1. Installing JAMP - VascoElbrecht/JAMP GitHub Wiki

JAMP is a R wrapper package that relies on VSEARCH, USEARCH, Cutadapt and other software. As most of the used programs are available for Linux/Mac only, JAMP will NOT work on windows (no support planned, sorry). Not all commandline tools have to be installed, but if you want to use all modules I recommend installing:

  • USEARCH
  • VSEARCH
  • Cutadapt (for the Cutadapt module -> Primer trimming)
  • FastQC (for the FastQC() module)
  • NCBI SRA Toolkit (Downloading sequences from NCBI sra, SRA())

Detailed installation instructions

Please make sure the following R packages are installed:

install.packages(c("bold", "XML", "rentrez", "seqinr"), dependencies=T)

Also, the following command line tools should be installed (and accessible via the terminal, by typing "Usearch", "Vsearch" or "Cutadapt")

  • Install Cutadapt v1.15 for primer trimming. Run the following command in the terminal:
sudo pip install cutadapt

If you have problems installing cutadapt type sudo su in the terminal and then run the command above again.

  • Next we want to install Usearch and Vsearch v2.6.2 which can be downloaded as already compiled programs. The 32 bit version of usearch is free, but you have to register on the website (the download link will be provided to you per mail). However, you have to move them to a folder to make them executable from the Terminal (path variable). You might need to change the file permissions, and also change the file name to Usearch / Vserch. Rename the usearch file to "usearch" and move it e.g. to the folder "/usr/local/bin/". Make sure you give the system permission to run the file with chmod(in the terminal):
cd path/to/usearch/file/on/your/computer # navigate to file
sudo mv usearch /usr/local/bin           # move it into the right place
chmod +x /usr/local/bin/usearch          # Allow your computer to use it

The same has to be done for vsearch.

  • Install the precompiled version of FastQC, and move all folder contents into /usr/local/bin.

  • Install the precompiled version of NCBI SRA Toolkit. Move all items in bin to /usr/local/bin.

You can check if all programs are installed correctly by typing vsearch, usearch, cutadapt, FastQC or fastq-dump in the terminal.

If you do not want to install the software in bin, you can also keep the executables anywhere on your system and specify the path to each program in R using the exe or exeV (does not work for cutadapt).

Initialling JAMP

To install JAMP locally from within R: Simply run the following commands in R.

# Installing dependencies needed fro JAMP
install.packages(c("bold", "XML", "seqinr", "devtools"), dependencies=T)
# Load devtools and install package directly from GitHub
library("devtools")
install_github("VascoElbrecht/PrimerMiner", subdir="PrimerMiner")
install_github("VascoElbrecht/JAMP", subdir="JAMP")

You can also download the latest release of JAMP or PrimerMiner, extract and intal within R using install.packages("JAMP", repos = NULL, type="source")

Example of a system-wide installation on an ubuntu|debian server:

wget https://github.com/VascoElbrecht/JAMP/archive/v0.35.tar.gz
tar -xzf v0.35.tar.gz
cd JAMP-0.35
sudo R CMD INSTALL JAMP