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Merge pull request #29 from monagrland/main
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Update Conda installation instructions
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adriantich authored Jan 24, 2024
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23 changes: 19 additions & 4 deletions README.md
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Expand Up @@ -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

Expand All @@ -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
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