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## Requirements

TL;DR: no external requirements needed. Both the `--recursive` Github clone as well as the bioconda package should work out-of-the-box.
TL;DR: no external requirements needed. Both the recursive GitHub clone as well as the bioconda package should work out-of-the-box.
<details><summary> 🛠️ Details to build from source </summary>
The <i>amplisim</i> software is intended for 64-bit POSIX compliant operating systems and was tested successfully under Ubuntu 22.04 LTS and macOS v12.5.1 (Monterey).
Building <i>amplisim</i> from source requires libraries for <i>lzma</i>, <i>libbz2</i> and <i>libcurl</i> on your system in order to compile <i>htslib</i>.
Both Linux and masOS operating systems typically provide them via their respective package managers.
Both Linux and masOS operating systems typically provide them via their respective package managers. See intructions below.
</details>

## Installation
### Build via conda
The easiest way to install _amplisim_ is via the conda package manager from the bioconda channel.
Please note that the conda installation is currently only available for Linux operating systems.

```
# create a new conda environment
conda create --name amplisim
# install the latest amplisim version from the bioconda channel
conda install -c bioconda amplisim
```
Please note that the bioconda installation is currently only available for Linux operating systems.

### Build from source
```
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### Minimal working examples
The minimal command to run _amplisim_ is to provide a reference genome in FASTA format and a set of primers in BED format (see chapter [Input and output](#input-and-output) for more details).
By default, _amplisim_ prints the amplicons sequences to the standard output, s.t. the user can either store the sequences or forward them to the next program.
By default, _amplisim_ prints the amplicons sequences to the standard output such that the user can either direct the sequences to a file or forward them to the next program.
```
amplisim <my_reference.fasta> <my_primers.bed> > <my_amplicons.fasta>
```
If you are just interested in the resulting FASTA file you can directly use the `-o` option.
If you want _amplisim_ to store the resulting amplicon sequences directly in a FASTA file you can use the `-o` option.
```
amplisim -o <my_amplicons.fasta> <my_reference.fasta> <my_primers.bed>
```
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