-
Notifications
You must be signed in to change notification settings - Fork 1
/
Dockerfile
137 lines (118 loc) · 6.47 KB
/
Dockerfile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
# Use Ubuntu as the base image
FROM dreg.cloud.sdu.dk/ucloud-apps/ubuntu:Apr2024-xfce
# Labels for the Dockerfile
LABEL software="Proteomics Sandbox"\
author="Jacob Fredegaard Hansen <jfredegaard@bmb.sdu.dk>"\
version="v2024.06"\
license="MIT"\
description="Proteomics sandbox with software for clinical proteomics data analysis."
# Set the working directory
WORKDIR /opt
## Installing dependencies for proteomics sandbox app
# Update package list and install python3-pip
RUN sudo apt-get update && \
sudo apt-get install -y software-properties-common && \
sudo add-apt-repository -y ppa:deadsnakes/ppa && \
sudo apt-get install -y python3.9 python3.9-venv python3.9-dev python3-pip && \
sudo apt-get install -y mono-devel && \
sudo apt install -y libgtk-3-dev && \
sudo apt install -y wmctrl && \
sudo apt-get purge -y -q firefox && \
sudo apt-get install -y -q firefox && \
sudo apt-get clean
#Installing pip for Python3.9
RUN sudo curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py && python3.9 get-pip.py
# Add Microsoft package signing key, repository, and install libicu
RUN wget https://packages.microsoft.com/config/ubuntu/24.04/packages-microsoft-prod.deb -O packages-microsoft-prod.deb && \
sudo dpkg -i packages-microsoft-prod.deb && \
sudo rm packages-microsoft-prod.deb && \
sudo apt-get update && \
wget http://archive.ubuntu.com/ubuntu/pool/main/i/icu/libicu70_70.1-2_amd64.deb && \
sudo dpkg -i libicu70_70.1-2_amd64.deb && \
sudo rm libicu70_70.1-2_amd64.deb
# Install .NET Core SDK 7.0 and ASP.NET Core Runtime 7.0
RUN sudo apt-get update && \
sudo apt-get install -y dotnet-sdk-7.0 aspnetcore-runtime-7.0 && \
sudo apt-get clean
# Upgrade pip and setuptools to ensure we have the latest versions
# Install specific versions and latest versions of required Python packages: easypqp and lxml and numpy (already installed) and pandas in Python3.9 for FragPipe and attrdict3, gooey, pyinstaller for the DIA-NN GUI
RUN sudo python3.9 -m pip install --upgrade pip setuptools && \
sudo python3.9 -m pip install pyopenms==2.6.0 easypqp lxml attrdict3 gooey pyinstaller && \
sudo python3.9 -m pip install --force numpy pandas
# Create the /usr/local directory in the container
RUN mkdir -p /usr/local
# Copy necessary files
COPY ./Installers /usr/local
COPY ./Scripts/ /opt
COPY ./cache.template /opt/fragpipe/cache
COPY ./launchers /usr/share/applications/launchers
# Unzip, install, and cleanup
RUN sudo chmod +x /opt/diann_install.sh && \
/opt/diann_install.sh && \
sudo rm /opt/diann_install.sh && \
sudo rm /opt/install_gooey.sh && \
sudo unzip /usr/local/MSFragger-4.1.zip -d /usr/local && \
sudo mv /usr/local/MSFragger-4.1 /opt/fragpipe/tools && \
sudo unzip /usr/local/IonQuant-1.10.27.zip -d /usr/local && \
sudo mv /usr/local/IonQuant-1.10.27 /opt/fragpipe/tools && \
sudo unzip /usr/local/diaTracer-1.1.3.zip -d /usr/local && \
sudo mv /usr/local/diaTracer-1.1.3 /opt/fragpipe/tools && \
sudo mkdir /usr/local/ProteoWizard && \
sudo tar xvjf /usr/local/pwiz-bin-linux-x86_64-gcc7-release-3_0_23007_23d2af0.tar.bz2 -C /usr/local/ProteoWizard && \
sudo unzip /usr/local/MaxQuant_v2.5.2.0.zip -d /usr/local && \
sudo tar xvzf /usr/local/vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar.gz -C /usr/local && \
sudo rm /usr/local/*.tar.gz && \
sudo rm /usr/local/*.zip && \
sudo rm /usr/local/*.tar.bz2
# Configure and install vmd
WORKDIR /usr/local/vmd-1.9.3
RUN sudo ./configure && \
cd src/ && \
sudo make install && \
cd /usr/local
#sudo rm -rf vmd-1.9.3
# Set the working directory
WORKDIR /opt
## Installing software for the proteomics sandbox app
# Install SearchGUI, FragPipe, Philosopher, PDV, PeptideShaker, ThermoRawFileParserGUI, and DIA-NN
RUN sudo wget https://genesis.ugent.be/maven2/eu/isas/searchgui/SearchGUI/4.3.9/SearchGUI-4.3.9-mac_and_linux.tar.gz && \
sudo tar -xzf SearchGUI-4.3.9-mac_and_linux.tar.gz && \
sudo rm SearchGUI-4.3.9-mac_and_linux.tar.gz && \
sudo wget https://github.com/Nesvilab/FragPipe/releases/download/22.0/FragPipe-22.0.zip && \
sudo unzip FragPipe-22.0.zip && \
sudo rm FragPipe-22.0.zip && \
sudo wget https://github.com/Nesvilab/philosopher/releases/download/v5.1.0/philosopher_v5.1.0_linux_amd64.zip && \
sudo unzip philosopher_v5.1.0_linux_amd64.zip && \
sudo rm philosopher_v5.1.0_linux_amd64.zip && \
sudo mv /opt/philosopher /opt/fragpipe/tools && \
sudo wget https://github.com/wenbostar/PDV/releases/download/v2.0.0/PDV-2.0.0.zip && \
sudo unzip PDV-2.0.0.zip && \
sudo rm PDV-2.0.0.zip && \
sudo wget https://genesis.ugent.be/maven2/eu/isas/peptideshaker/PeptideShaker/3.0.8/PeptideShaker-3.0.8.zip && \
sudo unzip PeptideShaker-3.0.8.zip && \
sudo rm PeptideShaker-3.0.8.zip && \
sudo wget https://genesis.ugent.be/maven2/no/uib/thermo-raw-file-parser-gui/ThermoRawFileParserGUI/1.7.3/ThermoRawFileParserGUI-1.7.3.zip && \
sudo unzip ThermoRawFileParserGUI-1.7.3.zip && \
sudo rm ThermoRawFileParserGUI-1.7.3.zip && \
sudo wget https://github.com/mzmine/mzmine3/releases/download/v4.0.3/mzmine-linux-installer_4.0.3.deb && \
sudo apt-get install -y ./mzmine-linux-installer_4.0.3.deb && \
sudo rm mzmine-linux-installer_4.0.3.deb
# Set permissions and configurations
RUN sudo chmod -R a+rwx /opt/SearchGUI-4.3.9/resources && \
sudo chmod -R a+rwx /opt/PeptideShaker-3.0.8/resources && \
sudo cp /usr/share/applications/launchers/*.desktop ~/Desktop && \
sudo chmod -R a+rwx ~/Desktop
# Change to /opt/fragpipe and create the 'updates' directory with superuser permissions
RUN cd /opt/fragpipe && \
sudo mkdir updates
# Set ownership for all .desktop files
RUN sudo chown $USER:$USER ~/Desktop/*.desktop
# Set permissions for .desktop files and update xfce-exe-checksum metadata
RUN chmod 775 "${HOME}"/Desktop/*.desktop \
&& for f in "${HOME}"/Desktop/*.desktop; do \
dbus-launch gio set -t string "$f" metadata::xfce-exe-checksum "$(sha256sum $f | awk '{print $1}')"; \
done
# Set the working directory
WORKDIR /work
# Run the Docker container locally. It can be accessed at localhost:6901
# docker run --rm -it -p 6901:6901 -e VNC_RESOLUTION=1920x1200 -e VNC_PW=vncpassword --name myimage myimage bash -c "vnc_startup.sh firefox https://github.com/hds-sandbox/proteomics-course"