From d018061f152b6af6257ad95937528f00e6e4d1b1 Mon Sep 17 00:00:00 2001 From: ChrisGadek1 Date: Mon, 15 Jun 2026 19:04:00 +0200 Subject: [PATCH] Fix typos and improve clarity in README instructions --- README.md | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index f0b69e8..3ad5112 100644 --- a/README.md +++ b/README.md @@ -58,12 +58,9 @@ pytest ./tests ## Running on AFDB structures locally -Requires having a directory with AFDB structures and a text file containing list of AFDB IDs with `\n` delimeter. +Requires having a directory with AFDB structures and a text file containing list of AFDB IDs with `\n` delimeter. Assuming all steps from `Instalation and activation` succeded ``` -# -# Assuming all steps from `Instalation and activation` succeded -# FRIDATA_PATH="" AFDB_PATH="" IDS_PATH="" @@ -107,8 +104,10 @@ python3 -m pip install -e . 2. Now FRIdata can be run as a CLI tool ``` -$ fridata <...> -```3dc54 (Use ids_file tokens (e.g. plain UniProt) plus chain as the canonical dataset index keys) +fridata <...> +``` + +(Use ids_file tokens (e.g. plain UniProt) plus chain as the canonical dataset index keys) ## Running on HPC @@ -122,7 +121,7 @@ Prerequisites: - `AFDB_PATH`: path to AFDB structures (can be empty directory - structures will be fetched there) - `DATA_PATH`: path to the parent diretory of all generated output data - Optional ENV vars with default values: - - `COMMON_SLURM_PATH`: path to common_slurn.sh, defaults to `$DEEPFRI_PATH/FRIdata/scripts/hpc/common_slurm.sh` + - `COMMON_SLURM_PATH`: path to common_slurm.sh, defaults to `$DEEPFRI_PATH/FRIdata/scripts/hpc/common_slurm.sh` - `LAUNCH_WORKER_SLURM_PATH`: path to launch_worker_slurm.sh, defaults to `$DEEPFRI_PATH/FRIdata/scripts/hpc/launch_workers_slurm.sh` - `MEMORY_LIMIT`: memory limit per Dask worker, defaults to `288GiB` - `IP_INTERFACE`: network unix interface, where dask workers are connected. Defaults to `ens1f0` @@ -151,7 +150,7 @@ chmod u+x -R scripts/hpc/cpu ./scripts/hpc/initialize_slurm.sh [--cpu] ``` -4. Schedule SBatch script into the HPC with all the args specified. Operations to be chosen are: `sequences`, `coordinates`, `embeddings` +4. Schedule sbatch script into the HPC with all the args specified. Operations to be chosen are: `sequences`, `coordinates`, `embeddings` For CPU: