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01_Install

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Ricardo H. Ramirez-Gonzalez edited this page Apr 9, 2022 · 1 revision

Installyng IBSpy

There easiest way to install IBSpy is to use pip3.

pip3 install IBSpy

If pip3 fails, you can clone the project and compiling it with:

pip3 install -r requirements.txt
python3 setup.py develop

Then you should have the IBSpy command available.

Optional kmer databases

IBSpy requires to have a kmer database from the sequencing files. Currently three formats are supported:

  1. KMC: If you want to use the KMC binder, install the KMC and compile the python instructions.
  2. Jellyfish: Follow the instructions in its website
  3. kmerGWAS: Has an adhoc file format that contains only the kmers in a binary representation, sorted. This option is faster than the jellyfish version, but creating the kmer table is less straight forward. The manual is here.

If neigher KMC or Jellyfish are detected, building the kmer database can be built using the format described by kmerGWAS within IBPspy.

KMC3

If you want to use the KMC binder, install the KMC and compile the python instructions.

This commands should setup the KMC envieronment for KMC. If you wa

wget https://github.com/refresh-bio/KMC/archive/refs/tags/v3.1.1.tar.gz
tar -xzf v3.1.1.tar.gz
cd KMC-3.1.1
make py_kmc_api
cd py_kmc_api
source set_path.sh 
cd ../..
echo $PYTHONPATH

If you don't want to have to source every time, you can add the bin folder to $PYTHONPATH in your envieronment

PYTHONPATH=$PYTHONPATH:$KMC_PATH/KMC-3.1.1/bin

Or, you can copy the .so compiled objects to your site-packages folder. This is the method used in the example singularity image. However, this is not recomended in other environments.

cp bin/*.so  /usr/local/lib/python3.9/site-packages/

Runn unit tests

To makes sure that your changes havent broken the core IBSpy, run the unit tests:

python3 setup.py test

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