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Include numpy matrix filename in labels csv.
[lightning.git]
/
cmd.go
diff --git
a/cmd.go
b/cmd.go
index a321848f589631c6ef40401a8ee96840021ddf92..5789fe4604d3b5f41b75215e762b89868503e821 100644
(file)
--- a/
cmd.go
+++ b/
cmd.go
@@
-8,6
+8,8
@@
import (
"os/exec"
"git.arvados.org/arvados.git/lib/cmd"
"os/exec"
"git.arvados.org/arvados.git/lib/cmd"
+ "github.com/mattn/go-isatty"
+ "github.com/sirupsen/logrus"
)
var (
)
var (
@@
-16,14
+18,28
@@
var (
"-version": cmd.Version,
"--version": cmd.Version,
"-version": cmd.Version,
"--version": cmd.Version,
+ "ref2genome": &ref2genome{},
+ "vcf2fasta": &vcf2fasta{},
"import": &importer{},
"import": &importer{},
+ "annotate": &annotatecmd{},
+ "export": &exporter{},
"export-numpy": &exportNumpy{},
"export-numpy": &exportNumpy{},
- "filter": &filterer{},
+ "numpy-comvar": &numpyComVar{},
+ "filter": &filtercmd{},
"build-docker-image": &buildDockerImage{},
"build-docker-image": &buildDockerImage{},
+ "pca-go": &goPCA{},
+ "pca-py": &pythonPCA{},
+ "plot": &pythonPlot{},
+ "diff-fasta": &diffFasta{},
+ "stats": &statscmd{},
+ "merge": &merger{},
})
)
func main() {
})
)
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))
}
os.Exit(handler.RunCommand(os.Args[0], os.Args[1:], os.Stdin, os.Stdout, os.Stderr))
}
@@
-37,19
+53,23
@@
func (cmd *buildDockerImage) RunCommand(prog string, args []string, stdin io.Rea
}
defer os.RemoveAll(tmpdir)
err = ioutil.WriteFile(tmpdir+"/Dockerfile", []byte(`FROM debian:10
}
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
+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)
`), 0644)
if err != nil {
fmt.Fprint(stderr, err)
return 1
}
docker := exec.Command("docker", "build", "--tag=lightning-runtime", tmpdir)
- docker.Stdout =
os.S
tdout
- docker.Stderr =
os.S
tderr
+ docker.Stdout =
s
tdout
+ docker.Stderr =
s
tderr
err = docker.Run()
if err != nil {
return 1
}
err = docker.Run()
if err != nil {
return 1
}
+ fmt.Fprintf(stderr, "built and tagged new docker image, lightning-runtime\n")
return 0
}
return 0
}