diff --git a/tensorqtl/1.0.8/.gitignore b/tensorqtl/1.0.8/.gitignore new file mode 100755 index 0000000..d037007 --- /dev/null +++ b/tensorqtl/1.0.8/.gitignore @@ -0,0 +1 @@ +tensorqtl* diff --git a/tensorqtl/1.0.8/README.md b/tensorqtl/1.0.8/README.md new file mode 100755 index 0000000..b39c565 --- /dev/null +++ b/tensorqtl/1.0.8/README.md @@ -0,0 +1,73 @@ +# Installation + +```bash +## Commands used for installing the software + +# Create and enter a python virtual environment (we'll actually need R and +# some system utilities made available through conda_R/4.3). Note that we're +# on the 'caracol' node! +module load conda_R/4.3 +python -m venv ./tensorqtl_venv +source tensorqtl_venv/bin/activate + +# Upgrade pip and install CUDA-aware pytorch +python -m pip install --upgrade pip +python -m pip install torch==1.11.0+cu113 -f https://download.pytorch.org/whl/torch_stable.html + +# Install tensorQTL 1.0.8 (The git repo doesn't have a 1.0.8 release yet, so +# we'll clone the latest commit) +git clone git@github.com:broadinstitute/tensorqtl.git +cd tensorqtl +git checkout 890f32977f36d7e5be2d0820c7f382764617b553 + +# Despite not explicitly installing tensorqtl==1.0.8 (which isn't available +# from pip yet!), it does appear to be installed as a dependency at version +# 1.0.8 +python -m pip install -r install/requirements.txt + +# Exit virtual environment +deactivate + +## Ignore all downloaded/installed files +echo "tensorqtl*" > .gitignore + +# Allow fairly relaxed permissions, but protect against accidental changes to +# the virtual environment +chmod -R 775 /jhpce/shared/jhpce/libd/tensorqtl/1.0.8 +chmod -R 755 /jhpce/shared/jhpce/libd/tensorqtl/1.0.8/tensorqtl_venv + +## Version control files +git add .gitignore +git add README.md +``` + +# Reproducibility + +```bash +## Evaluate the following commands +module list +date +echo "User: ${USER}" +echo "Hostname: ${HOSTNAME}" +``` + +```bash +## copy paste the output from the previous commands +$ 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 + + + +$ date +Fri Jun 16 11:44:40 EDT 2023 + +$ echo "User: ${USER}" +User: neagles + +$ echo "Hostname: ${HOSTNAME}" +Hostname: compute-126.cm.cluster +```