Added README; modified makefile

README.md

+### INF pipeline
+
+**Requirements**
+
+Python3 with mlpy (!), numpy, scikit-learn
+R >= 3.2.3 with cvTools, doParallel, TunePareto, igraph
+
+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"))`
+
+**Input files**
+
+* omics layer 1 data: samples x features, tab-separated, with row & column names
+* omics layer 2 data: same as above (**samples must be in the same order as the first file**)
+* omics layers 1+2 data: the juxtaposition of the above two files
+* labels file: one column, just the labels, no header (**same order as the data files**)
+
+**Example run**
+
+The original pipeline was reimplemented in a Makefile, with variables that can be set runtime.
+
+An example is given in the `runner.sh` script:
+
+```
+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
+```
+
+

run_INF_RF-KBest.mk

@@ -15,9 +15,9 @@ DATA2 ?= data/MAV-G_498_LIT_ALL_tr.txt
 ENDPOINT ?= ALL-EFS
 # added MF 20170710
 THREADS ?= 4
+OUTBASE ?= /path/to/out_tmp
 
-BINDIR := /Users/chierici/Documents/work/inf_test
-OUTBASE := /Users/chierici/Documents/work/inf_test/out_tmp
+BINDIR := /path/to/repo
 OUTDIR := $(OUTBASE)/$(ENDPOINT)
 
 # derived variables