From 5d4fcb53e164dac05884ed9fcc1a3bce88df2cdc Mon Sep 17 00:00:00 2001
From: ZhaoXiaofei <cndfeifei@hotmail.com>
Date: Thu, 21 Sep 2023 01:44:16 +0800
Subject: [PATCH] Re-added back the code for the work-around of using the
 optitype_env conda env to run optitype 1.3.2 instead of its latest version
 due to https://github.com/FRED-2/OptiType/issues/125 and added comments to
 explain the three work-arounds for this issue.

---
 install-step-1-by-conda.sh | 25 ++++++++++++++++---------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/install-step-1-by-conda.sh b/install-step-1-by-conda.sh
index a9fd98d..0af3855 100644
--- a/install-step-1-by-conda.sh
+++ b/install-step-1-by-conda.sh
@@ -27,7 +27,7 @@ conda create -y -n $neoheadhunter
 #   ASNEO requires 'biopython<=1.79' (ASNEO code can be refactored to upgrade biopython)
 #   ERGO-II requires pytorch-lightning=0.8, but we will change a few lines of source code in ERGO-II
 #     in the next installation step to make it work with higher versions of pytorch-lightning
-#   podman will be used to provide a work-around for https://github.com/FRED-2/OptiType/issues/125
+#   podman can be used to provide a work-around for https://github.com/FRED-2/OptiType/issues/125
 $conda install -y -n $neoheadhunter python=3.10 xlrd \
     gcc openjdk parallel perl podman sshpass tcsh \
     perl-carp-assert psutil pyyaml requests-cache zlib \
@@ -40,18 +40,25 @@ $conda install -y -n $neoheadhunter python=3.10 xlrd \
 #   to solve this error (namely, export CONDA_OVERRIDE_CUDA="11.8" && export CONDA_CUDA_OVERRIDE="11.8").
 
 conda run -n $neoheadhunter pip install sj2psi # for ASNEO.py
-conda run -n $neoheadhunter podman pull quay.io/biocontainers/optitype:1.3.2--py27_3 # work-around for https://github.com/FRED-2/OptiType/issues/125
 
-# The optitype environment should be able to provide a work-around for https://github.com/FRED-2/OptiType/issues/125
-# However, it seems that conda and mamba cannot install the obsolete python versions that the previous versions of optitype depend on
-# Therefore, we commented out the following 4 lines of code
-# optitype=optitype_env
-# conda create -y -n $optitype
-# $conda install -y -n $optitype optitype=1.3.2
-# conda env export -n ${optitype} > ${optitype}.freeze.yml &&  conda list -e -n ${optitype} > ${optitype}.requirements.txt
+# > First work-around for https://github.com/FRED-2/OptiType/issues/125 : use podman to run OptiType
+#   Please set IS_PODMAN_USED_TO_WORKAROUND_OPTITYPE_MEM_LEAK=True in the Snakefile to enable this work-around.
+#   On some platforms, the error '''Error: command required for rootless mode with multiple IDs: exec: "newuidmap": executable file not found in $PATH''' pop up for this work-around. 
+conda run -n $neoheadhunter podman pull quay.io/biocontainers/optitype:1.3.2--py27_3
+
+# > Second work-around for https://github.com/FRED-2/OptiType/issues/125 : use another conda env to run OptiType
+#   Please set OTITYPE_CONDA_ENV=optitype_env in the Snakefile to enable this work-around.
+#   On some platforms, conda and mamba cannot install the obsolete python versions that the previous versions of optitype depend on
+optitype=optitype_env
+conda create -y -n $optitype
+$conda install -y -n $optitype optitype=1.3.2
+conda run -n ${optitype} pip install --upgrade pyomo # pyomo=5.7.3
+
+# > Third work-around for https://github.com/FRED-2/OptiType/issues/125 : manually set the comma_sep_hla_list config param to skip HLA typing. 
 
 # The following commands can generate the requirements and freeze files
 if false; then
+    conda env export -n ${optitype} > env/${optitype}.freeze.env_export.yml &&  conda list -e -n ${optitype} > env/${optitype}.requirements.list_e.txt
     conda list       -n ${neoheadhunter} -e | grep -v "^sj2psi=" > env/requirements.list_e_no_pypi.txt
     conda env export -n ${neoheadhunter}                         > env/freeze.env_export.yml
     conda env export -n ${neoheadhunter} --no-builds             > env/freeze.env_export_no_builds.yml