Create new conda env for optitype to work-around the issue at FRED-2/…

…OptiType#125

install-step-1-by-conda.sh

@@ -7,26 +7,32 @@ bioconda="-c https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/" # -c
 pytorch="-c https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/" # -c pytorch
 
 conda=mamba
-neohunter=nhh # neohunter
+neoheadhunter=nhh # neoheadhunter
 
 conda install -y mamba -n base
-conda create -y -n $neohunter
+conda create -y -n $neoheadhunter
 
 # common bin, common lib, machine-learning lib, bioinformatics bin, bioinformatics lib 
 # note: 
 #   pyfasta is replaced by pyfaidx
 #   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
-$conda install -y -n $neohunter python=3.10 \
+$conda install -y -n $neoheadhunter python=3.10 \
     gcc openjdk parallel perl sshpass tcsh \
     perl-carp-assert psutil pyyaml requests-cache zlib \
     pandas pytorch pytorch-lightning scikit-learn xgboost \
     bcftools blast bwa ensembl-vep gatk kallisto mosdepth optitype samtools snakemake star 'star-fusion>=1.11' \
     'biopython<=1.79' pybiomart pyfaidx pysam
 
-pip install sj2psi # for ASNEO.py
+conda run -n $neoheadhunter pip install sj2psi # for ASNEO.py
+
+# The optitype environment provides a work-around for the issue at https://github.com/FRED-2/OptiType/issues/125
+optitype=optitype_env
+conda create -y -n $optitype
+$conda install -y -n $optitype optitype=1.3.2 
 
 # The following command can be run to generate the freeze and requirement files
-# conda env export > freeze.yml &&  conda list -e > requirements.txt
+# conda env export -n ${neoheadhunter} > ${neoheadhunter}.freeze.yml &&  conda list -e -n ${neoheadhunter} > ${neoheadhunter}.requirements.txt
+# conda env export -n ${optitype} > ${optitype}.freeze.yml &&  conda list -e -n ${optitype} > ${optitype}.requirements.txt
 

optitype_env.freeze.yml

@@ -0,0 +1,125 @@
+name: optitype_env
+channels:
+  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
+  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
+  - http://conda.anaconda.org/gurobi
+  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
+  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
+  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
+  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
+  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/fastai/
+  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
+  - appdirs=1.4.4=pyh9f0ad1d_0
+  - backports=1.0=pyhd8ed1ab_3
+  - backports.functools_lru_cache=1.6.1=py_0
+  - backports_abc=0.5=py_1
+  - blosc=1.21.4=h0f2a231_0
+  - bzip2=1.0.8=h7f98852_4
+  - c-ares=1.19.1=hd590300_0
+  - ca-certificates=2023.5.7=hbcca054_0
+  - certifi=2019.11.28=py27h8c360ce_1
+  - cycler=0.10.0=py_2
+  - dbus=1.13.6=hfdff14a_1
+  - enum34=1.1.10=py27h8c360ce_1
+  - expat=2.5.0=hcb278e6_1
+  - fontconfig=2.14.2=h14ed4e7_0
+  - freetype=2.12.1=hca18f0e_1
+  - funcsigs=1.0.2=py_3
+  - functools32=3.2.3.2=py_3
+  - future=0.18.2=py27h8c360ce_1
+  - futures=3.3.0=py27h8c360ce_1
+  - gettext=0.21.1=h27087fc_0
+  - glib=2.66.3=h58526e2_0
+  - glpk=5.0=h445213a_0
+  - gmp=6.2.1=h58526e2_0
+  - gst-plugins-base=1.14.5=h0935bb2_2
+  - gstreamer=1.14.5=h36ae1b5_2
+  - hdf5=1.10.5=nompi_h5b725eb_1114
+  - htslib=1.17=h6bc39ce_1
+  - icu=64.2=he1b5a44_1
+  - jpeg=9e=h0b41bf4_3
+  - keyutils=1.6.1=h166bdaf_0
+  - kiwisolver=1.1.0=py27h9e3301b_1
+  - krb5=1.20.1=hf9c8cef_0
+  - ld_impl_linux-64=2.40=h41732ed_0
+  - libblas=3.9.0=17_linux64_openblas
+  - libcblas=3.9.0=17_linux64_openblas
+  - libclang=9.0.1=default_hb4e5071_5
+  - libcurl=7.87.0=h6312ad2_0
+  - libdeflate=1.13=h166bdaf_0
+  - libedit=3.1.20191231=he28a2e2_2
+  - libev=4.33=h516909a_1
+  - libexpat=2.5.0=hcb278e6_1
+  - libffi=3.2.1=he1b5a44_1007
+  - libgcc-ng=13.1.0=he5830b7_0
+  - libgfortran-ng=13.1.0=h69a702a_0
+  - libgfortran5=13.1.0=h15d22d2_0
+  - libglib=2.66.3=hbe7bbb4_0
+  - libgomp=13.1.0=he5830b7_0
+  - libiconv=1.17=h166bdaf_0
+  - liblapack=3.9.0=17_linux64_openblas
+  - libllvm9=9.0.1=default_hc23dcda_7
+  - libnghttp2=1.51.0=hdcd2b5c_0
+  - libopenblas=0.3.23=pthreads_h80387f5_0
+  - libpng=1.6.39=h753d276_0
+  - libsqlite=3.42.0=h2797004_0
+  - libssh2=1.10.0=haa6b8db_3
+  - libstdcxx-ng=13.1.0=hfd8a6a1_0
+  - libuuid=2.38.1=h0b41bf4_0
+  - libxcb=1.15=h0b41bf4_0
+  - libxkbcommon=0.10.0=he1b5a44_0
+  - libxml2=2.9.10=hee79883_0
+  - libzlib=1.2.13=hd590300_5
+  - lz4-c=1.9.4=hcb278e6_0
+  - lzo=2.10=h516909a_1000
+  - matplotlib=2.2.5=ha770c72_3
+  - matplotlib-base=2.2.5=py27h250f245_1
+  - mock=3.0.5=py27h8c360ce_1
+  - ncurses=6.4=hcb278e6_0
+  - nose=1.3.7=py27h8c360ce_1004
+  - nspr=4.35=h27087fc_0
+  - nss=3.89=he45b914_0
+  - numexpr=2.7.1=py27hb3f55d8_0
+  - numpy=1.15.4=py27h8b7e671_1002
+  - openssl=1.1.1u=hd590300_0
+  - optitype=1.3.2=py27_3
+  - pandas=0.24.2=py27hb3f55d8_0
+  - pcre=8.45=h9c3ff4c_0
+  - pip=20.1.1=pyh9f0ad1d_0
+  - ply=3.11=py_1
+  - pthread-stubs=0.4=h36c2ea0_1001
+  - pyomo=5.6.9=py27h8c360ce_1
+  - pyparsing=2.4.7=pyh9f0ad1d_0
+  - pyqt=5.12.3=py27hcca6a23_1
+  - pysam=0.20.0=py27h7835474_0
+  - pytables=3.5.2=py27h9f153d1_2
+  - python=2.7.15=h5a48372_1011_cpython
+  - python-dateutil=2.8.1=py_0
+  - python_abi=2.7=1_cp27mu
+  - pytz=2020.1=pyh9f0ad1d_0
+  - pyutilib=6.0.0=pyh9f0ad1d_0
+  - qt=5.12.5=hd8c4c69_1
+  - razers3=3.5.8=h6dccd9a_4
+  - readline=8.2=h8228510_1
+  - samtools=1.17=hd87286a_1
+  - setuptools=44.0.0=py27_0
+  - singledispatch=3.6.1=pyh44b312d_0
+  - six=1.16.0=pyh6c4a22f_0
+  - snappy=1.1.10=h9fff704_0
+  - sqlite=3.42.0=h2c6b66d_0
+  - subprocess32=3.5.4=py27h516909a_0
+  - tk=8.6.12=h27826a3_0
+  - tornado=5.1.1=py27h14c3975_1000
+  - wheel=0.37.1=pyhd8ed1ab_0
+  - xorg-libxau=1.0.11=hd590300_0
+  - xorg-libxdmcp=1.1.3=h7f98852_0
+  - xz=5.2.6=h166bdaf_0
+  - zlib=1.2.13=hd590300_5
+  - zstd=1.5.2=hfc55251_7
+  - pip:
+      - pyqt5-sip==4.19.18
+      - pyqtwebengine==5.12.1
+prefix: /home/zhaoxiaofei/miniconda3/envs/optitype_env

optitype_env.requirements.txt

@@ -0,0 +1,114 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+_libgcc_mutex=0.1=conda_forge
+_openmp_mutex=4.5=2_gnu
+appdirs=1.4.4=pyh9f0ad1d_0
+backports=1.0=pyhd8ed1ab_3
+backports.functools_lru_cache=1.6.1=py_0
+backports_abc=0.5=py_1
+blosc=1.21.4=h0f2a231_0
+bzip2=1.0.8=h7f98852_4
+c-ares=1.19.1=hd590300_0
+ca-certificates=2023.5.7=hbcca054_0
+certifi=2019.11.28=py27h8c360ce_1
+cycler=0.10.0=py_2
+dbus=1.13.6=hfdff14a_1
+enum34=1.1.10=py27h8c360ce_1
+expat=2.5.0=hcb278e6_1
+fontconfig=2.14.2=h14ed4e7_0
+freetype=2.12.1=hca18f0e_1
+funcsigs=1.0.2=py_3
+functools32=3.2.3.2=py_3
+future=0.18.2=py27h8c360ce_1
+futures=3.3.0=py27h8c360ce_1
+gettext=0.21.1=h27087fc_0
+glib=2.66.3=h58526e2_0
+glpk=5.0=h445213a_0
+gmp=6.2.1=h58526e2_0
+gst-plugins-base=1.14.5=h0935bb2_2
+gstreamer=1.14.5=h36ae1b5_2
+hdf5=1.10.5=nompi_h5b725eb_1114
+htslib=1.17=h6bc39ce_1
+icu=64.2=he1b5a44_1
+jpeg=9e=h0b41bf4_3
+keyutils=1.6.1=h166bdaf_0
+kiwisolver=1.1.0=py27h9e3301b_1
+krb5=1.20.1=hf9c8cef_0
+ld_impl_linux-64=2.40=h41732ed_0
+libblas=3.9.0=17_linux64_openblas
+libcblas=3.9.0=17_linux64_openblas
+libclang=9.0.1=default_hb4e5071_5
+libcurl=7.87.0=h6312ad2_0
+libdeflate=1.13=h166bdaf_0
+libedit=3.1.20191231=he28a2e2_2
+libev=4.33=h516909a_1
+libexpat=2.5.0=hcb278e6_1
+libffi=3.2.1=he1b5a44_1007
+libgcc-ng=13.1.0=he5830b7_0
+libgfortran-ng=13.1.0=h69a702a_0
+libgfortran5=13.1.0=h15d22d2_0
+libglib=2.66.3=hbe7bbb4_0
+libgomp=13.1.0=he5830b7_0
+libiconv=1.17=h166bdaf_0
+liblapack=3.9.0=17_linux64_openblas
+libllvm9=9.0.1=default_hc23dcda_7
+libnghttp2=1.51.0=hdcd2b5c_0
+libopenblas=0.3.23=pthreads_h80387f5_0
+libpng=1.6.39=h753d276_0
+libsqlite=3.42.0=h2797004_0
+libssh2=1.10.0=haa6b8db_3
+libstdcxx-ng=13.1.0=hfd8a6a1_0
+libuuid=2.38.1=h0b41bf4_0
+libxcb=1.15=h0b41bf4_0
+libxkbcommon=0.10.0=he1b5a44_0
+libxml2=2.9.10=hee79883_0
+libzlib=1.2.13=hd590300_5
+lz4-c=1.9.4=hcb278e6_0
+lzo=2.10=h516909a_1000
+matplotlib=2.2.5=ha770c72_3
+matplotlib-base=2.2.5=py27h250f245_1
+mock=3.0.5=py27h8c360ce_1
+ncurses=6.4=hcb278e6_0
+nose=1.3.7=py27h8c360ce_1004
+nspr=4.35=h27087fc_0
+nss=3.89=he45b914_0
+numexpr=2.7.1=py27hb3f55d8_0
+numpy=1.15.4=py27h8b7e671_1002
+openssl=1.1.1u=hd590300_0
+optitype=1.3.2=py27_3
+pandas=0.24.2=py27hb3f55d8_0
+pcre=8.45=h9c3ff4c_0
+pip=20.1.1=pyh9f0ad1d_0
+ply=3.11=py_1
+pthread-stubs=0.4=h36c2ea0_1001
+pyomo=5.6.9=py27h8c360ce_1
+pyparsing=2.4.7=pyh9f0ad1d_0
+pyqt=5.12.3=py27hcca6a23_1
+pyqt5-sip=4.19.18=pypi_0
+pyqtwebengine=5.12.1=pypi_0
+pysam=0.20.0=py27h7835474_0
+pytables=3.5.2=py27h9f153d1_2
+python=2.7.15=h5a48372_1011_cpython
+python-dateutil=2.8.1=py_0
+python_abi=2.7=1_cp27mu
+pytz=2020.1=pyh9f0ad1d_0
+pyutilib=6.0.0=pyh9f0ad1d_0
+qt=5.12.5=hd8c4c69_1
+razers3=3.5.8=h6dccd9a_4
+readline=8.2=h8228510_1
+samtools=1.17=hd87286a_1
+setuptools=44.0.0=py27_0
+singledispatch=3.6.1=pyh44b312d_0
+six=1.16.0=pyh6c4a22f_0
+snappy=1.1.10=h9fff704_0
+sqlite=3.42.0=h2c6b66d_0
+subprocess32=3.5.4=py27h516909a_0
+tk=8.6.12=h27826a3_0
+tornado=5.1.1=py27h14c3975_1000
+wheel=0.37.1=pyhd8ed1ab_0
+xorg-libxau=1.0.11=hd590300_0
+xorg-libxdmcp=1.1.3=h7f98852_0
+xz=5.2.6=h166bdaf_0
+zlib=1.2.13=hd590300_5
+zstd=1.5.2=hfc55251_7