From b361fb705f5b6921aa6e6a9e6b656064bcf5525f Mon Sep 17 00:00:00 2001
From: don <donkirkby@gmail.com>
Date: Thu, 9 Aug 2018 12:40:21 -0700
Subject: [PATCH] Convert from Docker to Singularity for cfe-lab/Kive#737.

---
 .gitignore  |  1 +
 Singularity | 60 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 61 insertions(+)
 create mode 100644 Singularity

diff --git a/.gitignore b/.gitignore
index 78458412e..76e247925 100755
--- a/.gitignore
+++ b/.gitignore
@@ -21,6 +21,7 @@
 /micall/tests/working/*
 /micall/tests/microtest/Results
 !/micall/tests/working/*.launch
+/micall-*.simg
 /timing.*
 .DS_Store
 */.DS_Store
diff --git a/Singularity b/Singularity
new file mode 100644
index 000000000..a9f59102b
--- /dev/null
+++ b/Singularity
@@ -0,0 +1,60 @@
+# Generate the Singularity container to run MiCall on Kive.
+Bootstrap: docker
+From: python:3.4
+
+%help
+    MiCall maps all the reads from a sample against a set of reference
+    sequences, then stitches all the reads into consensus sequences and
+    coverage maps.
+
+    This Singularity container can be run on Kive: http://cfe-lab.github.io/Kive
+
+%label
+    MAINTAINER BC CfE in HIV/AIDS /~https://github.com/cfe-lab/MiCall
+
+%setup
+    # Unneeded once Singularity creates parent dirs:
+    # /~https://github.com/singularityware/singularity/issues/1549
+    mkdir ${SINGULARITY_ROOTFS}/opt/micall
+    mkdir ${SINGULARITY_ROOTFS}/opt/micall/micall
+
+%files
+    ## MiCall
+    micall_basespace.py /opt/micall/
+    micall_kive.py /opt/micall/
+    micall_kive_resistance.py /opt/micall/
+    micall/__init__.py /opt/micall/micall/
+    micall/project* /opt/micall/micall/
+
+    micall/core    /opt/micall/micall/core/
+    micall/drivers    /opt/micall/micall/drivers/
+    micall/g2p     /opt/micall/micall/g2p/
+    micall/resistance   /opt/micall/micall/resistance/
+    micall/monitor /opt/micall/micall/monitor/
+    micall/utils   /opt/micall/micall/utils/
+
+    ## Gotoh
+    micall/alignment /opt/micall/alignment
+    requirements.txt /opt/micall/
+    requirements-basespace.txt /opt/micall/
+
+%post
+    ## Prerequisites
+    apt-get update -qq --fix-missing
+    apt-get install -qq -y unzip wget
+    rm -rf /var/lib/apt/lists/*
+
+    ## bowtie2
+    wget -q -O bowtie2.zip /~https://github.com/BenLangmead/bowtie2/releases/download/v2.2.8/bowtie2-2.2.8-linux-x86_64.zip
+    unzip bowtie2.zip -d /opt/
+    ln -s /opt/bowtie2-2.2.8/ /opt/bowtie2
+    rm bowtie2.zip
+
+    ## Python packages, plus trigger matplotlib to build its font cache
+    cd /opt
+    pip install -r /opt/micall/requirements-basespace.txt
+    ln -s /usr/local/bin/cutadapt /usr/local/bin/cutadapt-1.11
+    /usr/local/bin/python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot'
+
+%environment
+    export PATH=$PATH:/opt/bowtie2
\ No newline at end of file