From 025c058ef15ef72e59f6ab0eebc542cb5110092c Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Thu, 24 Sep 2020 11:25:54 +0200
Subject: [PATCH] More precise definition of external dependencies
---
README.md | 11 ++++++-----
doc/source/starting.rst | 9 +++++----
2 files changed, 11 insertions(+), 9 deletions(-)
diff --git a/README.md b/README.md
index 7c77592f..1d8e88fe 100755
--- a/README.md
+++ b/README.md
@@ -46,11 +46,12 @@ Amandine PERRIN, Eduardo P.C. ROCHA (2020). PanACoTA: A modular tool for massiv
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) 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'):
+PanACoTA has several dependencies. Install only the one(s) you need, according to the module you want to use:
+- For prepare module: [**mash**](https://mash.readthedocs.io/en/latest/) (to filter genomes)
+- For annotate module: [**prokka**](https://github.com/tseemann/prokka) and/or [**prodigal**](https://github.com/hyattpd/Prodigal) (to uniformly annotate your genomes)
+- For pangenome module: [**mmseqs**](https://github.com/soedinglab/MMseqs2) (to generate pangenomes)
+- For align module: [**mafft**](http://mafft.cbrc.jp/alignment/software/) (to align persistent genome)
+- For tree module: At least one of those softwares, to infer a phylogenetic tree:
- [**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)
diff --git a/doc/source/starting.rst b/doc/source/starting.rst
index 1e121975..c7260a48 100755
--- a/doc/source/starting.rst
+++ b/doc/source/starting.rst
@@ -13,10 +13,11 @@ 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>`_ (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'):
+- For prepare module: `mash <https://mash.readthedocs.io/en/latest/>`_ (to filter genomes)
+- For annotate module: `prokka <https://github.com/tseemann/prokka>`_ and/or `prodigal <https://github.com/hyattpd/Prodigal>`_ (to uniformly annotate your genomes)
+- For pangenome module: `mmseqs <https://github.com/soedinglab/MMseqs2>`_ (to generate pangenomes)
+- For align module: `mafft <http://mafft.cbrc.jp/alignment/software/>`_ (to align persistent genome)
+- For tree module: At least one of those softwares:
- `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>`.
--
GitLab