From 44cf5809ad7c07049c5d1f70900d2151b455d14a Mon Sep 17 00:00:00 2001
From: Iago Bonnici <iago.bonnici@umontpellier.fr>
Date: Mon, 19 Jun 2023 14:49:01 +0200
Subject: [PATCH] Document container installation in README.

---
 README.md | 66 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 66 insertions(+)

diff --git a/README.md b/README.md
index 236341a..ba363b1 100644
--- a/README.md
+++ b/README.md
@@ -5,3 +5,69 @@ following its specifications within Nicolas Galtier's draft paper
 *Phylogenetic conflicts:
 distinguishing gene flow from incomplete lineage sorting* (2023),
 and the original C code.
+
+## Build instructions
+
+### With Apptainer/Singularity
+
+Aphid can be run from an apptainer
+provided you have [Apptainer] (aka. Singularity) installed.
+
+First, build the container image as root:
+
+```sh
+# Get definition file.
+curl -L \
+  https://gitlab.mbb.univ-montp2.fr/ibonnici/aphid/-/jobs/artifacts/main/raw/singularity.def?job=container-recipes \
+  > aphid.def # (or download by hand)
+
+# Build image.
+sudo apptainer build aphid.sif aphid.def
+```
+
+Then run the container as regular user:
+
+```sh
+./aphid.sif <my_input_files>
+```
+
+### With Docker
+
+Aphid can be run from a docker container,
+provided you have [Docker] installed.
+
+First, build the container image:
+```sh
+docker buildx build -t aphid \
+  https://gitlab.mbb.univ-montp2.fr/ibonnici/aphid/-/jobs/artifacts/main/raw/Dockerfile?job=container-recipes
+```
+
+Then run the container:
+```sh
+docker run --rm -it -v ${PWD}:/home/aphid aphid <my_input_files>
+```
+
+
+### Manual compilation
+
+The program is still fairly easy to compile yet,
+provided you have [git] and [gcc] installed.
+
+First clone and compile the project:
+
+```sh
+git clone --recursive https://gitlab.mbb.univ-montp2.fr/ibonnici/aphid/
+cd aphid
+gcc -lm aphid.*.c -o aphid
+```
+
+Then run the binary obtained:
+
+```sh
+./aphid <my_input_files>
+```
+
+[Apptainer]: https://apptainer.org/
+[Docker]: https://www.docker.com/
+[git]: https://git-scm.com/
+[gcc]: https://gcc.gnu.org/
-- 
GitLab