From 24f011801314157fbfcaace5af5b19fdfdf52e8d Mon Sep 17 00:00:00 2001
From: Arthur Zalevsky <aozalevsky@gmail.com>
Date: Thu, 29 Feb 2024 17:33:29 -0800
Subject: [PATCH] added singularity recipe file

---
 docker/README.md       | 15 ++++++++++
 docker/Singularity.def | 63 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 78 insertions(+)
 create mode 100644 docker/README.md
 create mode 100644 docker/Singularity.def

diff --git a/docker/README.md b/docker/README.md
new file mode 100644
index 00000000..5c86ab73
--- /dev/null
+++ b/docker/README.md
@@ -0,0 +1,15 @@
+# Building runtime image
+
+We switched from Docket to [Singularity](https://docs.sylabs.io/guides/4.1/user-guide/introduction.html) containers to run the validation pipeline. 
+
+To build the image:
+1. navigate to the directory holding `Singularity.def` file:
+`cd IHMValidation/docker`
+2. Download [ATSAS](https://www.embl-hamburg.de/biosaxs/download.html) `.deb` package for Ubuntu 22.04 and put into the same directory. The current pipeline was tested with `ATSAS-3.2.1` but newer versions should work too.
+3. Select an appropriate [timezone](https://en.wikipedia.org/wiki/List_of_tz_database_time_zones). For example `America/Los_Angeles`
+4. Build the image:
+`singularity build --build-arg TZ=America/Los_Angeles --build-arg ATSAS=./ATSAS-3.2.1-1_amd64.deb ihmv_$(date +%Y%m%d).sif Singularity.def`
+which will generate a `.sif` image using current date as a nametag (i.e. `ihmv_20240227.sif`)
+
+**NB 1**: It takes about ~25 minutes on a modern workstation to build the image from scratch. 
+**NB 2**: Due to the [Molprobity](https://github.com/rlabduke/MolProbity)'s rolling release model we can't freeze Molprobity version thus we can't guarantee the `IHMValidation` package will work with a freshly-built image. 
diff --git a/docker/Singularity.def b/docker/Singularity.def
new file mode 100644
index 00000000..cceb317f
--- /dev/null
+++ b/docker/Singularity.def
@@ -0,0 +1,63 @@
+Bootstrap: docker
+From: ubuntu:22.04
+Stage: spython-base
+
+%files
+
+    {{ ATSAS }} /ATSAS.deb
+
+%labels
+
+    MAINTAINER Arthur Zalevsky <aozalevsky@gmail.com>
+
+%post
+
+    TZ={{ TZ }}
+    DEBIAN_FRONTEND=noninteractive
+
+    # Install common dependencies
+    apt-get update -y && apt-get install -y wget curl git subversion build-essential
+
+    # Set up basic conda environment using conda-forge packages
+    curl -L https://github.com/conda-forge/miniforge/releases/download/23.3.1-1/Mambaforge-23.3.1-1-Linux-x86_64.sh -o miniforge.sh && echo "dbe92c011a1315b9626e2f93a165892f4b89177145bc350b3859a483a3642a24 miniforge.sh" sha256sum -c --status && bash ./miniforge.sh -b -p /opt/conda && rm -f miniforge.sh && /opt/conda/bin/conda init -q bash
+
+    # Ensure that we always use a shell with conda
+    PATH=/opt/conda/bin:${PATH}
+    echo "conda activate" >> ~/.bashrc
+
+    # Build molprobity from source code and put the binaries we need in /usr/bin/
+    mkdir /opt/molprobity && cd /opt/molprobity && curl -O https://raw.githubusercontent.com/rlabduke/MolProbity/master/install_via_bootstrap.sh && bash ./install_via_bootstrap.sh 4
+    PATH=${PATH}:/opt/molprobity/build/bin
+
+    # Install SAS tools: ATSAS and SASCIFTOOLS
+    apt-get update -y && apt-get install -y /ATSAS.deb && rm -f /ATSAS.deb
+    pip install git+https://git.embl.de/grp-svergun/sasciftools3.git@master#egg=sasciftools
+
+    # Install additional certificate for SASBDB
+    curl https://cacerts.digicert.com/ThawteEVRSACAG2.crt.pem -o ThawteEVRSACAG2.crt --output-dir /usr/local/share/ca-certificates/ && update-ca-certificates
+    REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt
+
+    # Install Python packages and other dependencies needed by IHMValidation
+    apt-get update -y && apt-get install -y xvfb libasound2 libdbus-glib-1-2 libgtk-3-0 && mamba install -y pip requests numpy pandas scikit-learn matplotlib "bokeh<3.0" selenium pyvirtualdisplay firefox geckodriver jinja2 && pip install -U iqplot pdfkit ihm && curl -L -O https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6.1-2/wkhtmltox_0.12.6.1-2.jammy_amd64.deb && apt install -y ./wkhtmltox_0.12.6.1-2.jammy_amd64.deb && rm -rf wkhtmltox_0.12.6.1-2.jammy_amd64.deb
+
+    # Hardcode selenium path
+    SE_MANAGER_PATH=/opt/conda/bin/selenium-manager
+
+    # Get IHMValidation
+    git clone --depth 1 https://github.com/salilab/IHMValidation.git /opt/IHMValidation
+
+    # Create input and output dirs
+    mkdir -p /ihmv/input /ihmv/output /ihmv/cache /ihmv/databases
+
+%environment
+
+    export TZ=${TZ}
+    export DEBIAN_FRONTEND=noninteractive
+    export PATH=/opt/conda/bin:${PATH}
+    export PATH=${PATH}:/opt/molprobity/build/bin
+    export REQUESTS_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt
+    export SE_MANAGER_PATH=/opt/conda/bin/selenium-manager
+
+%runscript
+
+    exec /bin/bash "$@"