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Reorder local installation steps in documentation #15

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Apr 23, 2021
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Reorder local installation steps in documentation #15

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7957b63
Reorder and improve steps in local installation
Apr 16, 2021
32389f5
WSL2: manual mounting of Windows filesystem
Apr 21, 2021
e727af9
Minor (add "e.g." to Windows file system path)
Apr 23, 2021
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27 changes: 13 additions & 14 deletions doc/source/installation.rst
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Expand Up @@ -82,25 +82,17 @@ Without the use of a container the installation of *ksrates* and its dependencie
.. note::
WSL2 (Windows Subsystem for Linux 2) is a native Windows 10 feature that allows to run a GNU/Linux terminal without the use of a VM. It can be installed following the official `documentation <https://docs.microsoft.com/en-us/windows/wsl/install-win10#requirements>`__.

1. Clone the *ksrates* repository from `GitHub <https://github.com/VIB-PSB/ksrates>`__::

git clone https://github.com/VIB-PSB/ksrates
1. Most of non-Python dependencies can be installed with the following commands::

2. Install the tool and its Python dependencies using ``pip3``::

cd ksrates
pip3 install .

3. Most of non-Python dependencies can be installed witht the following commands::

sudo apt-get -yq install default-jdk build-essential ncbi-blast+ muscle mafft prank fasttree mcl phyml
sudo apt-get update && sudo apt-get -yq install python3-pip default-jdk build-essential ncbi-blast+ muscle mafft prank fasttree mcl phyml
wget -qO- https://get.nextflow.io | bash

Optionally make Nextflow accessible through your ``$PATH`` variable, for example::

sudo mv nextflow /usr/local/bin

4. Install PAML 4.9j from source (for more infromation see PAML installation `page <http://abacus.gene.ucl.ac.uk/software/#phylogenetic-analysis-by-maximum-likelihood-paml>`__) to avoid compatibility issues::
2. Install PAML 4.9j from source (for more infromation see PAML installation `page <http://abacus.gene.ucl.ac.uk/software/#phylogenetic-analysis-by-maximum-likelihood-paml>`__) to avoid compatibility issues::

wget http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz
tar -xzf paml4.9j.tgz
Expand All @@ -115,15 +107,22 @@ Without the use of a container the installation of *ksrates* and its dependencie
* Or move ``codeml`` to another directory (here assumed to be ``~/bin``) and add this directory to ``$PATH``, for the Bash shell by copying the following line to the shell initialization file (e.g. ``.bashrc``)::

export PATH=$PATH:~/bin

Please refer to PAML `website <http://abacus.gene.ucl.ac.uk/software/paml.html#download>`__ for more information about its installation.

5. Install I-ADHoRe 3.0 from its GitHub `page <https://github.com/VIB-PSB/i-ADHoRe>`__ (required only for collinearity analysis of genome data).
3. Install I-ADHoRe 3.0 from its GitHub `page <https://github.com/VIB-PSB/i-ADHoRe>`__ (required only for collinearity analysis of genome data).

4. Clone the *ksrates* repository from `GitHub <https://github.com/VIB-PSB/ksrates>`__ and install the package and its Python dependencies::

git clone https://github.com/VIB-PSB/ksrates
cd ksrates
pip3 install .


Testing your installation
=========================

.. note::
WSL2 users can enter the Windows file system from the terminal through e.g. ``cd mnt/c/Users/your_username``.

1. Clone the *ksrates* repository from `GitHub <https://github.com/VIB-PSB/ksrates>`__ to get the use case dataset::

git clone https://github.com/VIB-PSB/ksrates
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