for storing intermediate and output data")
+       flags.StringVar(&cmd.projectUUID, "project", "", "project `UUID` for output data")
        flags.BoolVar(&cmd.runLocal, "local", false, "run on local host (default: run in an arvados container)")
        pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
        err = flags.Parse(args)
@@ -74,6 +74,8 @@ func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, std
                        Name:        "lightning import",
                        Client:      arvados.NewClientFromEnv(),
                        ProjectUUID: cmd.projectUUID,
+                       RAM:         30000000000,
+                       VCPUs:       16,
                }
                err = runner.TranslatePaths(&cmd.tagLibraryFile, &cmd.refFile, &cmd.outputFile)
                if err != nil {
@@ -118,33 +120,30 @@ func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, std
                }
        }()
 
-       var outfile *os.File
-       var w *bufio.Writer
+       var output io.WriteCloser
        if cmd.outputFile == "" {
-               w = bufio.NewWriter(stdout)
+               output = nopCloser{stdout}
        } else {
-               outfile, err = os.OpenFile(cmd.outputFile, os.O_CREATE|os.O_WRONLY, 0777)
+               output, err = os.OpenFile(cmd.outputFile, os.O_CREATE|os.O_WRONLY, 0777)
                if err != nil {
                        return 1
                }
-               defer outfile.Close()
-               w = bufio.NewWriter(outfile)
+               defer output.Close()
        }
-       cmd.encoder = gob.NewEncoder(w)
+       bufw := bufio.NewWriter(output)
+       cmd.encoder = gob.NewEncoder(bufw)
 
        err = cmd.tileInputs(tilelib, infiles)
        if err != nil {
                return 1
        }
-       err = w.Flush()
+       err = bufw.Flush()
        if err != nil {
                return 1
        }
-       if outfile != nil {
-               err = outfile.Close()
-               if err != nil {
-                       return 1
-               }
+       err = output.Close()
+       if err != nil {
+               return 1
        }
        return 0
 }