Updated README, runner.sh

README.md

@@ -2,14 +2,15 @@
 
 **Requirements**
 
-Python3 with mlpy (!), numpy, scikit-learn
-R >= 3.2.3 with cvTools, doParallel, TunePareto, igraph
+Python3 with mlpy (!), numpy, scikit-learn, pandas, snakemake
+
+R >= 3.2.3 with argparse, cvTools, doParallel, TunePareto, igraph, lubridate, data.table
 
 To install R via Anaconda: [doc](https://docs.anaconda.com/anaconda/user-guide/tasks/using-r-language/)
 
 To install the R dependencies, run the following command from the R prompt:
 
-`install.packages(c("cvTools", "doParallel", "TunePareto", "igraph"))`
+`install.packages(c("argparse", "cvTools", "doParallel", "TunePareto", "igraph", "lubridate", "data.table"))`
 
 **Input files**
 
@@ -20,21 +21,29 @@ To install the R dependencies, run the following command from the R prompt:
 
 **Example run**
 
-The original pipeline was reimplemented in a Makefile, with variables that can be set runtime.
+The INF pipeline is implemented as a Snakefile.
+
+The following directory tree is required:
+
+* {datafolder}/{dataset}/{layer1}_{layer2}_{tr,ts}.txt
+* {datafolder}/{dataset}/labels_{target}_{tr,ts}.txt
+* {datafolder}/{dataset}/{layer1,layer2}_{tr,ts}.txt
+* {outfolder}/{dataset}/{target}/{juxt,rSNF,rSNFi,single}/ _(these will be created if not present)_
 
-An example is given in the `runner.sh` script:
+All the {variables} can be specified either in a config.yaml file or on the command line; for example:
 
+```{python}
+snakemake --config datafolder="data" dataset="breast" target="ER" layer1="gene" layer2="cnv"
 ```
-make -f run_INF_RF-KBest.mk \
-         OUTBASE=${OUT} \
-         # layer1 dataset
-         DATA1=data/AG1-G_145_LIT_ALL_tr.txt \
-         # layer2 dataset
-         DATA2=data/CNV-G_145_LIT_ALL_tr.txt \
-         # layer1 + layer2 juxtaposed dataset
-         FILE=data/AG1-G_CNV-G_145_LIT_ALL_tr.txt \
-         # sample labels
-         LABEL=data/label_145_ALL-EFS_tr.lab
+
+A maximum number of cores can also be set:
+
+```{python}
+snakemake [--config etc.] --cores 12
 ```
 
+The pipeline can be "dry-run" using the `-n` flag:
 
+```{python}
+snakemake --cores 12 -n
+```

runner.sh

 #!/bin/bash
 # Example script for the INF pipeline
 
-# output folder
-OUT=results_breast
-DATA_FOLDER=data/TCGA_data/Breast/INF
+THREADS=12
 
+OUTFOLDER=results_breast
+DATAFOLDER=data/breast
 LAYER1=gene
 LAYER2=cnv
-# prepare output tree
-
+TARGET=ER
 
 # go!
-make all \
-	OUTBASE=${OUT} \
-	DATA1=${DATA_FOLDER}/${LAYER1}_tr.txt \
-	DATA2=${DATA_FOLDER}/${LAYER2}_tr.txt \
-	FILE=${DATA_FOLDER}/${LAYER1}_${LAYER2}_tr.txt \
-	LABEL=${DATA_FOLDER}/labels_ER_tr.txt \
-	ENDPOINT=breast_ER_${LAYER1}_${LAYER2}
-
+snakemake --cores $THREADS --config datafolder=$DATAFOLDER outfolder=$OUTFOLDER target=$TARGET layer1=$LAYER1 layer2=$LAYER2