setting up a unified data download handeling

data/.gitignore

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+# This gitignore contains all those data files, which are not kept on the repo
+# and thus have to be downloaded automatically or manually (in case registration
+# or journal access is needed)
+
+# The temporary download folder:
+tmp/
+
+
+################
+# PPIs
+#################
+
+# Bossi & Lehner PPI file
+ppis/CRG.integrated.human.interactome.txt
 

data/README.md

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+Data Sources
+============
+
+Protein-Protein Interaction Networks
+------------------------------------
+
+### Bossi & Lehner composite PPI network
+
+From the supplementary section of the paper ["Tissue specificity and the human protein interaction network"](http:https://www.ncbi.nlm.nih.gov/pubmed/19357639).
+
+This can be automatically downloaded via the download_data.sh script.
+
+

data/download_data.sh

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+#!/bin/bash
+
+# This script downloads all publicly available data into the correct folders.
+# Run this before using the pipeline.
+# Don't forget to download the data, that is not publicly available (see README.md for 
+# sources and further explainations)
+
+# A few settings
+TMP_FOLDER=tmp
+
+
+# make tmp folder
+rm -R $TMP_FOLDER
+mkdir -p $TMP_FOLDER
+
+
+####################
+# PPI networks 
+###################
+
+# 1.) Bossi & Lehner:
+BOSSI_URL=http:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683721/bin/msb200917-s2.zip
+BOSSI_ZIP=$TMP_FOLDER/bossi-lehner-suppl.zip
+
+curl -o $BOSSI_ZIP $BOSSI_URL
+unzip $BOSSI_ZIP -d $TMP_FOLDER
+cp $TMP_FOLDER/CRG-human-interactome/CRG.integrated.human.interactome.txt ppis/
+
+