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Separate pvcf/vcf output.
[lightning.git]
/
arvados.go
diff --git
a/arvados.go
b/arvados.go
index 6d76aded264124ff33d6bee7c24ef39346325145..ec2701bcdc7c96664601351225aedb83f3b5e16a 100644
(file)
--- a/
arvados.go
+++ b/
arvados.go
@@
-267,6
+267,9
@@
func (runner *arvadosContainerRunner) RunContext(ctx context.Context) (string, e
Preemptible: true,
Partitions: []string{},
},
Preemptible: true,
Partitions: []string{},
},
+ "environment": map[string]string{
+ "GOMAXPROCS": fmt.Sprintf("%d", rc.VCPUs),
+ },
},
})
if err != nil {
},
})
if err != nil {
@@
-511,7
+514,12
@@
var (
siteFSMtx sync.Mutex
)
siteFSMtx sync.Mutex
)
-func open(fnm string) (io.ReadCloser, error) {
+type file interface {
+ io.ReadCloser
+ Readdir(n int) ([]os.FileInfo, error)
+}
+
+func open(fnm string) (file, error) {
if os.Getenv("ARVADOS_API_HOST") == "" {
return os.Open(fnm)
}
if os.Getenv("ARVADOS_API_HOST") == "" {
return os.Open(fnm)
}
@@
-520,8
+528,8
@@
func open(fnm string) (io.ReadCloser, error) {
return os.Open(fnm)
}
uuid := m[2]
return os.Open(fnm)
}
uuid := m[2]
- mnt := "/mnt/" + uuid
+ "/"
- if
!strings.HasPrefix(fnm, mnt
) {
+ mnt := "/mnt/" + uuid
+ if
fnm != mnt && !strings.HasPrefix(fnm, mnt+"/"
) {
return os.Open(fnm)
}
return os.Open(fnm)
}
@@
-544,5
+552,5
@@
func open(fnm string) (io.ReadCloser, error) {
}
log.Infof("reading %q from %s using Arvados client", fnm[len(mnt):], uuid)
}
log.Infof("reading %q from %s using Arvados client", fnm[len(mnt):], uuid)
- return siteFS.Open("by_id/" + uuid +
"/" +
fnm[len(mnt):])
+ return siteFS.Open("by_id/" + uuid + fnm[len(mnt):])
}
}