diff --git a/docs/Installation.md.in b/docs/Installation.md.in index c6ff757a..bfd4d7d6 100644 --- a/docs/Installation.md.in +++ b/docs/Installation.md.in @@ -1,6 +1,6 @@ # Installing SingleM -There are several ways to install SingleM. +There are several ways to install SingleM. On the assumption that a standard internet connection speed is available, each of these methods should take substantially less than 1 hour, hopefully less than 15 minutes. ## Installation via conda SingleM can be installed through @@ -88,6 +88,21 @@ singlem -h After this, you'll also need to procure the reference data (the "metapackage"). See [singlem data](/tools/data). +# Example data + +To test the main subcommand of SingleM, [pipe](/tools/pipe) works, download a minimal dataset and generate a taxonomic profile like so: +``` +wget 'https://github.com/wwood/singlem/raw/44e1f81404c12931742259088999290edbb271b3/test/data/methanobacteria/genomes/GCA_000309865.1_genomic.fna' +singlem pipe -1 GCA_000309865.1_genomic.fna -p /dev/stdout +``` + +This should output a profile similar to the below. When tested, the `pipe` took a little less than 2 minutes: +``` +sample coverage taxonomy +GCA_000309865.1_genomic 0.39 Root; d__Archaea; p__Methanobacteriota; c__Methanobacteria; o__Methanobacteriales; f__Methanobacteriaceae; g__Methanobacterium +08/06/2024 04:50:25 PM INFO: Finished condense +``` + # Containerised SingleM installation examples To ensure that the instructions here work, they have been tested in containerised environments. Logs of this procedure are available at [https://github.com/wwood/singlem-installation](https://github.com/wwood/singlem-installation).