Export hgvs-onehot.

[lightning.git] / cmd.go

diff --git a/cmd.go b/cmd.go
index 8cbcdb681c11e33204cf16664c88ce39f676035b..d2f75c996ddc613a83c359ad7ba1f07e553e7c01 100644 (file)
--- a/cmd.go
+++ b/cmd.go
@@ -1,4 +1,4 @@
-package main
+package lightning
 
 import (
        "fmt"
@@ -21,11 +21,11 @@ var (
                "ref2genome":         &ref2genome{},
                "vcf2fasta":          &vcf2fasta{},
                "import":             &importer{},
-               "import-stats-plot":  &importstatsplot{},
                "annotate":           &annotatecmd{},
                "export":             &exporter{},
                "export-numpy":       &exportNumpy{},
-               "filter":             &filterer{},
+               "numpy-comvar":       &numpyComVar{},
+               "filter":             &filtercmd{},
                "build-docker-image": &buildDockerImage{},
                "pca-go":             &goPCA{},
                "pca-py":             &pythonPCA{},
@@ -33,10 +33,11 @@ var (
                "diff-fasta":         &diffFasta{},
                "stats":              &statscmd{},
                "merge":              &merger{},
+               "dumpgob":            &dumpGob{},
        })
 )
 
-func main() {
+func Main() {
        if !isatty.IsTerminal(os.Stderr.Fd()) {
                logrus.StandardLogger().Formatter = &logrus.TextFormatter{DisableTimestamp: true}
        }
@@ -52,11 +53,11 @@ func (cmd *buildDockerImage) RunCommand(prog string, args []string, stdin io.Rea
                return 1
        }
        defer os.RemoveAll(tmpdir)
-       err = ioutil.WriteFile(tmpdir+"/Dockerfile", []byte(`FROM debian:10
+       err = ioutil.WriteFile(tmpdir+"/Dockerfile", []byte(`FROM debian:bullseye
 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 install -y --no-install-recommends bcftools bedtools samtools python2 python3-sklearn python3-matplotlib ca-certificates && \
   apt-get clean
 `), 0644)
        if err != nil {