Add old demos

demos/old_demos/completeE.sh

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+# Demo for WGS data from a cancer patient
+: ex: set ft=markdown ;:<<'```shell' #
+
+The following CHISEL demo represents a guided example of the complete CHISEL pipeline starting from the barcoded [BAM file](https://support.10xgenomics.com/single-cell-dna/datasets/1.0.0/breast_tissue_E_2k) publicly available from 10X Genomics archive and obtained through 10X Chromium Single Cell CNV Solution for section E of a breast tumor. Simply run this file through BASH as a standard script to run the complete demo. The demo can also be considered as a guided example of a complete execution and is correspondingly commented.
+
+## Requirements and set up
+
+The demo requires that CHISEL has been succesfully installed, such that the python environment called by the command `python2.7` has the required packages, and both `samtools` and `awk` are available in `${PATH}`.
+
+```shell
+export CHISEL_HOME="../../" # This is CHISEL home by default, update if needed
+:<<'```shell' # Ignore this line
+```
+
+We also ask the demo to terminate in case of errors and to print a trace of the execution by the following commands
+```shell
+set -e
+set -o xtrace
+PS4='[\t]'
+:<<'```shell' # Ignore this line
+```
+
+## Downloading of data
+
+The demo auomatically downloads the required barcoded single-cell and matched-normal BAM files from 10X Genomics archive through the following commands in `data` folder.
+
+```shell
+# Creating data folder
+mkdir -p data
+
+# Downloading barcoded single-cell BAM of breast tumor section E
+wget -N -c http://s3-us-west-2.amazonaws.com/10x.files/samples/cell-dna/1.0.0/breast_tissue_E_2k/breast_tissue_E_2k_possorted_bam.bam -P data/
+wget -N -c http://cf.10xgenomics.com/samples/cell-dna/1.0.0/breast_tissue_E_2k/breast_tissue_E_2k_possorted_bam.bam.bai -P data/
+export TUM="data/breast_tissue_E_2k_possorted_bam.bam"
+
+# Downloading matched-normal BAM file as section A
+wget -N -c http://s3-us-west-2.amazonaws.com/10x.files/samples/cell-dna/1.0.0/breast_tissue_A_2k/breast_tissue_A_2k_possorted_bam.bam -P data/
+wget -N -c http://cf.10xgenomics.com/samples/cell-dna/1.0.0/breast_tissue_A_2k/breast_tissue_A_2k_possorted_bam.bam.bai -P data/
+export NOR="data/breast_tissue_A_2k_possorted_bam.bam"
+:<<'```shell' # Ignore this line
+```
+
+Next the corresponding reference genome is downloaded and unpacked
+
+```shell
+export REF="data/refdata-GRCh38-2.1.0/fasta/genome.fa"
+export DIC="data/refdata-GRCh38-2.1.0/fasta/genome.dict"
+if [[ ! -f "${REF}" || ! -f "${DIC}" ]]; then
+    wget -N -c http://cf.10xgenomics.com/supp/genome/refdata-GRCh38-2.1.0.tar.gz -P data/
+    tar -xzvf data/refdata-GRCh38-2.1.0.tar.gz -C data/
+    rm -f data/refdata-GRCh38-2.1.0.tar.gz
+fi
+:<<'```shell' # Ignore this line
+```
+
+Last, we download the pre-computed VCF with phased SNPs; the VCF has been computed following the reccommended instructions, using BCFtools to call germline SNPs and Eagle2 throught the Michigan Imputation Serverve with HRC panel to phase the SNPs.
+
+```shell
+wget -N -c https://github.com/raphael-group/chisel-data/raw/master/demos/completeE/phased.HRC.vcf.gz -P data/
+gzip -f -d data/phased.HRC.vcf.gz
+export PHA="data/phased.HRC.vcf"
+:<<'```shell' # Ignore this line
+```
+
+## Run CHISEL
+
+We now run the complete pipeline of CHISEL with the corresponding command `chisel`.
+
+```shell
+chisel -t ${TUM} -n ${NOR} -r ${REF} -l ${PHA} --seed 25
+exit $?
+```
+
+