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Installation
============

Requirements
------------

In order to run PSOT on your machine you need:

* git
* python >= 3
* nextflow
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* dbxref library
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* the bioinformatic tools you want to use

  * blastp
  * hmmscan
  * signalp
  * ghostx
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  * tmhmm
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  * targetp
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* the bioinformatic databases you want to use
  
  * PFAM
  * Swiss-Prot

Installation
------------

Install nextflow::
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    curl -fsSL get.nextflow.io | bash 

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(Optional) create a virtual env::

    virtualenv --python=python3 venv
    source venv/bin/activate

Install dbxref and psot::

    pip3 install git+https://git.computational.bio.uni-giessen.de/SOaAS/dbxref.git
    pip3 install git+https://git.computational.bio.uni-giessen.de/SOaAS/psot.git

Install a default repository for your profiles and modules::

    TODO

Developer setup
---------------

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Clone the git repository of PSOT::

    git clone git@git.computational.bio.uni-giessen.de:SOaAS/psot.git

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Install it into a virtualenv::
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    virtualenv --python=python3 venv; source venv/bin/activate;
    pip3 install git+https://git.computational.bio.uni-giessen.de/SOaAS/dbxref.git
    pip3 install -e .