-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
import (
"fmt"
"io/ioutil"
"os"
"os/exec"
+ "strings"
"git.arvados.org/arvados.git/lib/cmd"
"github.com/mattn/go-isatty"
"ref2genome": &ref2genome{},
"vcf2fasta": &vcf2fasta{},
"import": &importer{},
- "import-stats-plot": &importstatsplot{},
+ "annotate": &annotatecmd{},
"export": &exporter{},
"export-numpy": &exportNumpy{},
- "filter": &filterer{},
+ "flake": &flakecmd{},
+ "slice": &slicecmd{},
+ "slice-numpy": &sliceNumpy{},
+ "numpy-comvar": &numpyComVar{},
+ "filter": &filtercmd{},
"build-docker-image": &buildDockerImage{},
"pca-go": &goPCA{},
"pca-py": &pythonPCA{},
"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}
}
+ if len(os.Args) >= 2 && !strings.HasSuffix(os.Args[1], "version") {
+ cmd.Version.RunCommand("lightning", nil, nil, os.Stderr, os.Stderr)
+ }
os.Exit(handler.RunCommand(os.Args[0], os.Args[1:], os.Stdin, os.Stdout, os.Stderr))
}
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 {