PARTIE requires several tools to run and a database.
You will need to have the following software installed before you can run PARTIE
- curl This should be already installed, if not you can download it from here
- R and the randomForest library. Once you have R installed you can install that library with
install.packages(c("randomForest"), dependencies=TRUE); - bowtie2 Available from sourceforge
- jellyfish Available from github
- seqtk Available from github
- the NCBI SRA Toolkit. You should download the prebuilt binaries or check this NCBI page for the latest versions
- zotkill is used to write to a single file. This is an elegant file locking approach to combine multiple outputs into one file, e.g. while running on a cluster
Follow the installation instructions for each of those libraries.
Once the libraries are installed you can clone the code base from GitHub:
git clone https://github.com/linsalrob/partie.git
You will also need the databases that we have built.
We provide the databases in two formats, and there are two ways you can install them.
This is probably the best download, you can download the three databases we use already formatted for bowtie2. These three databases should end up in the db/ directory under PARTIE.
You can use make to install the files:
make indexes
Or you can download each of the three files separately (you don't need to do this if you did make):
- 16S (Note that this file is 14M)
- Phage (Note that this file is 225M)
- Prokaryotes (Note that this file is 7.3G)
- Human (Note that this file is 3.8G)
Once you have downloaded them you can extract them with:
tar xf 16SMicrobial.bowtie2indices.bz2
tar xf phage.bowtie2indices.bz2
tar xf prokaryotes.bowtie2indices.bz2
tar xf human.bowtie2indices.bz2
You can download each of the databases as a single file, but then you will need to use bowtie2 to build them. Again, we have a Makefile for this, or you can do them manually:
To install this way using make
make databases
Or you can download them from edwards.sdsu.edu (Note that this file is 2.3G) and then build them with bowtie2-build:
bowtie2-build db/16SMicrobial.fna db/16SMicrobial
bowtie2-build db/phages.fna db/phages
bowtie2-build db/prokaryotes.fna db/prokaryotes
bowtie2-build db/hg38.fa db/humanGenome
Once you have installed all the dependencies you should be able to run the test code for PARTIE.