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Include numpy matrix filename in labels csv.
[lightning.git]
/
cmd.go
diff --git
a/cmd.go
b/cmd.go
index 17578b43e7ab112d3f40a20b7545e75f421cd31c..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 (
@@
-19,15
+21,25
@@
var (
"ref2genome": &ref2genome{},
"vcf2fasta": &vcf2fasta{},
"import": &importer{},
"ref2genome": &ref2genome{},
"vcf2fasta": &vcf2fasta{},
"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": &pythonPCA{},
+ "pca-go": &goPCA{},
+ "pca-py": &pythonPCA{},
"plot": &pythonPlot{},
"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))
}
@@
-44,7
+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 && \
RUN DEBIAN_FRONTEND=noninteractive \
apt-get update && \
apt-get dist-upgrade -y && \
- apt-get install -y --no-install-recommends bcftools bedtools samtools python
3-sklearn python3-matplotlib
&& \
+ apt-get install -y --no-install-recommends bcftools bedtools samtools python
2 python3-sklearn python3-matplotlib ca-certificates
&& \
apt-get clean
`), 0644)
if err != nil {
apt-get clean
`), 0644)
if err != nil {