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emarinier authored Nov 1, 2024
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Expand Up @@ -19,9 +19,7 @@ This release provides fixes for ambiguous crashes as a consequence of inputs con

# Installation #

It is strongly recommended you refer to the
[documentation](https://phac-nml.github.io/neptune/install/) for full
installation instructions. Neptune may be installed on any 64-bit Linux system using Bioconda, preferably with [Mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html) or with the Mamba resolver under Conda:
It is strongly recommended you refer to the [documentation](https://phac-nml.github.io/neptune/install/) for full installation instructions. Neptune may be installed on any 64-bit Linux system using Bioconda, preferably with [Mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html) or with the Mamba resolver under Conda:

1. Install [Bioconda](https://bioconda.github.io/)
2. Create an environment for Neptune and install within it: `mamba create -n neptune bioconda::neptune -c conda-forge`
Expand All @@ -33,8 +31,7 @@ If you run into problems installing Neptune with Conda / Mamba, you can try the
- Modify your `~/.condarc` file to have `channel_priority: flexible`
- Modify your conda solver within `~/.condarc` to use Mamba: `solver: libmamba`

Neptune may also be installed directly and instructions are available in the
[documentation](https://phac-nml.github.io/neptune/install/).
Neptune may also be installed directly and instructions are available in the [documentation](https://phac-nml.github.io/neptune/install/).

# Running Neptune #

Expand All @@ -47,8 +44,7 @@ A simple example of running Neptune:
neptune --inclusion /path/to/inclusion/ --exclusion /path/to/exclusion/
--output /path/to/output/

Please refer to the
[documentation](https://phac-nml.github.io/neptune/parameters/) for more details.
Please refer to the [documentation](https://phac-nml.github.io/neptune/parameters/) for more details.

# Contact #

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Copyright Government of Canada 2015-2024

Written by: Eric Marinier, Public Health Agency of Canada,
National Microbiology Laboratory
Written by: Eric Marinier, Public Health Agency of Canada, National Microbiology Laboratory

Funded by the National Micriobiology Laboratory and the Genome Canada / Alberta Innovates Bio Solutions project "Listeria Detection and Surveillance using Next Generation Genomics"

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