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Microbiome Helper Tools Install
See the commands below for how to install the resources included with the Microbiome Helper VBox on a fresh Ubuntu 16.04.2 server. These commands will be updated over time as new resources are added.
Note that the versions aren't necessarily the most recent, but were when these commands were run.
This could be a useful resource to link to for users installing the microbiome helper tools themselves.
Cloned GitHub repository (I used sudo since this was run in /usr/local/prg) and entered directory.
sudo git clone https://github.com/LangilleLab/microbiome_helper.git
cd microbiome_helper
Made symbolic links of all scripts (files ending in .py, .pl, and .R) to /usr/local/bin.
for script in *.py; do sudo ln -s $PWD/$script /usr/local/bin/$script; done
for script in *.pl; do sudo ln -s $PWD/$script /usr/local/bin/$script; done
for script in *.R; do sudo ln -s $PWD/$script /usr/local/bin/$script; done
Installed Perl dependencies:
cpan App::cpanminus # Use sudo option to install globally
sudo cpanm Parallel::ForkManager
sudo apt-get install perl-doc
First installed required python packages with pip:
Note that numpy is installed automatically with the below command.
pip install h5py
wget https://github.com/picrust/picrust/releases/download/1.1.1/picrust-1.1.1.tar.gz
tar -zxvf picrust-1.1.1.tar.gz
rm picrust-1.1.1.tar.gz
cd picrust-1.1.1
At this stage one would usually download the pre-calculated files of interest from the PICRUSt website e.g. with wget. I had previously downloaded these files and placed them in our scratch data folder (which is specific to our server) so instead I created symbolic links to these files.
First I entered picrust/data:
cd picrust/data
Then made symbolic links to the pre-calculated tables of counts:
ln -s /scratch/db/picrust_precalculated_v1.1.1/13_5/16S_13_5_precalculated.tab.gz $PWD/16S_13_5_precalculated.tab.gz
ln -s /scratch/db/picrust_precalculated_v1.1.1/13_5/ko_13_5_precalculated.tab.gz $PWD/ko_13_5_precalculated.tab.gz
ln -s /scratch/db/picrust_precalculated_v1.1.1/13_5/cog_13_5_precalculated.tab.gz $PWD/cog_13_5_precalculated.tab.gz
ln -s /scratch/db/picrust_precalculated_v1.1.1/13_5/rfam_13_5_precalculated.tab.gz $PWD/rfam_13_5_precalculated.tab.gz
And also to the pre-calculated tables of variances so that confidence intervals can be calculated:
ln -s /scratch/db/picrust_precalculated_v1.1.1/13_5/variances/16S_13_5_precalculated_variances.tab.gz $PWD/16S_13_5_precalculated_variances.tab.gz
ln -s /scratch/db/picrust_precalculated_v1.1.1/13_5/variances/cog_13_5_precalculated_variances.tab.gz $PWD/cog_13_5_precalculated_variances.tab.gz
ln -s /scratch/db/picrust_precalculated_v1.1.1/13_5/variances/ko_13_5_precalculated_variances.tab.gz $PWD/ko_13_5_precalculated_variances.tab.gz
ln -s /scratch/db/picrust_precalculated_v1.1.1/13_5/variances/rfam_13_5_precalculated_variances.tab.gz $PWD/rfam_13_5_precalculated_variances.tab.gz
Finally to install PICRUSt I navigated to the folder containing setup.py and ran pip install.
cd ../..
pip install
- biom-format (v2.1.6)
- click (v6.7)
- cogent (v1.5.3)
- future (v0.16.0)
- scipy (v0.19.1)
- pandas (v.0.19.2)
- pyqi (v0.3.2)
- pytz (v2017)
- python_dateutil (v2.6.1)
There are good instructions here for how to install R on ubuntu 16.04: https://www.digitalocean.com/community/tutorials/how-to-install-r-on-ubuntu-16-04-2
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo add-apt-repository 'deb [arch=amd64,i386] https://cran.rstudio.com/bin/linux/ubuntu xenial/'
sudo apt-get update
I was missing the add-apt-repository command and had to install software-properties-common to fix this problem:
sudo apt-get install software-properties-common
sudo apt-get install r-base
R packages can be installed within an R environment by starting the program with sudo -i R so that they will be installed globally.
Start R environment as root and install.
sudo -i R
install.package("ape") # In R environment
Download, extract and link MetaPhlAn2:
curl -o /tmp/metaphlan2.zip \
https://bitbucket.org/biobakery/metaphlan2/get/2.6.0.zip
sudo unzip /tmp/metaphlan2.zip -d /usr/local/prg/
sudo mv /usr/local/prg/biobakery-metaphlan2-c43e40a443ed/ \
/usr/local/prg/metaphlan2-2.6.0
sudo ln -s \
/usr/local/prg/metaphlan2-2.6.0/{metaphlan2,strainphlan}.py /usr/local/bin/
rm /tmp/metaphlan2.zip
Install dependencies:
sudo /usr/bin/pip install numpy biom-format
HUMAnN2, by default, also installs compatible versions of both DIAMOND and Bowtie 2.
sudo /usr/bin/pip install humann2
Download and configure the default HUMAnN2 databases:
sudo mkdir /scratch/db/humann2
sudo humann2_databases --download utility_mapping full /scratch/db/humann2
sudo humann2_databases --download uniref uniref90_diamond /scratch/db/humann2
sudo humann2_databases --download chocophlan full /scratch/db/humann2
You may wish to download Bowtie 2 databases to use with contaminant filters, like Phi X. Store them in /scratch/db/bowtie/ and symlink them to /home/shared/bowtiedb/ (to work with the metagenomics protocol).
Note that Trimmomatic depends on Java, which can be installed with sudo apt-get install default-jre on Ubuntu 16.04.
curl -o /tmp/trimmomatic.zip \
-L http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip
sudo unzip /tmp/trimmomatic.zip -d /usr/local/prg/
rm /tmp/trimmomatic.zip
sudo apt-get install fastx-toolkit
curl -o /tmp/fastqc.zip \
-L http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip
sudo unzip /tmp/fastqc.zip -d /usr/local/prg/
sudo chmod 755 /usr/local/prg/FastQC/fastqc
sudo ln -s /usr/local/prg/FastQC/fastqc /usr/local/bin/
Went to https://sco.h-its.org/exelixis/web/software/pear/ and hit new downloads page. Selected academic license and filled in required information. Uploaded to /usr/local/prg and put in folder pear with LICENSE.
cd pear/pear-0.9.10-linux-x86_64/bin/
sudo ln -s /usr/local/prg/pear/pear-0.9.10-linux-x86_64/bin/pear /usr/local/bin/pear
Downloaded BBMAP from https://sourceforge.net/projects/bbmap/. Uploaded to /usr/local/prg.
sudo gunzip BBMap_37.50.tar.gz
sudo tar -xf BBMap_37.50.tar
BBMAP files are now in the folder /usr/local/prg/bbmap.
cd /usr/local/prg
sudo wget https://github.com/torognes/vsearch/releases/download/v2.4.4/vsearch-2.4.4-linux-x86_64.tar.gz
sudo gunzip vsearch-2.4.4-linux-x86_64.tar.gz
sudo tar -xf vsearch-2.4.4-linux-x86_64.tar
cd vsearch-2.4.4-linux-x86_64/bin
sudo ln -s $PWD/vsearch /usr/local/bin/vsearch
cd /usr/local/prg
sudo wget http://bioinfo.lifl.fr/RNA/sortmerna/code/sortmerna-2.1-linux-64-multithread.tar.gz
sudo gunzip sortmerna-2.1-linux-64-multithread.tar.gz
sudo tar -xf sortmerna-2.1-linux-64-multithread.tar
cd sortmerna-2.1b
sudo ln -s /usr/local/prg/sortmerna-2.1b/sortmerna /usr/local/bin/sortmerna
sudo ln -s /usr/local/prg/sortmerna-2.1b/indexdb_rna /usr/local/bin/indexdb_rna
sudo wget https://git.metabarcoding.org/obitools/sumatra/uploads/251020bbbd6c6595cb9fce6077e29952/sumatra_v1.0.20.tar.gz
sudo tar -zxvf sumatra_v1.0.20.tar.gz
cd sumatra_v1.0.20
sudo make
sudo ln -s /usr/local/prg/sumatra_v1.0.20/sumatra /usr/local/bin/sumatra
- Getting Started in the Lab
- Funding Opportunities
- Registering New Computer on Dal Network
- Conferences & Travel
- Setting up a Miniconda Environment
- tmux Quick Reference
- Customizing Matplotlib
- SSH Tunneling to use RStudio Server
- SSH Tunneling to use Jupyter Notebooks