diff --git a/README.rst b/README.rst index b5357fef..2d1a2b8f 100644 --- a/README.rst +++ b/README.rst @@ -19,9 +19,10 @@ BIDS App Bootstrap (BABS) is a reproducible, generalizable, and scalable Python package for BIDS App analysis of large datasets. It uses `DataLad `_ and adopts the `FAIRly big framework `_. -Currently it is compatible with SGE and Slurm clusters. +Currently, BABS supports jobs submissions and audits on Sun Grid Engine (SGE) and Slurm +high performance computing (HPC) clusters. -BABS functions +BABS programs --------------------- .. image:: https://github.com/PennLINC/babs/raw/main/docs/source/_static/babs_cli.png @@ -32,3 +33,19 @@ Schematic of BABS workflow ---------------------------- .. image:: https://github.com/PennLINC/babs/raw/main/docs/source/_static/babs_workflow.png .. Note: this image is taken from the main branch, so it's normal that docs built from branches is not up-to-date. + +Background and Significance +------------------------------- + +Neuroimaging research faces a crisis of reproducibility. +With massive sample sizes and greater data complexity, this problem becomes more acute. +The BIDS Apps - the software operating on BIDS data - have provided a substantial advance. +However, even using BIDS Apps, a full audit trail of data processing is a necessary prerequisite for fully reproducible research. +Obtaining a faithful record of the audit trail is challenging - especially for large datasets. +Recently, the `FAIRly big framework `_ +was introduced as a way to facilitate reproducible processing of large-scale data +by leveraging `DataLad `_ - a version control system for data management. +However, the current implementation of this framework remains challenging to general users. + +BABS was developed to address these challenges +and to facilitate the reproducible application of BIDS Apps to large-scale datasets. diff --git a/docs/source/index.rst b/docs/source/index.rst index fad28eb6..7a955d5c 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -2,11 +2,14 @@ .. include:: ../../README.rst .. include:: links.rst -Documentations +Documentation ================== +Please follow the instructions in this documentation to use BABS. +Currently there is no alternative usage of BABS. + .. toctree:: - :maxdepth: 2 + :maxdepth: 1 overview installation diff --git a/docs/source/installation.rst b/docs/source/installation.rst index ea3d0cfc..1581a4cd 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -4,6 +4,20 @@ Installation .. contents:: Table of Contents +Step 0. System requirement +============================================= + +Currently BABS supports applications on high performance computing (HPC) clusters, +specifically, Sun Grid Engine (SGE) and Slurm clusters. +Please make sure Singularity or one of its successors +(i.e. SingularityCE or Apptainer which BABS currently supports) is available on the cluster. + +Currently, BABS is **not** compatible with: + +* cloud-based computing platforms (e.g., Amazon Web Services [AWS]); +* local computers where a job scheduling system or Singularity software is not installed; +* computing nodes without job scheduling systems. + Step 1. Prepare a conda environment for BABS =============================================