mirror of
https://github.com/RosettaCommons/foundry.git
synced 2026-06-04 13:24:22 +08:00
63 lines
2.5 KiB
Bash
63 lines
2.5 KiB
Bash
# USAGE INSTRUCTIONS:
|
||
# - copy this file and rename it to `.env` to use it.
|
||
# - do not commit the `.env` file to version control.
|
||
# - you will need to set the paths below as appropriate for your environment.
|
||
# We provide examples in the comments to give you an idea of the expected format.
|
||
|
||
# --- Mirrors to RCSB data ---
|
||
|
||
# The `PDB_MIRROR_PATH` is a path to a local mirror of the PDB database. It's
|
||
# expected that you use the same saving conventions as the RCSB PDB, which means:
|
||
# `1a2b` --> /path/to/pdb_mirror/a2/1a2b.cif.gz
|
||
# To set up a mirror, you can use tha atomworks commandline: `atomworks pdb sync /path/to/mirror`
|
||
PDB_MIRROR_PATH=
|
||
|
||
# The `CCD_MIRROR_PATH` is a path to a local mirror of the CCD database.
|
||
# It's expected that you use the same saving conventions as the RCSB CCD, which means:
|
||
# `HEM` --> /path/to/ccd_mirror/H/HEM/HEM.cif
|
||
# To set up a mirror, you can use the atomworks commandline: `atomworks ccd sync /path/to/mirror`
|
||
# If no mirror is provided, the internal biotite CCD will be used as a fallback. To provide a
|
||
# custom CCD for a ligand, you can place it in the in the CCD mirror path following the CCDs pattern.
|
||
# Example: /path/to/ccd_mirror/M/MYLIGAND1/MYLIGAND1.cif
|
||
CCD_MIRROR_PATH=
|
||
|
||
# --- Local MSA directories ---
|
||
LOCAL_MSA_DIRS=
|
||
|
||
|
||
# --- External tools ---
|
||
# The HBPLUS_PATH is a path to the hbplus tool, which is used for hydrogen bond calculation
|
||
# during training and during metrics computation.
|
||
# Example: /path/to/hbplus
|
||
HBPLUS_PATH=
|
||
|
||
# The `X3DNA_PATH` is a path to the x3dna tool, which is used for DNA structure analysis.
|
||
# Example: /path/to/x3dna-v2.4
|
||
X3DNA_PATH=
|
||
|
||
# For secondary structure prediction (not currently used)
|
||
DSSP_PATH=
|
||
|
||
# The `HHFILTER_PATH` is a path to the hhfilter tool from the HH-suite, which is used for
|
||
# filtering MSAs to reduce redundancy.
|
||
# Example: /path/to/hhsuite/build/bin/hhfilter
|
||
HHFILTER_PATH=
|
||
|
||
# The `MMSEQS2_PATH` is a path to the mmseqs2 tool, which is used for fast sequence searching.
|
||
# Example: /path/to/mmseqs-gpu/bin/mmseqs
|
||
MMSEQS2_PATH=
|
||
|
||
# CollabFold MMseqs2 database paths for GPU and CPU usage.
|
||
|
||
# Local access (preferred)
|
||
# NOTE: MMseqs2 databases are best stored on local drives of compute nodes for performance
|
||
COLABFOLD_LOCAL_DB_PATH_GPU=
|
||
COLABFOLD_LOCAL_DB_PATH_CPU=
|
||
|
||
# Network access (fallback; may cause IO-related issues)
|
||
COLABFOLD_NET_DB_PATH_GPU=
|
||
COLABFOLD_NET_DB_PATH_CPU=
|
||
|
||
# Foundry checkpoint directories (colon-separated list). Example:
|
||
# /path/to/user/install/dir:/home/username/.foundry/checkpoints
|
||
FOUNDRY_CHECKPOINT_DIRS= |