Skip to content

Commit

Permalink
Installation: Add install time and demo.
Browse files Browse the repository at this point in the history
  • Loading branch information
wwood committed Aug 6, 2024
1 parent 87f75db commit 20e0900
Showing 1 changed file with 16 additions and 1 deletion.
17 changes: 16 additions & 1 deletion docs/Installation.md.in
Original file line number Diff line number Diff line change
@@ -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
Expand Down Expand Up @@ -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).

0 comments on commit 20e0900

Please sign in to comment.