02. Installation

You can install PopDel from Bioconda or download the binary of the latest version from the release page. To build PopDel from source, first clone the repository:

git clone https://github.com/kehrlab/PopDel-develop.git

Then, inside the source directory, simply run make install. If you don't have writing access to 'usr/local/bin/', run the command with sudo. You can specify the target directory for the PopDel binary by appending 'PREFIX=/your/preferred/location' to the make install command, which will then create the binary as '/your/preferred/location/bin/popdel'. Alternatively you can also run make all to create the binary in the source directory without copying it anywhere. A (very slow) debug build can be created with make debug. The installation process should not take more than 5 minutes of time for the average user.

Before building, please make sure that all of PopDel's dependencies are fulfilled (see. 01. Dependencies).

# In source-directory
sudo make install

Without sudo privileges simply run 'make all' and move the binary to your preferred location (or use it directly from the source directory):

# In source-directory
make all
mv popdel /wherever/you/want/

To uninstall PopDel after installing it via 'make install' use:

# In source-directory
sudo make uninstall

To instead install PopDel using conda:

conda install popdel

Please make sure that you have added the required channels to your conda installation as described in 01. Dependencies. Otherwise the dependencies of HTSlib might not be resolved properly and you will only be abled to install PopDel v1.2.2 or below.

Note: We observed that PopDel takes 50% more time for calling variants when installed via conda. It still is considerably faster than most other tools, but if you want to use it on a bigger cohort or want to save some time, please consider installing PopDel from GitHub until the problem has been resolved.

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