X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/afcd9e08f6274c58262b81d94ed160bda79d8fa5..56bfceeaedc235866704decc588f56c67edd4605:/cmd.go

diff --git a/cmd.go b/cmd.go
index 713e1d815d..514bd1ebb4 100644
--- a/cmd.go
+++ b/cmd.go
@@ -1,4 +1,8 @@
-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
 
 import (
 	"fmt"
@@ -6,8 +10,12 @@ import (
 	"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 (
@@ -16,12 +24,43 @@ var (
 		"-version":  cmd.Version,
 		"--version": cmd.Version,
 
-		"gvcf2numpy":         &gvcf2numpy{},
+		"ref2genome":         &ref2genome{},
+		"vcf2fasta":          &vcf2fasta{},
+		"import":             &importer{},
+		"annotate":           &annotatecmd{},
+		"export":             &exporter{},
+		"export-numpy":       &exportNumpy{},
+		"flake":              &flakecmd{},
+		"slice":              &slicecmd{},
+		"slice-numpy":        &sliceNumpy{},
+		"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{},
 	})
 )
 
-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") {
+		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))
 }
 
@@ -34,20 +73,24 @@ 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
-RUN apt-get update
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends bcftools samtools
+	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 ca-certificates && \
+  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
 }