This is a fork of the original project CoNVaDING That project is the official one and I make no claims to be a replacement of it.
If you want to follow the official project please go to:
https://molgenis.gitbooks.io/convading/
This fork was created by Duarte Molha to implement features not provided by the original project.
You can read more about how it differs from the original software here:
https://github.com/duartemolha/CoNVaDING_reload/wiki/CoNVaDING_reload
Sequentially again forked by mmterpstra who added an amplicon mode to CountFromBam, implemented the perl build system and misc bugfixes.
How to install on ubuntu 18.04 to your home:
# install bedtools / samtools
sudo apt install bedtools samtools
#install mosdepth
wget https://github.com/brentp/mosdepth/releases/download/v0.2.6/mosdepth && chmod +x ./mosdepth && export PATH=$(pwd):$PATH
#make sure it is included on your path
# install convading
cpanm --installdeps --notest .
perl Makefile.PL PREFIX=~/
make
make install
# change depending on your preferences
# preferably fork first
git clone https://github.com/duartemolha/CoNVaDING_reload.git
git branch feature-tag
git checkout feature-tag
# edit some files
# test by using the following commands
(export PERL5LIB="blib/lib/:$PERL5LIB";perl Makefile.PL && make && make test)
# add, commit and push changed files
# create pull request on github