From 52b00f96a322739d2b20e651196019fb3a87c8cc Mon Sep 17 00:00:00 2001 From: Brandon Seah Date: Wed, 24 Jan 2024 10:25:25 +0100 Subject: [PATCH] Update Conda installation instructions --- README.md | 23 +++++++++++++++++++---- 1 file changed, 19 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 0e42abe..9c6e38e 100644 --- a/README.md +++ b/README.md @@ -131,17 +131,30 @@ python3 -m nuitka --static-libpython=no --standalone dnoise/DnoisE.py #### __B. INSTALLATION FROM CONDA__ #### __1. Install package__ +From version v1.4.0 onwards, DnoisE is also available via the +[Bioconda](https://bioconda.github.io/) channel of the [Conda package +manager](https://docs.conda.io/en/latest/), under the package name `dnoise`. + +Install `dnoise` to the current Conda environment: + ```bash -conda install -c adriantich dnoise +conda install -c conda-forge -c bioconda -c defaults --strict-channel-priority dnoise ``` -Different python versions (3.6, 3.7 and 3.8) are available at the [conda repository](https://anaconda.org/adriantich/dnoise/files). -However the *Levenshtein* package is not available so its installation must be done manually as follows +It is not recommended to install new packages to the default Conda `base` +environment, so you may wish to create a new environment instead. The following +command creates a new Conda environment named `dnoise-env` with `dnoise`: ```bash -pip3 install levenshtein +conda create -n dnoise-env -c conda-forge -c bioconda -c defaults --strict-channel-priority dnoise ``` +Refer to the [Bioconda documentation +("Usage")](https://bioconda.github.io/index.html) for an explanation of why the +channels (`conda-forge`, `bioconda`, `defaults`) have to be specified in the +order given. + + #### __2. Create an executable file (optional)__ To create a binary file of the program run @@ -161,6 +174,8 @@ large files). It also accepts .fastq input files. DnoisE can be called from the executable created by *nuitka* or directly from the python script. See example below: +From v1.4.0 onwards, the executable is named `dnoise`. + ```bash > ./dnoise/DnoisE.bin -h > python3 ./dnoise/DnoisE.py -h