Install Pyinseq

Install Python on the remote instance

cd Downloads/

wget https://repo.continuum.io/archive/Anaconda3-5.2.0-Linux-x86_64.sh

chmod +x Anaconda3-5.2.0-Linux-x86_64.sh

./Anaconda3-5.2.0-Linux-x86_64.sh

yes to license Default install location (hit enter) yes to prepend in path no to install VSCode

cd ..

source ~/.bashrc

python

Should now see:

Python 3.6.5 |Anaconda, Inc.| (default, Apr 29 2018, 16:14:56)
[GCC 7.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>

This is the python shell (also called the REPL). You can now run python on your remote instance, and the command python points to the version to just installed. Type exit() to return to the bash shell, which will look something like this:

mmandel@js-170-233:~$

Install Pyinseq

Install the latest version from GitHub:

pip install --upgrade pip

pip install git+git://github.com/mandel01/pyinseq

If you want to install the version registered in the Python Package Index, instead type pip install pyinseq.

Upload data to the instance

Make and enter the data directory

mkdir data

cd data

Download the sample data

wget https://www.dropbox.com/s/icroinqkyev4bb3/pyinseq_example_files.tar.gz

tar -zxvf pyinseq_example_files.tar.gz

Run pyinseq

Check out the required arguments:

pyinseq

Run a tiny dataset:

cd

pyinseq -i data/pyinseq_example_files/example01.fastq -s data/pyinseq_example_files/example01.txt -g data/pyinseq_example_files/ES114v2.gb -e example1

Run a larger dataset:

cd

pyinseq -i data/pyinseq_example_files/example02.fastq.gz -s data/pyinseq_example_files/example02.txt -g data/pyinseq_example_files/ES114v2.gb -e example2