-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"
+ "runtime/debug"
+ "strings"
"git.arvados.org/arvados.git/lib/cmd"
+ "github.com/mattn/go-isatty"
+ "github.com/sirupsen/logrus"
)
var (
"ref2genome": &ref2genome{},
"vcf2fasta": &vcf2fasta{},
"import": &importer{},
+ "annotate": &annotatecmd{},
+ "export": &exporter{},
"export-numpy": &exportNumpy{},
- "filter": &filterer{},
+ "flake": &flakecmd{},
+ "slice": &slicecmd{},
+ "slice-numpy": &sliceNumpy{},
+ "tiling-stats": &tilingStats{},
+ "anno2vcf": &anno2vcf{},
+ "numpy-comvar": &numpyComVar{},
+ "filter": &filtercmd{},
"build-docker-image": &buildDockerImage{},
- "pca-go": &goPCA{},
- "pca-py": &pythonPCA{},
"plot": &pythonPlot{},
"diff-fasta": &diffFasta{},
+ "stats": &statscmd{},
+ "merge": &merger{},
+ "dump": &dump{},
+ "dumpgob": &dumpGob{},
+ "choose-samples": &chooseSamples{},
})
)
-func main() {
+func init() {
+ if os.Getenv("GOGC") == "" {
+ debug.SetGCPercent(30)
+ }
+}
+
+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") {
+ // print version (then run subcommand)
+ 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 {