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MPBA
INF
Commits
738f883d
Commit
738f883d
authored
Mar 31, 2020
by
Alessia Marcolini
Browse files
Update runner
parent
d49cbf46
Changes
1
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Side-by-side
runner.sh
View file @
738f883d
#!/bin/bash
# Example script for the INF pipeline
THREAD
S
=
12
CORE
S
=
12
OUTFOLDER
=
results
DATAFOLDER
=
data
DATASET
=
tcga_
breast
DATASET
=
tcga_
aml
LAYER1
=
gene
LAYER2
=
cnv
TARGET
=
ER
MODEL
=
LSVM
LAYER2
=
meth
LAYER3
=
mirna
TARGET
=
OS
MODEL
=
randomForest
N_SPLITS_START
=
0
N_SPLITS_END
=
10
RANDOM_LABELS
=
tru
e
RANDOM_LABELS
=
fals
e
# go!
for
((
i
=
$N_SPLITS_START
;
i<
$N_SPLITS_END
;
i++
))
do
snakemake
-s
Snakefile_split
--cores
$
THREAD
S
--config
datafolder
=
$DATAFOLDER
outfolder
=
$OUTFOLDER
dataset
=
$DATASET
target
=
$TARGET
layer1
=
$LAYER1
layer2
=
$LAYER2
model
=
$MODEL
random
=
$RANDOM_LABELS
split_id
=
$i
-p
snakemake
-s
Snakefile_split
--cores
$
CORE
S
--config
datafolder
=
$DATAFOLDER
outfolder
=
$OUTFOLDER
dataset
=
$DATASET
target
=
$TARGET
layer1
=
$LAYER1
layer2
=
$LAYER2
layer3
=
$LAYER3
model
=
$MODEL
random
=
$RANDOM_LABELS
split_id
=
$i
-p
done
if
[
$RANDOM_LABELS
=
true
]
...
...
@@ -29,16 +30,16 @@ fi
for
MODE
in
juxt rSNF rSNFi single
do
python postprocessing/compute_all_metrics.py
--outfolder
$OUTFOLDER
--dataset
$DATASET
--target
$TARGET
--layers
$LAYER1
$LAYER2
--model
$MODEL
--n_splits_end
$N_SPLITS_END
--n_splits_start
$N_SPLITS_START
--mode
$MODE
python postprocessing/compute_all_metrics.py
--outfolder
$OUTFOLDER
--dataset
$DATASET
--target
$TARGET
--layers
$LAYER1
$LAYER2
$LAYER3
--model
$MODEL
--n_splits_end
$N_SPLITS_END
--n_splits_start
$N_SPLITS_START
--mode
$MODE
done
for
MODE
in
juxt rSNF
do
python postprocessing/borda_global_juxt_rSNF.py
--datafolder
$DATAFOLDER
--outfolder
$OUTFOLDER
--dataset
$DATASET
--target
$TARGET
--layers
$LAYER1
$LAYER2
--model
$MODEL
--n_splits_end
$N_SPLITS_END
--n_splits_start
$N_SPLITS_START
--mode
$MODE
python postprocessing/borda_global_juxt_rSNF.py
--datafolder
$DATAFOLDER
--outfolder
$OUTFOLDER
--dataset
$DATASET
--target
$TARGET
--layers
$LAYER1
$LAYER2
$LAYER3
--model
$MODEL
--n_splits_end
$N_SPLITS_END
--n_splits_start
$N_SPLITS_START
--mode
$MODE
done
python postprocessing/borda_global_rSNFi.py
--datafolder
$DATAFOLDER
--outfolder
$OUTFOLDER
--dataset
$DATASET
--target
$TARGET
--layers
$LAYER1
$LAYER2
--model
$MODEL
--n_splits_end
$N_SPLITS_END
--n_splits_start
$N_SPLITS_START
--mode
rSNFi
python postprocessing/borda_global_rSNFi.py
--datafolder
$DATAFOLDER
--outfolder
$OUTFOLDER
--dataset
$DATASET
--target
$TARGET
--layers
$LAYER1
$LAYER2
$LAYER3
--model
$MODEL
--n_splits_end
$N_SPLITS_END
--n_splits_start
$N_SPLITS_START
--mode
rSNFi
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