Pass gvcf_regions.py via mount.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

diff --git a/vcf2fasta.go b/vcf2fasta.go
index bc44424543645bb0194f4e58dc82474d46851d84..00e62f549e43acd3c092736487de0eb71e2dc324 100644 (file)
--- a/vcf2fasta.go
+++ b/vcf2fasta.go
@@ -14,6 +14,7 @@ import (
        "os/exec"
        "path/filepath"
        "runtime"
+       "strings"
        "sync"
 
        "git.arvados.org/arvados.git/sdk/go/arvados"
@@ -69,6 +70,13 @@ func (cmd *vcf2fasta) RunCommand(prog string, args []string, stdin io.Reader, st
                }()
        }
 
+       if cmd.mask {
+               err = cmd.loadRegionsPy()
+               if err != nil {
+                       return 1
+               }
+       }
+
        if !cmd.runLocal {
                if cmd.outputDir != "" {
                        err = errors.New("cannot specify output dir in non-local mode")
@@ -91,6 +99,12 @@ func (cmd *vcf2fasta) RunCommand(prog string, args []string, stdin io.Reader, st
                        RAM:         2<<30 + int64(cmd.vcpus)<<28,
                        VCPUs:       cmd.vcpus,
                        Priority:    *priority,
+                       Mounts: map[string]map[string]interface{}{
+                               "/gvcf_regions.py": map[string]interface{}{
+                                       "kind":    "text",
+                                       "content": string(cmd.gvcfRegionsPyData),
+                               },
+                       },
                }
                err = runner.TranslatePaths(&cmd.refFile)
                if err != nil {
@@ -103,7 +117,7 @@ func (cmd *vcf2fasta) RunCommand(prog string, args []string, stdin io.Reader, st
                                return 1
                        }
                }
-               runner.Args = append([]string{"vcf2fasta", "-local=true", "-ref", cmd.refFile, fmt.Sprintf("-mask=%v", cmd.mask), "-gvcf-regions.py", cmd.gvcfRegionsPy, "-output-dir", "/mnt/output"}, inputs...)
+               runner.Args = append([]string{"vcf2fasta", "-local=true", "-ref", cmd.refFile, fmt.Sprintf("-mask=%v", cmd.mask), "-gvcf-regions.py", "/gvcf_regions.py", "-output-dir", "/mnt/output"}, inputs...)
                var output string
                output, err = runner.Run()
                if err != nil {
@@ -113,23 +127,6 @@ func (cmd *vcf2fasta) RunCommand(prog string, args []string, stdin io.Reader, st
                return 0
        }
 
-       if cmd.mask {
-               var resp *http.Response
-               resp, err = http.Get(cmd.gvcfRegionsPy)
-               if err != nil {
-                       return 1
-               }
-               if resp.StatusCode != http.StatusOK {
-                       err = fmt.Errorf("get %q: http status %d", cmd.gvcfRegionsPy, resp.StatusCode)
-                       return 1
-               }
-               cmd.gvcfRegionsPyData, err = ioutil.ReadAll(resp.Body)
-               if err != nil {
-                       err = fmt.Errorf("get %q: read body: %s", cmd.gvcfRegionsPy, err)
-                       return 1
-               }
-       }
-
        infiles, err := listInputFiles(flags.Args())
        if err != nil {
                return 1
@@ -278,3 +275,28 @@ func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
        }
        return nil
 }
+
+func (cmd *vcf2fasta) loadRegionsPy() error {
+       if strings.HasPrefix(cmd.gvcfRegionsPy, "http") {
+               resp, err := http.Get(cmd.gvcfRegionsPy)
+               if err != nil {
+                       return err
+               }
+               if resp.StatusCode != http.StatusOK {
+                       return fmt.Errorf("get %q: http status %d", cmd.gvcfRegionsPy, resp.StatusCode)
+               }
+               buf, err := ioutil.ReadAll(resp.Body)
+               if err != nil {
+                       return fmt.Errorf("get %q: read body: %s", cmd.gvcfRegionsPy, err)
+               }
+               cmd.gvcfRegionsPyData = buf
+               return nil
+       } else {
+               buf, err := ioutil.ReadFile(cmd.gvcfRegionsPy)
+               if err != nil {
+                       return err
+               }
+               cmd.gvcfRegionsPyData = buf
+               return nil
+       }
+}