Environment variables

Most wrappers find their tool from an explicit constructor argument first, then an environment variable, then conventional locations such as ~/<Tool>, then a mhctools fetch snapshot. The exact order varies a little by wrapper, and mhctools ls shows which one was found. "Interpreter" variables name a separate Python that has the model's dependencies, so heavy stacks (torch, TensorFlow) stay out of the environment mhctools runs in.

Locating tools and models

Variable	Used by	Meaning
MHCTOOLS_DATA_DIR	fetch, ls, every fetched snapshot	Root for mhctools-managed snapshots. Default is the platform user-data directory.
NETMHC_BUNDLE_HOME	NetChop	A bundle directory that contains your licensed DTU tools.
NETCHOP_HOME	NetChop	The directory containing bin/netChop.
IEDB_MHCI_EXECUTABLE	SMM, SMM-PMBEC	Launcher that runs IEDB's predict_binding.py.
MIXMHCPRED_PATH	MixMHCpred	Your MixMHCpred release.
PRIME_EXECUTABLE	PRIME	The PRIME executable.
BIGMHC_DIR	BigMHC	A BigMHC clone.
CAPHLA_HOME	CapHLA	A CapHLA snapshot.
DEEPIMMUNO_HOME	DeepImmuno	A DeepImmuno checkout.
DEEPTAP_HOME	DeepTAP	A DeepTAP checkout.
ERAMER_HOME, ERAMER_PWM	ERAMER, eramer-step	An ERAMER checkout, or the path to its PWM.xlsx.
MIXTCRPRED_HOME	MixTCRpred	A MixTCRpred checkout.
NETCLEAVE_DIR	NetCleave	A NetCleave clone.
NETTCR_DIR	NetTCR	A NetTCR checkout.
PEPTIVERSE_HOME, PEPTIVERSE_ESM_HOME	PeptiVerse	The pinned PeptiVerse snapshot and local ESM2 weights.
PLIFEPRED2_HOME, PFEATURE_HOME	PlifePred2	The plifepred2 package and the pinned Pfeature checkout.
TLIMMUNO2_HOME	TLimmuno2	A TLimmuno2 clone.
TULIP_HOME	Tulip	A TULIP-TCR checkout.

Choosing an interpreter

Variable	Used by	Needs
DEEPIMMUNO_PYTHON	DeepImmuno	TensorFlow with Keras 2, or newer TensorFlow plus tf-keras
TLIMMUNO2_PYTHON	TLimmuno2	Same as DeepImmuno
DEEPTAP_PYTHON	DeepTAP	torch, pytorch_lightning, numpy, pandas
MIXTCRPRED_PYTHON	MixTCRpred	torch, torchvision, pytorch_lightning, numpy, pandas, scipy, sklearn
TULIP_PYTHON	Tulip	An isolated Python 3.11 with torch and transformers==4.32.1
PEPTIVERSE_PYTHON	PeptiVerse	torch, transformers==4.46.0, xgboost, lightning
PLIFEPRED2_PYTHON	PlifePred2	The plifepred2 runtime
NETCLEAVE_PYTHON	NetCleave	The NetCleave runtime
PEPSICKLE_PYTHON	Pepsickle	Interpreter for subprocess-isolated inference
PEPSICKLE_GB_PYTHON	Pepsickle gradient-boosted models	A Python 3.8 runtime with scikit-learn 0.23.2; see cleavage models

A *_PYTHON path that does not exist raises an error rather than falling back. Sidecar interpreters run with PYTHONNOUSERSITE=1, so packages installed with pip install --user are invisible to them; install into the interpreter itself.

TF_USE_LEGACY_KERAS=1 is set by the DeepImmuno and TLimmuno2 wrappers for their subprocess; you do not need to set it yourself.

Testing

Variable	Meaning
MHCTOOLS_TEST_ENV	Path to an activate.sh for ./test.sh; /dev/null disables it. See testing.
TEST_SH_MAX, TEST_SH_MIN, PER_WORKER_GB	Worker limits for ./test.sh.