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Beatrice Tan
CNAprioritization
Commits
3aa9679c
Commit
3aa9679c
authored
Feb 01, 2018
by
Beatrice Tan
Browse files
Enabled installing gistic when directory already exists.
parent
46b3980c
Changes
1
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rules/GISTIC2.smk
View file @
3aa9679c
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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