-
Notifications
You must be signed in to change notification settings - Fork 0
/
Dockerfile
executable file
·226 lines (187 loc) · 7 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
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
# Use the latest version of the official Ubuntu image as the base image
FROM ubuntu:latest
# Set the maintainer label
LABEL maintainer="[email protected]"
# for easy upgrade later. ARG variables only persist during image build
ARG SAMTOOLSVER=1.18
ARG R_VERSION=4.0.4
ARG SALMON_VERSION=1.10.0
ENV DEBIAN_FRONTEND=noninteractive
# RUN apt update && apt install -y --no-install-recommends python-is-python3 r-base-core=${R_VERSION} r-base-dev=${R_VERSION}
RUN apt update && apt install -y python-is-python3 r-base r-base-dev
# RUN java -version
# Update the package list and install curl and git
RUN apt-get update && apt-get install -y \
apt-transport-https \
autoconf \
bedtools \
build-essential \
bzip2 \
ca-certificates \
curl \
g++ \
gawk \
gcc \
git \
gnupg \
gnuplot \
libboost-all-dev \
libncurses5-dev \
libbz2-dev \
liblzma-dev \
libcurl4 \
libxml2-dev \
libssl-dev \
littler \
make \
nq \
openjdk-17-jdk \
openjdk-17-jre \
perl \
software-properties-common \
unzip \
wget \
zlib1g-dev && rm -rf /var/lib/apt/lists/*
# clean \
# libcurl4-gnutls-dev \
# libcurl4-openssl-dev \
RUN wget https://bootstrap.pypa.io/get-pip.py
RUN python get-pip.py
# install conda
# Install miniconda
ENV CONDA_DIR /opt/conda
RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
/bin/bash ~/miniconda.sh -b -p /opt/conda
# Put conda in path so we can use conda activate
ENV PATH=$CONDA_DIR/bin:$PATH
# install bioconda
RUN conda config --add channels defaults
RUN conda config --add channels bioconda
RUN conda config --add channels conda-forge
RUN conda config --set channel_priority strict
# Update pip to latest version
RUN python -m pip install --upgrade pip
# Update pip to latest version
RUN pip install nf-core
# install nextflow
WORKDIR /usr/local/
RUN mkdir nextflow_directory && cd nextflow_directory
RUN curl -s https://get.nextflow.io | bash
RUN mv nextflow /usr/local/bin
RUN chmod +x /usr/local/bin/nextflow
# # ENV PATH /usr/local/nextflow_directory:$PATH
# ENV PATH="/usr/local/nextflow_directory:$PATH"
# install apptainer
RUN apt update && apt install -y software-properties-common && add-apt-repository -y ppa:apptainer/ppa && apt update && apt install -y apptainer
# download pipeline
WORKDIR /usr/local/
RUN mkdir /usr/local/singularity_images
RUN mkdir /usr/local/nf-core-rnaseq
# RUN nextflow run hello
ENV NXF_SINGULARITY_CACHEDIR=/usr/local/singularity_images
RUN nf-core download rnaseq -r 3.12.0 --outdir /usr/local/nf-core-rnaseq --container-system singularity --compress none -d -u copy --force
# # install fq
# RUN conda install fq=0.11.0
# # Install dependencies
# COPY requirements.txt requirements.txt
# RUN python -m pip install -r requirements.txt
# #install samtools
# RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLSVER}/samtools-${SAMTOOLSVER}.tar.bz2 && \
# tar -xjf samtools-${SAMTOOLSVER}.tar.bz2 && \
# rm samtools-${SAMTOOLSVER}.tar.bz2 && \
# cd samtools-${SAMTOOLSVER} && \
# ./configure && \
# make && \
# make install
# # Install nf-core
# #COPY setup.py setup.py
# #COPY pyproject.toml pyproject.toml
# # RUN python -m pip install .
# # install STAR
# RUN git clone https://github.com/alexdobin/STAR.git
# RUN cd STAR/source
# RUN make STAR
# #install rsem
# WORKDIR /usr/local/
# RUN pwd
# RUN git clone https://github.com/deweylab/RSEM.git
# WORKDIR /usr/local/RSEM
# RUN pwd
# RUN git checkout v1.3.3
# RUN make
# RUN make install
# ENV PATH /usr/local/RSEM:$PATH
# #install umi-tools
# RUN pip install umi_tools
# # INSTALL QUALIMAP
# RUN ln -s /usr/lib/x86_64-linux-gnu/libncursesw.so.6 /usr/lib/x86_64-linux-gnu/libncursesw.so.5
# #Install R 3.6
# # RUN apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 51716619E084DAB9 && add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran35/" && apt update && apt install -y r-base
# #Install Bioconductor packages required by Qualimap
# RUN Rscript -e "install.packages('optparse')"
# RUN Rscript -e "install.packages('BiocManager', repos = 'http://cran.us.r-project.org')"
# RUN Rscript -e "BiocManager::install(c('NOISeq', 'Repitools','Rsamtools', 'GenomicFeatures', 'rtracklayer','DESeq2'))"
# #Install Qualimap
# RUN cd /opt && wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.3.zip && unzip qualimap_v2.3.zip && rm qualimap_v2.3.zip
# # RUN Rscript /opt/qualimap_v2.3/scripts/installDependencies.r
# ENV PATH="/opt/qualimap_v2.3:$PATH"
# # install salmon
# WORKDIR /usr/local/
# RUN wget https://github.com/COMBINE-lab/salmon/releases/download/v${SALMON_VERSION}/salmon-${SALMON_VERSION}_linux_x86_64.tar.gz && tar xzf salmon-${SALMON_VERSION}_linux_x86_64.tar.gz
# ENV PATH="/usr/local/salmon-latest_linux_x86_64/bin:$PATH"
# # Set the working directory inside the container
# WORKDIR /app
# #install string tie
# ARG STRINGTIE_VERSION=2.2.1
# WORKDIR /usr/local/
# RUN cd /usr/local/
# # RUN wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-${STRINGTIE_VERSION}.tar.gz
# # RUN tar xvfz ./stringtie-${STRINGTIE_VERSION}.tar.gz
# # RUN cd stringtie-${STRINGTIE_VERSION}
# # RUN make release
# # RUN conda install -c bioconda stringtie
# # RUN git clone https://github.com/gpertea/stringtie
# # RUN cd stringtie
# # RUN make release
# RUN wget https://github.com/gpertea/stringtie/releases/download/v${STRINGTIE_VERSION}/stringtie-${STRINGTIE_VERSION}.Linux_x86_64.tar.gz
# RUN tar xvfz stringtie-${STRINGTIE_VERSION}.Linux_x86_64.tar.gz
# ENV PATH="/usr/local/stringtie-${STRINGTIE_VERSION}.Linux_x86_64:$PATH"
# #INSTALL multiqc
# WORKDIR /usr/local/
# ARG MULTIQC_VERSION=1.16
# RUN pip install multiqc
# #INSTALL RSeQC
# WORKDIR /usr/local/
# ARG RSEQC_VERSION=5.0.1
# RUN pip install RSeQC
# #INSTALL dupRadar (should move up to other R when optimizing)
# WORKDIR /usr/local/
# ARG DUPRADAR=1.30.0
# RUN Rscript -e "BiocManager::install(c('dupRadar'))"
# #INSTALL picard
# RUN conda config --add channels defaults
# RUN conda config --add channels bioconda
# RUN conda config --add channels conda-forge
# RUN conda config --set channel_priority strict
# WORKDIR /usr/local/
# ARG PICARD_VERSION=3.0.0
# # RUN mamba install -y picard=${PICARD_VERSION}
# RUN conda install -y picard=${PICARD_VERSION}
# # RUN conda install -c "bioconda/label/cf201901" picard
# #update conda
# # RUN conda update -n base -c defaults conda
# # RUN conda update -y conda
# #install bedgraphtobigwig
# RUN conda config --add channels defaults
# RUN conda config --add channels bioconda
# RUN conda config --add channels conda-forge
# RUN conda config --set channel_priority strict
# ARG BEDGRAPHTOBIGWIG_VERSION=377
# WORKDIR /usr/local/
# # RUN conda install -c "bioconda/label/cf201901" ucsc-bedgraphtobigwig
# # RUN conda install -y -c bioconda ucsc-bedgraphtobigwig=${BEDGRAPHTOBIGWIG_VERSION}
# RUN conda install -y ucsc-bedgraphtobigwig=${BEDGRAPHTOBIGWIG_VERSION}
# # Set an environment variable
# ENV MY_ENV_VARIABLE=value
# When the container is started, run the bash shell by default
CMD ["/bin/bash"]