From 20e3d17f14231cece387a5f93e8b8625b45897f7 Mon Sep 17 00:00:00 2001
From: MatthewThe <matthew.the@scilifelab.se>
Date: Wed, 17 Jun 2020 11:59:51 +0200
Subject: [PATCH] Fixing Dinosaur permission command

---
 Singularity | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/Singularity b/Singularity
index 1b434d4..cfec100 100644
--- a/Singularity
+++ b/Singularity
@@ -61,7 +61,7 @@ From:chambm/wine-dotnet:4.7-x64  # Prebuilt, WIP trying to convert to Ubuntu 18.
     rm -r ui/
     chmod -R a+x /var/local/quandenser_ui/*  # So everybody can access the files
 
-    echo "Installling packages with apt-get"
+    echo "Installing packages with apt-get"
     apt-get update
     apt-get -y install wget
     wget -nc https://dl.winehq.org/wine-builds/winehq.key  # Add key, since it does not exist in image.
@@ -104,7 +104,7 @@ From:chambm/wine-dotnet:4.7-x64  # Prebuilt, WIP trying to convert to Ubuntu 18.
     ln -sf /usr/local/bin/python3 /usr/local/bin/python
     ln -sf /usr/local/bin/pip /usr/local/bin/pip3
 
-    echo "Installling packages with pip"
+    echo "Installing packages with pip"
     # psutil requires gcc
     pip install psutil
     pip install PySide2
@@ -115,7 +115,7 @@ From:chambm/wine-dotnet:4.7-x64  # Prebuilt, WIP trying to convert to Ubuntu 18.
     pip install tqdm
     #apt-get -y install python3.6-tk
 
-    echo "Installling dependencies for OpenGL and X11"
+    echo "Installing dependencies for OpenGL and X11"
     # Qt dependencies
     apt-get -y install build-essential cmake qt5-default libxml2 libxslt1.1 qtbase5-dev
     apt-get -y install qttools5-dev-tools libqt5clucene5 libqt5concurrent5 libqt5core5a libqt5dbus5 libqt5designer5 libqt5designercomponents5 libqt5feedback5 libqt5gui5 libqt5help5 libqt5multimedia5 libqt5network5 libqt5opengl5 libqt5opengl5-dev libqt5organizer5 libqt5positioning5 libqt5printsupport5 libqt5qml5 libqt5quick5 libqt5quickwidgets5 libqt5script5 libqt5scripttools5 libqt5sql5 libqt5sql5-sqlite libqt5svg5 libqt5test5 libqt5webkit5 libqt5widgets5 libqt5xml5 libqt5xmlpatterns5 libqt5xmlpatterns5-dev
@@ -123,29 +123,30 @@ From:chambm/wine-dotnet:4.7-x64  # Prebuilt, WIP trying to convert to Ubuntu 18.
     # Downloading tmp files here
     cd $(mktemp -d)
 
-    echo "Installling quandenser"
+    echo "Installing quandenser"
     # wget -nc https://github.com/statisticalbiotechnology/quandenser/releases/download/rel-0-01/quandenser-v0-01-linux-amd64.deb
     git clone --recursive https://github.com/statisticalbiotechnology/quandenser.git
     cd quandenser
     # git checkout e07136fdc1ba5fd61f2b41462ef19a82847824aa
     git checkout quandenser-pipeline
+    git submodule update --recursive
     ./quickbuild.sh
     cd ..
     dpkg -i ./release/ubuntu64/quandenser-*-linux-amd64.deb
     # Weird stuff with permissions. Fixing
     chmod 755 /usr/bin/quandenser
     chmod 755 /usr/share/java/advParams_dinosaur_targeted.txt
-    chmod 755 /usr/share/java/Dinosaur-1.1.3.free.jar
+    chmod 755 /usr/share/java/Dinosaur-*.free.jar
     apt-get install -f
 
-    echo "Installling triqler (quandenser-pipeline version)"
+    echo "Installing triqler (quandenser-pipeline version)"
     pip install triqler
     #git clone -b quandenser-pipeline https://github.com/statisticalbiotechnology/triqler.git
     #cd triqler
     #pip install .
     #cd ..
 
-    echo "Installling crux"
+    echo "Installing crux"
     wget -nc https://noble.gs.washington.edu/crux-downloads/crux-3.2/crux-3.2.Linux.x86_64.zip  # -nc checks if it exist
     unzip -uq crux-3.2.Linux.x86_64.zip
     cp -f crux-3.2.Linux.x86_64/bin/crux /usr/local/bin/