From 4b1879300816af414eb788c7dfc9e47c6098a186 Mon Sep 17 00:00:00 2001
From: Stephen Kelly <stevekm@users.noreply.github.com>
Date: Tue, 10 Nov 2020 21:11:42 -0500
Subject: [PATCH] remove old Singularity container recipe and run script

---
 Singularity        | 28 ----------------------------
 run.Singularity.sh | 22 ----------------------
 2 files changed, 50 deletions(-)
 delete mode 100644 Singularity
 delete mode 100755 run.Singularity.sh

diff --git a/Singularity b/Singularity
deleted file mode 100644
index 428a294..0000000
--- a/Singularity
+++ /dev/null
@@ -1,28 +0,0 @@
-BootStrap: docker
-From: ubuntu:16.04
-
-%post
-    apt-get update && \
-    apt-get install -y wget \
-    unzip \
-    default-jdk \
-    xvfb \
-    xorg \
-    python
-
-    wget http://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_2.4.10.zip && \
-    unzip IGV_2.4.10.zip && \
-    rm -f unzip IGV_2.4.10.zip
-
-    export PATH="/IGV_2.4.10/:${PATH}"
-
-    # make a dummy batch script in order to load the hg19 genome into the container
-    # https://software.broadinstitute.org/software/igv/PortCommands
-    printf 'new\ngenome hg19\nexit\n' > /genome.bat
-    xvfb-run --auto-servernum --server-num=1 igv.sh -b /genome.bat
-
-%test
-    which igv.sh
-
-%environment
-    export PATH="/IGV_2.4.10/:${PATH}"
diff --git a/run.Singularity.sh b/run.Singularity.sh
deleted file mode 100755
index 5fff741..0000000
--- a/run.Singularity.sh
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/bin/bash
-
-# example wrapper script to launch the snapshot script inside a Singularity container (needed if xvfb is not installed)
-
-# default path to Singularity container file
-container="${1:-IGV.simg}"
-
-# need to load Singularity if running on Big Purple HPC
-if [ "$(hostname  | grep -q 'bigpurple' ; echo $?)" -eq 0 ]; then
-    module load singularity/2.5.2
-
-    # command to launch Singularity container and run commands inside the container
-    # NOTE: you may need to make sure that the directory filesystem root and the current dir are bound to the container with `-B`
-    singularity exec \
-    -B /gpfs \
-    -B "${PWD}" \
-    "${container}" \
-    /bin/bash -c " \
-    cd ${PWD}
-    python make_IGV_snapshots.py test_data/test_alignments.bam test_data/test_alignments2.bam
-    "
-fi