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Fix typos and improve clarity in README instructions #16

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PawelSzczerbiak merged 1 commit into from
Jun 18, 2026
Merged

Fix typos and improve clarity in README instructions #16

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15 changes: 7 additions & 8 deletions README.md
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Expand Up @@ -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="<repository path>"
AFDB_PATH="<AFDB structures directory path>"
IDS_PATH="<AFDB IDs file path>"
Expand Down Expand Up @@ -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

Expand All @@ -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`
Expand Down Expand Up @@ -151,7 +150,7 @@ chmod u+x -R scripts/hpc/cpu
./scripts/hpc/initialize_slurm.sh <path to .conda> [--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:
Expand Down
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