ChromImpute needs large files to work. Developers provided examples files ~1GB.
We cannot include these large files in a package, so we cannot write an autopkgtest. 

Quick instructions on running ChromImpute on the example data (chr21 of eight primary marks from the Roadmap Epigenomics project):
1. Install Java 1.6 or later if not already installed.
2. Unzip the file ChromImpute.zip.
3. Unzip the file EXAMPLE.zip and place in the ChromImpute directory.
4. From a command line go to the directory in which ChromImpute.jar is installed.
5. To try out ChromImpute imputing H3K9ac for sample E034 (Primary T cells from peripheral blood) based on pre-computed predictors enter the command:
java -mx4000M -jar ChromImpute.jar Apply EXAMPLE/CONVERTEDDATADIR EXAMPLE/DISTANCEDIR EXAMPLE/PREDICTORDIR EXAMPLE/tier1_samplemarktable.txt EXAMPLE/hg19sizes_chr21.txt EXAMPLE/OUTPUTDATA E034 H3K9ac
In ~20min this will generate a chr21_impute_E034_H3K9ac.wig.gz file in the directory EXAMPLE/OUTPUTDATA

# Get ChromImpute
apt install chromimpute
# wget http://www.biolchem.ucla.edu/labs/ernst/ChromImpute/ChromImpute.zip
# unzip ChromImpute.zip


# Get examples files
wget http://www.broadinstitute.org/~jernst/EXAMPLE.zip
unzip EXAMPLE.zip

# Run ChromImpute
CHROMIMPUTE='java -mx4000M -jar /usr/share/java/chromimpute.jar'
# CHROMIMPUTE='java -mx4000M -jar ChromImpute/ChromImpute.jar'
${CHROMIMPUTE} Apply EXAMPLE/CONVERTEDDATADIR EXAMPLE/DISTANCEDIR EXAMPLE/PREDICTORDIR EXAMPLE/tier1_samplemarktable.txt EXAMPLE/hg19sizes_chr21.txt EXAMPLE/OUTPUTDATA E034 H3K9ac
