Install tensorQTL 1.0.8. Needed to independently install appropriate …

…R and python versions (and their dependencies), as conda_R/4.3 is a bit different at SLURM. This approach also doesn't rely on user-specific R packages ('qvalue')

tensorqtl/1.0.8/README.md

@@ -16,24 +16,37 @@ rm v1.0.8.tar.gz
 source /jhpce/shared/jhpce/core/conda/miniconda3-23.3.1/etc/profile.d/conda.sh
 conda create -y -p $PWD/tensorqtl_env -c conda-forge mamba
 conda activate $PWD/tensorqtl_env
-mamba install -y -c anaconda python==3.8.5
-mamba install -y -c conda-forge r-base==4.2.0
 
-#  Install their recommended python dependencies, a version of PyTorch
-#  compatible with our CUDA/ GPU hardware, and the tensorQTL package itself
+#  'rpy2' seems to need a very recent version of python, but recent versions of
+#  python don't have versions of torch + CUDA compatible with our GPUs. So we
+#  have to be careful about the versions of python, rpy2, and torch here
+mamba install -y -c anaconda python==3.9
+pip install rpy2==3.5.12
 pip install torch==1.11.0+cu113 -f https://download.pytorch.org/whl/torch_stable.html
+
+#  Otherwise, install dependencies as recommended in the repo, and add some more
+#  packages we frequently use
 pip install -r tensorqtl-1.0.8/install/requirements.txt
+pip install session-info pyhere plotnine
 
+#  Now install tensorqtl itself
 pip install tensorqtl==1.0.8
 
+#  'rpy2' needs R and the 'qvalue' package
+mamba install -y -c conda-forge r-base==4.2.0
+mamba install -y -c bioconda bioconductor-qvalue
+
 conda deactivate
 
 ## Ignore all downloaded/installed files
 echo "tensorqtl*" > .gitignore
 
 #  Allow fairly relaxed permissions, but protect against accidental changes to
 #  the conda environment
-chmod -R 775 .
+chmod 775 .
+chmod 775 -R tensorqtl-1.0.8
+chmod 775 README.md
+chmod 775 .gitignore
 chmod -R 555 tensorqtl_env
 
 ## Version control files
@@ -56,18 +69,14 @@ echo "Node name: ${SLURMD_NODENAME}"
 $ module list
 
 Currently Loaded Modules:
-  1) matlab/R2019a     4) sge/8.1.9                       7) JHPCE_CENTOS7_DEFAULT_ENV
-  2) stata/17          5) gcc/4.4.7                       8) conda/3-4.11.0
-  3) JHPCE_tools/1.0   6) COMMUNITY_CENTOS7_DEFAULT_ENV   9) conda_R/4.3
-
+  1) JHPCE_tools/3.0
 
+
 
 $ date
-Fri Jun 16 11:44:40 EDT 2023
-
+Tue Sep 26 03:40:36 PM EDT 2023
 $ echo "User: ${USER}"
 User: neagles
-
-$ echo "Hostname: ${HOSTNAME}"
-Hostname: compute-126.cm.cluster
+$ echo "Node name: ${SLURMD_NODENAME}"
+Node name: compute-070
 ```