Commit 3aa9679c authored by Beatrice Tan's avatar Beatrice Tan

Enabled installing gistic when directory already exists.

parent 46b3980c
import datetime
import os.path
rule install_gistic:
"""Install GISTIC2 to a directory of choice."""
output:
os.path.join(config["gisticdir"], "gistic2")
params:
config["gisticdir"]
shell:
"{workflow.basedir}/scripts/install_gistic2.sh {output}"
"{workflow.basedir}/scripts/install_gistic2.sh {params}"
rule run_gistic:
"""Run GISTIC2 for the tumor segmentation data."""
input:
gistic_directory=config["gisticdir"],
os.path.join(config["gisticdir"], "gistic2"),
seg="Input/Segments_tumor.txt"
output:
"GISTIC/all_lesions.conf_" + config["gistic_precision"] + ".txt",
......
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