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diff --git a/reproduce/software/containers/README-apptainer.md b/reproduce/software/containers/README-apptainer.md deleted file mode 100644 index a7826ec..0000000 --- a/reproduce/software/containers/README-apptainer.md +++ /dev/null @@ -1,71 +0,0 @@ -# Maneage'd projects in Apptainer - -Copyright (C) 2025-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>\ -Copyright (C) 2025-2025 Giacomo Lorenzetti <glorenzetti@cefca.es>\ -See the end of the file for license conditions. - -For an introduction on containers, see the "Building in containers" section -of the `README.md` file within the top-level directory of this -project. Here, we focus on Apptainer with a simple checklist on how to use -the `apptainer-run.sh` script that we have already prepared in this -directory for easy usage in a Maneage'd project. - - - - - -## Building your Maneage'd project in Apptainer - -Through the steps below, you will create an Apptainer image that will only -contain the software environment and keep the project source and built -analysis files (data and PDF) on your host operating system. This enables -you to keep the size of the image to a minimum (only containing the built -software environment) to easily move it from one computer to another. - - 1. Using your favorite text editor, create a `run.sh` in your top Maneage - directory (as described in the comments at the start of the - `apptainer.sh` script in this directory). Just add `--build-only` on - the first run so it doesn't go onto doing the analysis and just sets up - the software environment. Set the respective directory(s) based on your - filesystem (the software directory is optional). The `run.sh` file name - is already in `.gitignore` (because it contains local directories), so - Git will ignore it and it won't be committed by mistake. - - 2. Make the script executable with `chmod +x ./run.sh`, and run it with - `./run.sh`. - - 3. Once the build finishes, the build directory (on your host) will - contain two Singularity Image Format (SIF) files listed below. You can - move them to any other (more permanent) positions in your filesystem or - to other computers as needed. - * `maneage-base.sif`: image containing the base operating system that - was used to build your project. You can safely delete this unless you - need to keep it for future builds without internet (you can give it - to the `--base-name` option of this script). If you want a different - name for this, put the same option in your - * `maneaged.sif`: image with the full software environment of your - project. This file is necessary for future runs of your project - within the container. - - 3. To execute your project remote the `--build-only` and use `./run.sh` to - execute it. If you want to enter your Maneage'd project shell, add the - `--project-shell` option to the call inside `./run.sh`. - - - - - -## Copyright information - -This file is free software: you can redistribute it and/or modify it under -the terms of the GNU General Public License as published by the Free -Software Foundation, either version 3 of the License, or (at your option) -any later version. - -This file is distributed in the hope that it will be useful, but WITHOUT -ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or -FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for -more details. - -You should have received a copy of the GNU General Public License along -with this file. If not, see <https://www.gnu.org/licenses/>. |