docs(README): include install instructions

Since the snakemake workflow catalog does not seem to be updating automatically, manual install instructions are provided.

README.md

@@ -25,7 +25,97 @@ we can run the whole thing in an isolated environment.
 
 ## Notes on Installation
 
-HOLDING
+### Necessary Software
+
+This pipeline needs [conda][conda]
+and [snakemake][sm]
+installed,
+and runs best if you also have [singularity][sing]
+installed,
+though it's not required.
+
+Snakemake recommends using [mambaforge][mambaforge]
+as your base conda,
+which I would also recommend.
+Installation instructions are at the above link.
+If you prefer a vanilla conda installation,
+you can always try `mamba` following the instructions at the above snakemake link.
+Once you have conda installed,
+install snakemake as outlined on their page
+(again, see the above link)
+and activate your snakemake environment.
+
+If you are running on a Linux system,
+then singularity can be installed from conda like so:
+
+```shell
+conda install -n snakemake -c conda-forge singularity
+```
+
+It's a bit more challenging for other operating systems.
+Your best bet is to follow their instructions
+[here][sing_install].
+But don't worry!
+**Singularity is _not_ regquired!**
+Snakemake will still run each step in its own Conda environment,
+it just won't put each Conda environment in a container.
+
+### Get the Source Code
+
+Navigate to our [release][releases]
+page on github and download the most recent version.
+The following will do the trick:
+
+```shell
+curl -s https://api.github.com/repos/IMS-Bio2Core-Facility/GTExSnake/releases/latest |
+grep tarball_url |
+cut -d " " -f 4 |
+tr -d '",' |
+xargs -n1 curl -sL |
+tar xzf -
+```
+
+After querying the github api to get the most recent release information,
+we grep for the desired URL,
+split the line and extract the field,
+trim superfluous characters,
+use `xargs` to pipe this to `curl` while allowing for re-directs,
+and un-tar the files.
+Easy!
+
+Alternatively,
+for the bleeding edge,
+please clone the repo like so:
+
+```shell
+git clone https://github.com/IMS-Bio2Core-Facility/GTExSnake
+```
+
+> :warning: **Heads Up!**
+> The bleeding edge may not be stable,
+> as it contains all active development.
+
+However you choose to install it,
+`cd` into the directory.
+
+### Running
+
+Once you've installed the above software,
+and fetched the code,
+running the pipeline is as simple as:
+
+```shell
+snakemake --use-conda --use-singularity --cores 6
+```
+
+If you aren't using `singularity`,
+then leave off the apropriate flag, as so:
+
+```shell
+snakemake --use-conda --cores 6
+```
+
+And `snakemake` will automatically leave it off.
 
 ## Notes on Configuration
 
@@ -76,3 +166,6 @@ and general analysis and data handling with `scanpy`.
 [sm]: https://snakemake.readthedocs.io/en/stable/index.html "Snakemake"
 [conda]: https://docs.conda.io/en/latest/ "Conda"
 [sing]: https://sylabs.io/singularity/ "Singularity"
+[mambaforge]: https://github.com/conda-forge/miniforge#mambaforge "Mambaforge"
+[sing_install]: https://sylabs.io/guides/3.8/admin-guide/installation.html#installation-on-windows-or-mac "Singularity Install"
+[releases]: https://github.com/IMS-Bio2Core-Facility/single_snake_sequencing/releases "Releases"