added install instructions

Former-commit-id: 5c4afe3

README.md

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+# Mutationseq
+
+
+## Install
+1. Create a directory to store temporary files:
+    ```
+    mkdir -p $HOME/museq/
+    cd $HOME/museq
+    ```
+2. Download and install Miniconda for python 2.7:
+
+    Download miniconda
+    ```
+    wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh
+    ```
+    Run
+    ```
+    sh Miniconda2-latest-Linux-x86_64.sh
+    ```
+    and follow the instructions. When you have finished following the instructions, you should have python installed:
+    ```
+    which python
+    ~/miniconda2/bin/python
+    ```
+3. clone the mutationseq repo.
+    ```
+    git clone -b easy_install https://dgrewal@svn.bcgsc.ca/bitbucket/scm/museq/mutationseq.git
+    ```
+4. create a conda environment:
+    ```
+    conda create --name mutationseq python=2.7 --file $HOME/museq/mutationseq/conda_packages.txt
+    ```
+
+3. activate the environment:
+    ```
+    conda activate mutationseq
+    ```
+4. Install mutationseq:
+
+    download boost:
+    ```
+    wget https://sourceforge.net/projects/boost/files/boost/1.57.0/boost_1_57_0.tar.gz/download -O boost.tar.gz
+    ```
+    At the moment mutationseq only supports boost 1.57.0 or older. Newer versions will run into installation issues.
+    extract boost:
+    ```
+    tar -xvf boost.tar.gz
+    ```
+    install mutationseq:
+    ```
+    cd $HOME/museq/mutationseq/
+    python setup.py install --boost_source=$HOME/museq/boost_1_57_0
+    ```
+
+## Running Mutationseq:
+To call variants using MutationSeq, we use the following command:
+```
+mkdir -p museq/results; \
+museq \
+  normal:bam/HCC1395_exome_normal.sort.markdup.17.7MB-8MB.bam \
+  tumour:bam/HCC1395_exome_tumour.sort.markdup.17.7MB-8MB.bam \
+  reference:refs/GRCh37-lite.fa \
+  -o museq/results/HCC1395_exome_tumour_normal_17.vcf
+```

conda_packages.txt

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+numpy
+scipy
+matplotlib
+scikit-learn
+intervaltree