# -*- coding: utf-8 -*-
from anadama2 import Workflow
workflow = Workflow(remove_options=["input", "output"])
workflow.do("ls /usr/bin/ | sort > [t:global_exe.txt]")
workflow.do("ls $HOME/.local/bin/ | sort > [t:local_exe.txt]")
workflow.do("join [d:global_exe.txt] [d:local_exe.txt] > [t:match_exe.txt]")
workflow.go()
# -*- coding: utf-8 -*-
from anadama2 import Workflow
ctx = Workflow(remove_options=["input", "output"])
ctx.do("wget -qO- checkip.dyndns.com > [t:my_ip.txt]")
ctx.do(r"sed 's|.*Address: \(.*[0-9]\)<.*|\1|' [d:my_ip.txt] > [t:ip.txt]")
ctx.do("whois $(cat [d:ip.txt]) > [t:whois.txt]")
ctx.go()
desc="Number of lines to trim [default: 10]",
default="10")
workflow.add_argument(
name="metadata",
desc="Metadata for performing analysis [default: input/metadata.tsv]",
default="input/metadata.tsv")
# Parsing the workflow arguments
args = workflow.parse_args()
#Loading the config setting
args.config = 'etc/config.ini'
# AnADAMA2 example workflow.do
workflow.do("ls /usr/bin/ | sort > [t:output/global_exe.txt]") #Command
workflow.do("ls $HOME/.local/bin/ | sort > [t:output/local_exe.txt]") #Command
# Task0 sample python analysis module - src/trim.py
workflow.add_task(
"src/trim.py --lines [args[0]] --output [targets[0]] --input " +
args.input, #Command
depends=[TrackedExecutable("src/trim.py")
], #Tracking executable dependencies
targets=args.output, #Output target directory
args=[args.lines]) #Additional arguments
# Task1 sample python visualization module - src/plot.py
workflow.add_task(
"src/plot.py --output [targets[0]] --input " + args.input, #Command
depends=[TrackedExecutable("src/plot.py")
