Add source-related files for tensorqtl 1.0.8

tensorqtl/1.0.8/.gitignore

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+tensorqtl*

tensorqtl/1.0.8/README.md

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+# 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 [email protected]: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
+```