X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/20123d5f8ceb57ea4e5253cb0c57da194d66da63..149b80b48df7b0da269004b3ff5b2ce7e9dedbb6:/cmd.go

diff --git a/cmd.go b/cmd.go
index 8fc3636d6c..5789fe4604 100644
--- a/cmd.go
+++ b/cmd.go
@@ -8,6 +8,8 @@ import (
 	"os/exec"
 
 	"git.arvados.org/arvados.git/lib/cmd"
+	"github.com/mattn/go-isatty"
+	"github.com/sirupsen/logrus"
 )
 
 var (
@@ -19,18 +21,25 @@ var (
 		"ref2genome":         &ref2genome{},
 		"vcf2fasta":          &vcf2fasta{},
 		"import":             &importer{},
+		"annotate":           &annotatecmd{},
+		"export":             &exporter{},
 		"export-numpy":       &exportNumpy{},
-		"filter":             &filterer{},
+		"numpy-comvar":       &numpyComVar{},
+		"filter":             &filtercmd{},
 		"build-docker-image": &buildDockerImage{},
 		"pca-go":             &goPCA{},
 		"pca-py":             &pythonPCA{},
 		"plot":               &pythonPlot{},
 		"diff-fasta":         &diffFasta{},
-		"stats":              &stats{},
+		"stats":              &statscmd{},
+		"merge":              &merger{},
 	})
 )
 
 func main() {
+	if !isatty.IsTerminal(os.Stderr.Fd()) {
+		logrus.StandardLogger().Formatter = &logrus.TextFormatter{DisableTimestamp: true}
+	}
 	os.Exit(handler.RunCommand(os.Args[0], os.Args[1:], os.Stdin, os.Stdout, os.Stderr))
 }
 
@@ -47,7 +56,7 @@ func (cmd *buildDockerImage) RunCommand(prog string, args []string, stdin io.Rea
 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 {