From f0c38ee2fbf7ae5b6885a6efc65e5305dda381c7 Mon Sep 17 00:00:00 2001 From: Leonardo Cristella Date: Fri, 8 Nov 2024 16:30:41 +0100 Subject: [PATCH] Remove BB5 reference from ReadMe --- readme.md | 55 ++----------------------------------------------------- 1 file changed, 2 insertions(+), 53 deletions(-) diff --git a/readme.md b/readme.md index b2cd85b..5380c0b 100644 --- a/readme.md +++ b/readme.md @@ -4,7 +4,6 @@ - [**Introduction**](#introduction) - [**Installation**](#installation) - [Git repository](#git-repository) - - [Singularity image on BB5](#singularity-image-on-bb5) - [Docker image](#docker-image) - [**Run the pipeline**](#run-the-pipeline) - [Running the reference Atlas pipeline](#running-the-reference-atlas-pipeline) @@ -35,15 +34,8 @@ To view the command for creating the Atlas as it is pushed to Nexus and consumed The Blue Brain Atlas Pipeline (BBAP) can be installed in three different ways: - via this [Git repository](#git-repository), -- via a [Singularity image](#singularity-image-on-bb5) (recommended), - via a [Docker image](#docker-image). -For computation time reason and ease of installation, it is recommended to run the pipeline -on the BB5 cluster via the Singularity image described [hereafter](#singularity-image-on-bb5). -You can log in to the cluster with -`ssh -l bbpv1.epfl.ch` -and your Gaspar password, or via the [OpenOnDemand service](https://bbpteam.epfl.ch/project/spaces/display/SDKB/JupyterHub+on+BB5). - Once the installation step is completed, go to [Run the pipeline](#run-the-pipeline) for the instructions to run the pipeline. ### Git repository @@ -67,55 +59,12 @@ Each package run as part of the pipeline is considered a pipeline dependency: - [bba-data-integrity-check](https://bbpteam.epfl.ch/project/spaces/display/BBKG/bba-data-check) - [bba-data-push](https://bbpteam.epfl.ch/project/spaces/display/BBKG/bba-data-push) -On BB5, most packages are available also as modules: -``` -module load unstable \ -snakemake \ -py-token-fetch \ -py-nexusforge \ -py-bba-datafetch \ -py-atlas-building-tools \ -py-bba-webexporter \ -py-data-integrity-check \ -py-bba-data-push -``` -Or they can be installed following the ‘Installation’ section in their Confluence documentation page. - -Now you can go to [Run the pipeline](#run-the-pipeline) for the instructions to run the pipeline. - - -### Singularity image on BB5 -A Singularity image (created from the [Docker image](#docker-image)) is available on BB5 in: -`/gpfs/bbp.cscs.ch/data/project/proj84/atlas_singularity_images/` - -The folder contains -- `blue_brain_atlas_pipeline_dev.sif`: development image regularly updated, -- `blue_brain_atlas_pipeline_.sif`: production image corresponding to a repository [tag](https://bbpgitlab.epfl.ch/dke/apps/blue_brain_atlas_pipeline/-/tags) - (such as `v0.5.2`). - -One can spawn the corresponding container with (example with dev) -1. `module load unstable singularityce` -2. `singularity shell /gpfs/bbp.cscs.ch/data/project/proj84/atlas_singularity_images/blue_brain_atlas_pipeline_dev.sif` -and run the following commands to copy the pipeline files in a path (e.g `$HOME`) where snakemake can write: -3. `cp -r /pipeline/blue_brain_atlas_pipeline $HOME` -4. `cd blue_brain_atlas_pipeline` - Now you can go to [Run the pipeline](#run-the-pipeline) for the instructions to run the pipeline. ### Docker image -A [Docker](https://docs.docker.com/reference) image containing all the pipeline dependencies is available in the Git [registry](https://bbpgitlab.epfl.ch/dke/apps/blue_brain_atlas_pipeline/container_registry/159): -`bbpgitlab.epfl.ch:5050/dke/apps/blue_brain_atlas_pipeline:` -where `` = `dev` or a repository tag. - -It can be pulled and run with -1. `docker login bbpgitlab.epfl.ch:5050 -u -p ` -2. `docker pull bbpgitlab.epfl.ch:5050/dke/apps/blue_brain_atlas_pipeline:` -3. `docker run -it bbpgitlab.epfl.ch:5050/dke/apps/blue_brain_atlas_pipeline: bash` -4. `cd blue_brain_atlas_pipeline` - -or converted into an **Apptainer** image with -`apptainer pull --docker-login docker://bbpgitlab.epfl.ch:5050/dke/apps/blue_brain_atlas_pipeline:` +A [Docker](https://docs.docker.com/reference) image containing all the pipeline dependencies +can be generated from the [`Dockerfile`](https://github.com/BlueBrain/bbp-atlas-pipeline/blob/develop/Dockerfile) provided in this repository. A benchmark of the resources to provision as required by the different pipeline steps is available [here](#profiling).