inputFilename := flags.String("i", "-", "input `file`")
sampleCSVFilename := flags.String("labels-csv", "", "use first two columns of `labels.csv` as id->color mapping")
sampleFastaDirname := flags.String("sample-fasta-dir", "", "`directory` containing fasta input files")
+ priority := flags.Int("priority", 500, "container request priority")
err = flags.Parse(args)
if err == flag.ErrHelp {
err = nil
Name: "lightning plot",
Client: arvados.NewClientFromEnv(),
ProjectUUID: *projectUUID,
- RAM: 1 << 30,
+ RAM: 4 << 30,
VCPUs: 1,
+ Priority: *priority,
Mounts: map[string]map[string]interface{}{
"/plot.py": map[string]interface{}{
"kind": "text",
}
runner.Prog = "python3"
runner.Args = []string{"/plot.py", *inputFilename, *sampleCSVFilename, *sampleFastaDirname, "/mnt/output/plot.png"}
- err = runner.Run()
+ var output string
+ output, err = runner.Run()
if err != nil {
return 1
}
+ fmt.Fprintln(stdout, output+"/plot.png")
return 0
}
'PJL': 'blueviolet',
}
for fnm in sorted(labels.keys()):
- colors.append(labelcolors[labels[fnm]])
+ if labels[fnm] in labelcolors:
+ colors.append(labelcolors[labels[fnm]])
+ else:
+ colors.append('black')
from matplotlib.figure import Figure
from matplotlib.patches import Polygon