įinally, we need a few of the UCSC utilities. makeĪs for our other tools, add samtools to our PATH environment variable: export PATH='$PATH:/path/to/pepatac_tutorial/tools/samtools-1.10/' Learn more about the -prefix option here. git clone git:///GregoryFaust/samblaster.gitĮxport PATH='$PATH:/path/to/pepatac_tutorial/tools/samblaster/'Īlternatively, if you do not have the ability to install samtools to the default location, you can specify using the -prefix=/install/destination/dir/ option. For a full guide, check out the samblaster installation instructions. wget Īdd to PATH! export PATH='$PATH:/path/to/peppro_tutorial/tools/preseq_v2.0/' Check out the author's page for more instruction. The pipeline uses preseq to calculate library complexity.

export PATH='$PATH:/path/to/pepatac_tutorial/tools/bedtools2/bin/'Īgain, let's add bowtie2 to our PATH environment variable: export PATH='$PATH:/path/to/pepatac_tutorial/tools/bowtie2-2.4.1/' Look here to learn more about the concept of environment variables if you are unfamiliar. Now, let's add bedtools to our PATH environment variable. We're going to install from source, but if you would prefer to install from a package manager, you can follow the instructions in the bedtools' installation guide. Let's start right at the beginning and install bedtools. We'll install each of these pieces of software before moving forward. The following tools are used by the pipeline: The complete list (including optional tools) is specified in the pipeline configuration file tools section. We will need some common bioinformatics tools installed. You can do a user-specific install using the included requirements.txt file in the pipeline directory: pip install -user -upgrade -r requirements.txt For peak calling, the pipeline uses MACS2 as the default. The pipeline uses pypiper to run a single sample, looper to handle multi-sample projects (for either local or cluster computation), and pararead for parallel processing sequence reads. This guide walks you through the nitty-gritty of how to install each prerequisite package.

Samtools install