Enable -skip-ooo in example.

[lightning.git] / cmd.go

diff --git a/cmd.go b/cmd.go
index 713e1d815dd9bcd24065b9c16fdca3b84209ffd4..c40c06369e8fcd94a20aacc0bc2dce6abd55c965 100644 (file)
--- a/cmd.go
+++ b/cmd.go
@@ -16,8 +16,15 @@ var (
                "-version":  cmd.Version,
                "--version": cmd.Version,
 
-               "gvcf2numpy":         &gvcf2numpy{},
+               "ref2genome":         &ref2genome{},
+               "vcf2fasta":          &vcf2fasta{},
+               "import":             &importer{},
+               "export-numpy":       &exportNumpy{},
+               "filter":             &filterer{},
                "build-docker-image": &buildDockerImage{},
+               "pca":                &pythonPCA{},
+               "plot":               &pythonPlot{},
+               "diff-fasta":         &diffFasta{},
        })
 )
 
@@ -35,19 +42,23 @@ func (cmd *buildDockerImage) RunCommand(prog string, args []string, stdin io.Rea
        }
        defer os.RemoveAll(tmpdir)
        err = ioutil.WriteFile(tmpdir+"/Dockerfile", []byte(`FROM debian:10
-RUN apt-get update
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends bcftools samtools
+RUN DEBIAN_FRONTEND=noninteractive \
+  apt-get update && \
+  apt-get dist-upgrade -y && \
+  apt-get install -y --no-install-recommends bcftools bedtools samtools python2 python3-sklearn python3-matplotlib && \
+  apt-get clean
 `), 0644)
        if err != nil {
                fmt.Fprint(stderr, err)
                return 1
        }
        docker := exec.Command("docker", "build", "--tag=lightning-runtime", tmpdir)
-       docker.Stdout = os.Stdout
-       docker.Stderr = os.Stderr
+       docker.Stdout = stdout
+       docker.Stderr = stderr
        err = docker.Run()
        if err != nil {
                return 1
        }
+       fmt.Fprintf(stderr, "built and tagged new docker image, lightning-runtime\n")
        return 0
 }