forked from adeslatt/sqanti3-docker
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Dockerfile
141 lines (114 loc) · 6.05 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
138
139
140
141
# Dockerfile for SQANTI3
# https://github.com/ConesaLab/SQANTI3
FROM python:3
MAINTAINER Joel Nitta [email protected]
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update
#########################
### install miniconda ###
#########################
ENV MINICONDA_VERSION py37_4.9.2
ENV CONDA_DIR /miniconda3
RUN wget https://repo.anaconda.com/miniconda/Miniconda3-$MINICONDA_VERSION-Linux-x86_64.sh -O ~/miniconda.sh && \
chmod +x ~/miniconda.sh && \
~/miniconda.sh -b -p $CONDA_DIR && \
rm ~/miniconda.sh
# make non-activate conda commands available
ENV PATH=$CONDA_DIR/bin:$PATH
# make conda activate command available from /bin/bash --login shells
RUN echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> ~/.profile
# make conda activate command available from /bin/bash --interative shells
RUN conda init bash
########################################
### build conda environment: SQANTI3 ###
########################################
# Clone SQANTI3 repo
ENV APPNAME SQANTI3
ENV APPS_HOME /apps
RUN mkdir $APPS_HOME
WORKDIR $APPS_HOME
RUN git clone https://github.com/ConesaLab/SQANTI3.git
WORKDIR $APPS_HOME/$APPNAME
# Checkout most recent version at time of building docker image (806893d = v1.6 on Dec 17, 2020)
RUN git checkout 806893d5ef8d26c6177fe3f34a1ad7c25724bf20
# Build SQANTI3 conda environment
ENV ENV_PREFIX /env/$APPNAME
RUN conda update --name base --channel defaults conda && \
conda env create --prefix $ENV_PREFIX --file $APPS_HOME/$APPNAME/$APPNAME.conda_env.yml --force && \
conda clean --all --yes
# Install gtfToGenePred dependency
# "that seems to have some issues with Python 3.7 (or openssl) when installed though conda"
RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/gtfToGenePred -P $APPS_HOME/$APPNAME/utilities/ && \
chmod +x $APPS_HOME/$APPNAME/utilities/gtfToGenePred
# Install C-DNA cupcake dependency
# Checkout most recent version at time of building docker image (6cefd47 = v19.0.0 on Jan 18, 2021)
# need to switch shell from default /sh to /bash so that `source` works
SHELL ["/bin/bash", "-c"]
RUN source $CONDA_DIR/etc/profile.d/conda.sh && \
conda activate /env/$APPNAME && \
git clone https://github.com/Magdoll/cDNA_Cupcake.git && \
cd cDNA_Cupcake && \
git checkout 6cefd4769318712478b0c5adacceae167d19776c && \
python setup.py build && \
python setup.py install && \
conda deactivate
SHELL ["/bin/sh", "-c"]
### Make shell scripts to run conda apps in conda environment ###
# e.g., SQANTI3 scripts can be run with `sqanti3_qc.py --help`
# Make python scripts executable
# sqanti3_RulesFilter.py lacks a shebang. add it here for now, but remove
# this if that gets fixed in the future.
RUN sed -i '1s/^/#!\/usr\/bin\/env python\n/' sqanti3_RulesFilter.py && \
chmod +x $APPS_HOME/$APPNAME/sqanti3_qc.py && \
chmod +x $APPS_HOME/$APPNAME/sqanti3_RulesFilter.py
# Make wrapper for sqanti3_qc.py
# needs to SQANTI3 conda env and export path to cDNA cupcake
ENV TOOLNAME sqanti3_qc.py
RUN echo '#!/bin/bash' >> /usr/local/bin/$TOOLNAME && \
echo "source $CONDA_DIR/etc/profile.d/conda.sh" >> /usr/local/bin/$TOOLNAME && \
echo "conda activate /env/$APPNAME" >> /usr/local/bin/$TOOLNAME && \
echo "export PYTHONPATH=$PYTHONPATH:$APPS_HOME/$APPNAME/cDNA_Cupcake/sequence/" >> /usr/local/bin/$TOOLNAME && \
echo "$APPS_HOME/$APPNAME/$TOOLNAME \"\$@\"" >> /usr/local/bin/$TOOLNAME && \
chmod 755 /usr/local/bin/$TOOLNAME
# Make wrapper for sqanti3_RulesFilter.py
ENV TOOLNAME sqanti3_RulesFilter.py
RUN echo '#!/bin/bash' >> /usr/local/bin/$TOOLNAME && \
echo "source $CONDA_DIR/etc/profile.d/conda.sh" >> /usr/local/bin/$TOOLNAME && \
echo "conda activate /env/$APPNAME" >> /usr/local/bin/$TOOLNAME && \
echo "export PYTHONPATH=$PYTHONPATH:$APPS_HOME/$APPNAME/cDNA_Cupcake/sequence/" >> /usr/local/bin/$TOOLNAME && \
echo "$APPS_HOME/$APPNAME/$TOOLNAME \"\$@\"" >> /usr/local/bin/$TOOLNAME && \
chmod 755 /usr/local/bin/$TOOLNAME
# Now add new tools and make wrapper for protein_classification.py
# First copy new tool from our local forked repo
COPY src/protein_classification.py $APPS_HOME/$APPNAME
RUN chmod +x $APPS_HOME/$APPNAME/protein_classification.py
ENV TOOLNAME protein_classification.py
RUN echo '#!/bin/bash' >> /usr/local/bin/$TOOLNAME && \
echo "source $CONDA_DIR/etc/profile.d/conda.sh" >> /usr/local/bin/$TOOLNAME && \
echo "conda activate /env/$APPNAME" >> /usr/local/bin/$TOOLNAME && \
echo "export PYTHONPATH=$PYTHONPATH:$APPS_HOME/$APPNAME/cDNA_Cupcake/sequence/" >> /usr/local/bin/$TOOLNAME && \
echo "$APPS_HOME/$APPNAME/$TOOLNAME \"\$@\"" >> /usr/local/bin/$TOOLNAME && \
chmod 755 /usr/local/bin/$TOOLNAME
# Now add new tools and make wrapper for protein_classification.py first by
# First copy new tool from our local forked repo
COPY src/sample_and_ref_gtf_file_rename_cds_to_exon.py $APPS_HOME/$APPNAME
RUN chmod +x $APPS_HOME/$APPNAME/sample_and_ref_gtf_file_rename_cds_to_exon.py
ENV TOOLNAME sample_and_ref_gtf_file_rename_cds_to_exon.py
RUN echo '#!/bin/bash' >> /usr/local/bin/$TOOLNAME && \
echo "source $CONDA_DIR/etc/profile.d/conda.sh" >> /usr/local/bin/$TOOLNAME && \
echo "conda activate /env/$APPNAME" >> /usr/local/bin/$TOOLNAME && \
echo "export PYTHONPATH=$PYTHONPATH:$APPS_HOME/$APPNAME/cDNA_Cupcake/sequence/" >> /usr/local/bin/$TOOLNAME && \
echo "$APPS_HOME/$APPNAME/$TOOLNAME \"\$@\"" >> /usr/local/bin/$TOOLNAME && \
chmod 755 /usr/local/bin/$TOOLNAME
# Now add new tools and make wrapper for protein_classification.py first by
# First copy new tool from our local forked repo
COPY src/sqanti3_protein.py $APPS_HOME/$APPNAME
RUN chmod +x $APPS_HOME/$APPNAME/sqanti3_protein.py
ENV TOOLNAME sqanti3_protein.py
RUN echo '#!/bin/bash' >> /usr/local/bin/$TOOLNAME && \
echo "source $CONDA_DIR/etc/profile.d/conda.sh" >> /usr/local/bin/$TOOLNAME && \
echo "conda activate /env/$APPNAME" >> /usr/local/bin/$TOOLNAME && \
echo "export PYTHONPATH=$PYTHONPATH:$APPS_HOME/$APPNAME/cDNA_Cupcake/sequence/" >> /usr/local/bin/$TOOLNAME && \
echo "$APPS_HOME/$APPNAME/$TOOLNAME \"\$@\"" >> /usr/local/bin/$TOOLNAME && \
chmod 755 /usr/local/bin/$TOOLNAME
WORKDIR /root