Repo for running FeatureREDUCE in a virtual environment
Please install Anaconda personal addition for linux.
- Create a virtual environment
run_freduce
conda create -n run_freduce python=3.6
- Activate the virtual environment
run_freduce
:
conda activate run_freduce
- Install required packages
sh install_packages.sh
- Unzip the FeatureREDUCE package
unzip FeatureREDUCE-master.zip
- Go to
FeatureREDUCE-master/freduce/src
and run:
javac FeatureReduce.java
cp *.class ../bin
- Copy envrc
FeatureREDUCE-master/freduce/.envrc
cp envrc FeatureREDUCE-master/freduce/.envrc
Please see the .envrc
file already present there and change the path accordingly. Here are the tips:
-
Used the command
which R
to find the path ofR
and set it asR_HOME
-
You will find
rJava
in$R_HOME/library/rJava
: set that asRJAVA_HOME
-
You need to put
libjvm.so
inLD_LIBRARY_PATH
.libjvm.so
can be found in you virtual library'slib/server
directory -
In your CLASSPATH,
JRI.jar
should be present. This jar file can be found in$RJAVA_HOME/jri/
- Source the
.envrc
file
source FeatureREDUCE-master/freduce/.envrc
- Run the snakemake pipeline to generate results (first run with
-np
flag to see if dry run looks good, then remove-np
flag and run to generate the result)
snakemake -np --snakefile run_feature_reduce.smk correlation_and_rsq/{max,mef2b,p53}_trial_{01..10}.tsv --configfile configs/config.yaml -j3