From 9dc05c9e97edf5553a7dc19731ca975c173787dd Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Wed, 2 Sep 2020 15:36:43 +0200
Subject: [PATCH] update documentation with github link
---
README.md | 12 ++++++------
doc/source/about.rst | 2 +-
doc/source/develop.rst | 2 ++
doc/source/starting.rst | 18 ++++++++++--------
4 files changed, 19 insertions(+), 15 deletions(-)
diff --git a/README.md b/README.md
index 0c8a5ea5..57d5364a 100755
--- a/README.md
+++ b/README.md
@@ -26,10 +26,10 @@ PanACoTA is a software providing tools for large scale comparative genomics:
PanACoTA is written in **python3**. So, you need python3 (and pip3 for installation) to run it.
Its external dependencies are:
-- [**prokka**](https://github.com/tseemann/prokka) (to annotate the genomes) and/or [**prodigal**](https://github.com/hyattpd/Prodigal)
-- [**mmseqs**](https://github.com/soedinglab/MMseqs2) (to generate pangenomes)
-- [**mafft**](http://mafft.cbrc.jp/alignment/software/) (to align persistent genome)
-- At least one of those softwares, to infer a phylogenetic tree:
+- [**prokka**](https://github.com/tseemann/prokka) and/or [**prodigal**](https://github.com/hyattpd/Prodigal) (for 'annotate module' - to uniformly annotate your genomes)
+- [**mmseqs**](https://github.com/soedinglab/MMseqs2) ('pangenome module' - to generate pangenomes)
+- [**mafft**](http://mafft.cbrc.jp/alignment/software/) ('align module' - to align persistent genome)
+- At least one of those softwares, to infer a phylogenetic tree ('tree module'):
- [**IQ Tree**](http://www.iqtree.org/)
- [**FastTreeMP**](http://www.microbesonline.org/fasttree/#Install): We advise to download C code, and compile as described here above.
- [**FastME**](http://www.atgc-montpellier.fr/fastme/binaries.php)
@@ -102,7 +102,7 @@ If you installed it by downloading a zip file, [Uninstall it](#uninstall), and [
`PanACoTA` contains 6 different subcommands:
-- `prepare` (download and prepare your dataset, with several controls)
+- `prepare` (download genomes from refseq if you want to, or give your input database, to run a filtering quality control)
- `annotate` (annotate all genomes of the dataset, after a quality control)
- `pangenome` (generate pan-genome)
- `corepers` (generate core-genome or persistent-genome)
@@ -132,7 +132,7 @@ You can find more information in [PanACoTA documentation](http://aperrin.pages.p
This part is for people who want to work on developing `PanACoTA` package. In the documentation, there is a part dedicated to [developers](http://aperrin.pages.pasteur.fr/pipeline_annotation/html-doc/develop.html).
-PanACoTA is also hosted in gitlab, where all CI is done. Here is the link: https://gitlab.pasteur.fr/aperrin/pipeline_annotation.git
+PanACoTA is also hosted in gitlab, where all CI is done. Here is the link: https://gitlab.pasteur.fr/aperrin/pipeline_annotation
## Installing `PanACoTA` (development mode)
diff --git a/doc/source/about.rst b/doc/source/about.rst
index 4ebcc19e..526b7fb5 100644
--- a/doc/source/about.rst
+++ b/doc/source/about.rst
@@ -3,7 +3,7 @@ About PanACoTA
==============
-PanACoTA program is available at `<https://gitlab.pasteur.fr/aperrin/PanACoTA>`_.
+PanACoTA program is available at `<https://github.com/gem-pasteur/PanACoTA>`_.
Copyright © `GEM <https://research.pasteur.fr/fr/team/microbial-evolutionary-genomics/>`_ - Institut Pasteur, CNRS UMR3525
diff --git a/doc/source/develop.rst b/doc/source/develop.rst
index 00b35ce6..971a5e57 100755
--- a/doc/source/develop.rst
+++ b/doc/source/develop.rst
@@ -4,6 +4,8 @@ Work on PanACoTA code
This part is for people who want to work on developing `PanACoTA` package: adding new features, correcting bugs etc.
+PanACoTA is also hosted in gitlab, where all CI is done. Here is the link: https://gitlab.pasteur.fr/aperrin/pipeline_annotation
+
Installing ``PanACoTA`` in development mode
===========================================
diff --git a/doc/source/starting.rst b/doc/source/starting.rst
index 935637a1..1bfad9e7 100755
--- a/doc/source/starting.rst
+++ b/doc/source/starting.rst
@@ -3,19 +3,18 @@ Starting with PanACoTA
======================
-``PanACoTA`` is a Python package, developed in Python 3.
+``PanACoTA`` is a Python package, developed in Python 3.6.
Downloading and updating
========================
-You can download ``PanACoTA`` source code by downloading an archive (zip, tar.gz), or by cloning its github repository. By cloning the github repository, you will then be able to update the code to new versions very easily and quickly. Here is how to clone the repository:
+You can download ``PanACoTA`` source code by downloading an archive of a given release (zip, tar.gz), or by cloning its github repository. By cloning the github repository, you will then be able to update the code to new versions very easily and quickly. Here is how to clone the repository:
.. code-block:: bash
git clone https://github.com/gem-pasteur/PanACoTA.git
-
-When asked, give your github login, and password.
+ve your github login, and password.
This will create a repository called ``PanACoTA``. Go inside this repository (``cd PanACoTA``) to install the software, as described hereafter.
@@ -39,10 +38,10 @@ Dependencies
There are several external dependencies, and you can install only the ones you need for your study:
-- `prokka <https://github.com/tseemann/prokka>`_ and/or `prodigal <https://github.com/hyattpd/Prodigal>`_ (if you want to uniformly annotate your genomes)
-- `mmseqs <https://github.com/soedinglab/MMseqs2>`_ (if you want to generate pangenomes)
-- `mafft <http://mafft.cbrc.jp/alignment/software/>`_ (if you want to align persistent genome)
-- At least one of those softwares, if you want to infer a phylogenetic tree:
+- `prokka <https://github.com/tseemann/prokka>`_ and/or `prodigal <https://github.com/hyattpd/Prodigal>`_ (for 'annotate module' - to uniformly annotate your genomes)
+- `mmseqs <https://github.com/soedinglab/MMseqs2>`_ ('pangenome module' - to generate pangenomes)
+- `mafft <http://mafft.cbrc.jp/alignment/software/>`_ ('align module' - to align persistent genome)
+- At least one of those softwares, if you want to infer a phylogenetic tree ('tree module'):
- `IQtree <http://www.iqtree.org/>`_
- `FastTreeMP <http://www.microbesonline.org/fasttree/#Install>`_: We advise to download C code, and compile as described :ref:`here above <fasttree>`.
@@ -90,6 +89,7 @@ just as any other software.
.. warning:: If you plan to work on the scripts, choose the development installation (see :doc:`Developer documentation <develop>`).
+.. _uninstall:
Uninstalling ``PanACoTA``
----------------------------
@@ -116,6 +116,8 @@ If you want to install a new version of ``PanACoTA``:
.. note:: If you have permission issues, and installed the package as root, use ``sudo`` before the second command line (``sudo ./make upgrade``) to upgrade. Or, if you installed the package locally, use ``./make upgrade --user`` to upgrade this local version.
+If you installed it by downloading a zip file, see :ref:`Uninstall it <uninstall>`), and install the new version (by cloning gitlab repository, or downloading the new zip file).
+
Quick run
=========
--
GitLab