CoNVaDING_reload

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/

History

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.

Install

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

Developing

# 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