Use podman image instead of another conda env to work-around the issu…

…e at FRED-2/OptiType#125 (this commit only affect the installation scripts.)

nhh.freeze.yml → freeze.yml

@@ -55,6 +55,8 @@ dependencies:
   - click=8.1.3=unix_pyhd8ed1ab_2
   - clustalo=1.2.4=hdbdd923_7
   - clustalw=2.1=h4ac6f70_9
+  - cni=1.0.1=ha975731_1
+  - cni-plugins=1.0.1=ha8f183a_0
   - coin-or-cbc=2.10.10=h9002f0b_0
   - coin-or-cgl=0.60.7=h516709c_0
   - coin-or-clp=1.17.8=h1ee7a9c_0
@@ -67,7 +69,9 @@ dependencies:
   - conda-package-handling=2.0.2=pyh38be061_0
   - conda-package-streaming=0.8.0=pyhd8ed1ab_0
   - configargparse=1.5.3=pyhd8ed1ab_0
+  - conmon=2.1.7=h748d886_0
   - connection_pool=0.0.3=pyhd3deb0d_0
+  - containers-common=0.31.1=ha770c72_0
   - contourpy=1.1.0=py310hd41b1e2_0
   - cryptography=39.0.0=py310h65dfdc0_0
   - cuda-version=11.8=h70ddcb2_2
@@ -122,6 +126,7 @@ dependencies:
   - google-crc32c=1.1.2=py310he8fe98e_4
   - google-resumable-media=2.5.0=pyhd8ed1ab_0
   - googleapis-common-protos=1.59.1=pyhd8ed1ab_0
+  - gpgme=1.18.0=h27087fc_0
   - graphite2=1.3.13=h58526e2_1001
   - grpcio=1.51.1=py310h5b20944_0
   - gsl=2.7=he838d99_0
@@ -144,6 +149,7 @@ dependencies:
   - jmespath=1.0.1=pyhd8ed1ab_0
   - joblib=1.2.0=pyhd8ed1ab_0
   - jpeg=9e=h0b41bf4_3
+  - jq=1.6=h36c2ea0_1000
   - jsonpatch=1.32=pyhd8ed1ab_0
   - jsonpointer=2.0=py_0
   - jsonschema=4.17.3=pyhd8ed1ab_0
@@ -158,6 +164,7 @@ dependencies:
   - lerc=4.0.0=h27087fc_0
   - libabseil=20220623.0=cxx17_h05df665_6
   - libarchive=3.6.2=hc8874e4_0
+  - libassuan=2.5.6=h59595ed_0
   - libblas=3.9.0=17_linux64_openblas
   - libbrotlicommon=1.0.9=h166bdaf_9
   - libbrotlidec=1.0.9=h166bdaf_9
@@ -180,6 +187,7 @@ dependencies:
   - libgfortran5=13.1.0=h15d22d2_0
   - libglib=2.76.3=hebfc3b9_0
   - libgomp=13.1.0=he5830b7_0
+  - libgpg-error=1.47=h71f35ed_0
   - libgrpc=1.51.1=h05bd8bd_0
   - libhwloc=2.9.1=hd6dc26d_0
   - libiconv=1.17=h166bdaf_0
@@ -196,6 +204,8 @@ dependencies:
   - libpng=1.6.39=h753d276_0
   - libprotobuf=3.21.12=h3eb15da_0
   - libsanitizer=13.1.0=hfd8a6a1_0
+  - libseccomp=2.4.4=h166bdaf_3
+  - libslirp=4.4.0=h329b89f_1
   - libsodium=1.0.18=h36c2ea0_1
   - libsolv=0.7.24=hfc55251_1
   - libsqlite=3.42.0=h2797004_0
@@ -239,6 +249,7 @@ dependencies:
   - numpy=1.25.0=py310ha4c1d20_0
   - oauth2client=4.1.3=py_0
   - oauthlib=3.2.2=pyhd8ed1ab_0
+  - oniguruma=6.9.8=h166bdaf_0
   - openjdk=17.0.3=h58dac75_5
   - openjpeg=2.5.0=h7d73246_1
   - openssl=1.1.1u=hd590300_0
@@ -371,6 +382,7 @@ dependencies:
   - pluggy=1.2.0=pyhd8ed1ab_0
   - ply=3.11=py_1
   - poa=2.0=h031d066_5
+  - podman=4.5.1=hc02c970_0
   - pooch=1.7.0=pyha770c72_3
   - prettytable=3.7.0=pyhd8ed1ab_0
   - protobuf=4.21.12=py310heca2aa9_0
@@ -424,6 +436,7 @@ dependencies:
   - rsa=4.9=pyhd8ed1ab_0
   - ruamel.yaml=0.17.32=py310h2372a71_0
   - ruamel.yaml.clib=0.2.7=py310h1fa729e_1
+  - runc=1.1.0=h77c71de_0
   - s3transfer=0.6.1=pyhd8ed1ab_0
   - samtools=1.6=hcd7b337_9
   - scikit-learn=1.2.2=py310hf7d194e_2
@@ -434,6 +447,7 @@ dependencies:
   - slacker=0.14.0=py_0
   - slclust=02022010=1
   - sleef=3.5.1=h9b69904_2
+  - slirp4netns=1.1.8=h329b89f_0
   - smart_open=6.3.0=pyhd8ed1ab_1
   - smmap=3.0.5=pyh44b312d_0
   - snakemake=7.29.0=hdfd78af_0

install-step-1-by-conda.sh

@@ -12,27 +12,31 @@ neoheadhunter=nhh # neoheadhunter
 conda install -y mamba -n base
 conda create -y -n $neoheadhunter
 
-# common bin, common lib, machine-learning lib, bioinformatics bin, bioinformatics lib 
+# Order of packages: 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
+#   podman will be used to provide a work-around for https://github.com/FRED-2/OptiType/issues/125
 $conda install -y -n $neoheadhunter python=3.10 \
-    gcc openjdk parallel perl sshpass tcsh \
+    gcc openjdk parallel perl podman 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
 
 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 
+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 3-4 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
 
 # The following command can be run to generate the freeze and requirement files
-# 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
+# conda env export -n ${neoheadhunter} > freeze.yml &&  conda list -e -n ${neoheadhunter} > requirements.txt