Installing the workshop software

ALL of this can be done on the head node

We are going to install the software needed for this workshop

  1. FLASH2 to overlap reads (https://github.com/dstreett/FLASH2)
  2. RDP to classify reads into taxon (https://github.com/rdpstaff/RDPTools)
  3. dbcAmplicons pipeline for processing amplicon sequences to abundance tables (https://github.com/msettles/dbcAmplicons)

optional

  1. bowtie2 (https://github.com/BenLangmead/bowtie2)

System Requirements

1. First, create a directory for the workshop in your home directory:

cd 
mkdir mca_example

and two other directors

mkdir mca_example/src
mkdir mca_example/bin

2. Now lets add the new bin directory to our PATH in a mca_profile file

using your favorite text editor, nano is simple, add the line

export PATH=~/mca_example/bin:$PATH
module load bowtie2/2.2.8

to a file named mca_profile in your home directory. Then on the command line, so that we don’t have to first log out then log back in.

source mca_profile

3. Install FLASH2 into src and link the exectuable into bin

cd mca_example/src
git clone https://github.com/dstreett/FLASH2.git
cd FLASH2/
make
ln -s ~/mca_example/src/FLASH2/flash2 ~/mca_example/bin/.
# test installation, should see help documentation
flash2 -h
cd ..

4.a Need Apache Ant and Java JDK 1.8 or higher to install

4.b Install the Ribsomal Database Project (RDP) into src

git clone https://github.com/rdpstaff/RDPTools.git
cd RDPTools/
git submodule init
git submodule update
make
# test installation, should see help documentation for classify
java -jar classifier.jar classify
cd ..

4.b RDP may not install correctly, if so copy over my version

module load java/1.8
cp /home/msettles/RDPTools.tar.gz .
tar zxvf RDPTools.tar.gz

4.c Add the location of classifier.jar as a variable in our mca_profile

using your favorite text editor, nano is simple, add the line

module load java/1.8
export RDP_PATH=~/mca_example/src/RDPTools

to a file named ~/mca_profile, then source it

source ~/mca_profile

5.a Setup a python virtual environment for dbcAmplicons

module load python/2.7.13
virtualenv dbcA_virtualenv

5.b now lets set the virtual environment to activate on login by adding it to our mca_profile

using your favorite text editor, nano is simple, add the lines

module load python/2.7.13
source ~/mca_example/src/dbcA_virtualenv/bin/activate
ulimit -S -v 4194304

to a file named ~/mca_profile, then source it

source ~/mca_profile

6. install dbcAmplicons

pip install numpy scipy pandas
git clone https://github.com/msettles/dbcAmplicons.git
cd dbcAmplicons/
python setup.py install
# test installation, should see help documentation
dbcAmplicons -h
cd ..

(Optional) You could also test the dbcAmplicons installation by running the script, test_dbAmplicons.sh, under the tests folds (in dbcAmplicions).

Lets Review

We created a directory for the workshop, in that directory we created two folders src and bin. We’ve installed FLASH2, RDP and dbcAmplicons. We’ve placed the executable for flash in a bin folder and added the folder to our PATH. We created an environment variable for the RDP classifier. We’ve created a python virtual environment and then installed the python package biom-format using pip and the dbcAmplions package using setup.py.

  1. You should have verified all the software works by viewing their help docs
  2. Verify that the flash executable is indeed in the bin folder
  3. We’ve modified your PATH and added 1 new environment variable, RDP_PATH, verify the PATH and the new env variable.
  4. We added a multiple lines to your mca_profile. How many lines?

Now log out, log back in and verify that each application still works. Ex.

source ~/mca_profile
flash2 -h

To verify RDP use

java -jar $RDP_PATH/classifier.jar classify
dbcAmplicons -h

You can check the current version of everything with, we usually save the output of this in the project file to remind ourselves which versions were run.

dbcVersionReport.sh

You can test the dbcAmplicons installation buy running the script test_dbAmplicons.sh, in the tests folder.

7. Last lets copy the workshop data into our home directory.

cd 
cd mca_example
cp /home/msettles/Illumina_Reads.tar.gz .
tar zxvf Illumina_Reads.tar.gz

Take a look at the files … what is inside the Illumina_Reads folder?