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Amanda Sullivan
committed
clean up docker files
1 parent f1e347f commit 7da0ba7

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lines changed

‎CHANGELOG.md

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@@ -7,6 +7,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### Credits
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- [Amanda Sullivan](https://github.com/mandysulli)
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### Enhancements
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-
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### Parameters
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| Old parameter | New parameter |
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| ------------- | ---------------------------- |
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| | |
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## v1.2.0 - 2024.11.07
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### Credits
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- [Amanda Sullivan](https://github.com/mandysulli)
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- [Reina Chau](https://github.com/rchau88)
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- [Arumugam Rajarethinam](https://github.com/lochanaarumugam)

‎Dockerfile

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@@ -34,7 +34,7 @@ COPY . ${PROJECT_DIR}
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############# Install python packages ##################
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# Copy all files to docker images
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COPY requirements.txt ${PROJECT_DIR}/requirements.txt
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COPY docker_files/requirements.txt ${PROJECT_DIR}/requirements.txt
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# Install python requirements
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RUN pip install --no-cache-dir -r ${PROJECT_DIR}/requirements.txt
@@ -53,13 +53,13 @@ RUN chmod a+x ${PROJECT_DIR}/MIRA_nextflow.sh
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############# Fix vulnerablities pkgs ##################
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# Copy all files to docker images
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COPY fixed_vulnerability_pkgs.txt ${PROJECT_DIR}/fixed_vulnerability_pkgs.txt
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COPY docker_files/fixed_vulnerability_pkgs.txt ${PROJECT_DIR}/docker_files/fixed_vulnerability_pkgs.txt
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# Copy all files to docker images
59-
COPY fixed_vulnerability_pkgs.sh ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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COPY docker_files/fixed_vulnerability_pkgs.sh ${PROJECT_DIR}/docker_files/fixed_vulnerability_pkgs.sh
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# Convert bash script from Windows style line endings to Unix-like control characters
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RUN dos2unix ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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RUN dos2unix ${PROJECT_DIR}/docker_files/fixed_vulnerability_pkgs.sh
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# Allow permission to excute the bash script
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RUN chmod a+x ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
@@ -70,10 +70,10 @@ RUN bash ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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############# Remove vulnerability pkgs ##################
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# Copy all files to docker images
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COPY remove_mira_nf_vulnerability_pkgs.txt ${PROJECT_DIR}/remove_vulnerability_pkgs.txt
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COPY docker_files/remove_mira_nf_vulnerability_pkgs.txt ${PROJECT_DIR}/remove_vulnerability_pkgs.txt
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# Copy all files to docker images
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COPY remove_vulnerability_pkgs.sh ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
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COPY docker_files/remove_vulnerability_pkgs.sh ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
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# Convert bash script from Windows style line endings to Unix-like control characters
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RUN dos2unix ${PROJECT_DIR}/remove_vulnerability_pkgs.sh

‎Dockerfile-bbtools

Lines changed: 13 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -15,27 +15,27 @@ ENV python_version=${python_version:-python3.10}
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COPY ca.crt /root/ca.crt
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# Put certs in /etc/ssl/certs location
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RUN cat /root/ca.crt >> /etc/ssl/certs/ca-certificates.crt
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RUN cat /root/ca.crt >>/etc/ssl/certs/ca-certificates.crt
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# Install system libraries of general use
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RUN apk update && apk add --no-cache \
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openjdk21-jre=21.0.5_p11-r0 \
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bash \
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vim \
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tar \
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dos2unix \
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&& pip install --upgrade pip
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dos2unix &&
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pip install --upgrade pip
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# Set up project directory
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ENV PROJECT_DIR=/bbtools
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############# Install bbtools ##################
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# Copy all files to docker images
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COPY bbtools/* ${PROJECT_DIR}/
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COPY docker_files/bbtools/* ${PROJECT_DIR}/
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# Copy all files to docker images
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COPY bbtools/install_bbtools.sh ${PROJECT_DIR}/install_bbtools.sh
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COPY docker_files/bbtools/install_bbtools.sh ${PROJECT_DIR}/install_bbtools.sh
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# Convert bash script from Windows style line endings to Unix-like control characters
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RUN dos2unix ${PROJECT_DIR}/install_bbtools.sh
@@ -49,7 +49,7 @@ RUN bash ${PROJECT_DIR}/install_bbtools.sh
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############# Fix vulnerablities pkgs ##################
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# Copy all files to docker images
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COPY fixed_vulnerability_pkgs.txt ${PROJECT_DIR}/fixed_vulnerability_pkgs.txt
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COPY docker_files/fixed_vulnerability_pkgs.txt ${PROJECT_DIR}/docker_files/fixed_vulnerability_pkgs.txt
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# Copy all files to docker images
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COPY fixed_vulnerability_pkgs.sh ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
@@ -61,15 +61,15 @@ RUN dos2unix ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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RUN chmod a+x ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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# Execute bash script to wget the file and tar the package
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RUN bash ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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RUN bash ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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############# Remove vulnerability pkgs ##################
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# Copy all files to docker images
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COPY remove_bbtools_vulnerability_pkgs.txt ${PROJECT_DIR}/remove_vulnerability_pkgs.txt
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COPY docker_files/remove_bbtools_vulnerability_pkgs.txt ${PROJECT_DIR}/remove_vulnerability_pkgs.txt
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# Copy all files to docker images
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COPY remove_vulnerability_pkgs.sh ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
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COPY docker_files/remove_vulnerability_pkgs.sh ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
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# Convert bash script from Windows style line endings to Unix-like control characters
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RUN dos2unix ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
@@ -83,9 +83,9 @@ RUN bash ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
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############# Remove the vendor packages ##################
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# Clean up and remove unwanted files
86-
RUN rm -rf /usr/local/lib/${python_version}/site-packages/pip/_vendor \
87-
&& rm -rf /usr/local/lib/${python_version}/site-packages/pipenv/patched/pip/_vendor \
88-
&& rm -rf /usr/local/lib/${python_version}/site-packages/examples
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RUN rm -rf /usr/local/lib/${python_version}/site-packages/pip/_vendor &&
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rm -rf /usr/local/lib/${python_version}/site-packages/pipenv/patched/pip/_vendor &&
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rm -rf /usr/local/lib/${python_version}/site-packages/examples
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############# Set up working directory ##################
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VOLUME ${WORKDIR}
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# Set up working directory in docker
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WORKDIR ${WORKDIR}
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WORKDIR ${WORKDIR}
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# Export project directory to PATH
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ENV PATH "$PATH:${PROJECT_DIR}/bbmap"
103-

‎Dockerfile-cutadapt

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Original file line numberDiff line numberDiff line change
@@ -19,26 +19,26 @@ ENV cutadapt_version=${cutadapt_version:-4.4}
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COPY ca.crt /root/ca.crt
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# Put certs in /etc/ssl/certs location
22-
RUN cat /root/ca.crt >> /etc/ssl/certs/ca-certificates.crt
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RUN cat /root/ca.crt >>/etc/ssl/certs/ca-certificates.crt
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# Install system libraries of general use
2525
RUN apk update && apk add --no-cache \
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openjdk21-jre=21.0.5_p11-r0 \
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bash \
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vim \
29-
&& pip install --upgrade pip \
30-
&& pip install --no-cache-dir cutadapt==${cutadapt_version}
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vim &&
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pip install --upgrade pip &&
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pip install --no-cache-dir cutadapt==${cutadapt_version}
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# Set up project directory
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ENV PROJECT_DIR=/cutadapt
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############# Fix vulnerablities pkgs ##################
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# Copy all files to docker images
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COPY fixed_vulnerability_pkgs.txt ${PROJECT_DIR}/fixed_vulnerability_pkgs.txt
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COPY docker_files/fixed_vulnerability_pkgs.txt ${PROJECT_DIR}/fixed_vulnerability_pkgs.txt
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# Copy all files to docker images
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COPY fixed_vulnerability_pkgs.sh ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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COPY docker_files/fixed_vulnerability_pkgs.sh ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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# Convert bash script from Windows style line endings to Unix-like control characters
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RUN dos2unix ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
@@ -47,15 +47,15 @@ RUN dos2unix ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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RUN chmod a+x ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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# Execute bash script to wget the file and tar the package
50-
RUN bash ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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RUN bash ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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############# Remove vulnerability pkgs ##################
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# Copy all files to docker images
55-
COPY remove_cutadapt_vulnerability_pkgs.txt ${PROJECT_DIR}/remove_vulnerability_pkgs.txt
55+
COPY docker_files/remove_cutadapt_vulnerability_pkgs.txt ${PROJECT_DIR}/remove_vulnerability_pkgs.txt
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# Copy all files to docker images
58-
COPY remove_vulnerability_pkgs.sh ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
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COPY docker_files/remove_vulnerability_pkgs.sh ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
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# Convert bash script from Windows style line endings to Unix-like control characters
6161
RUN dos2unix ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
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6969
############# Remove the vendor packages ##################
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7171
# Clean up and remove unwanted files
72-
RUN rm -rf /usr/local/lib/${python_version}/site-packages/pip/_vendor \
73-
&& rm -rf /usr/local/lib/${python_version}/site-packages/pipenv/patched/pip/_vendor \
74-
&& rm -rf /usr/local/lib/${python_version}/site-packages/examples
72+
RUN rm -rf /usr/local/lib/${python_version}/site-packages/pip/_vendor &&
73+
rm -rf /usr/local/lib/${python_version}/site-packages/pipenv/patched/pip/_vendor &&
74+
rm -rf /usr/local/lib/${python_version}/site-packages/examples
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7676
############# Set up working directory ##################
7777

@@ -82,6 +82,4 @@ ENV WORKDIR=/data
8282
VOLUME ${WORKDIR}
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# Set up working directory in docker
85-
WORKDIR ${WORKDIR}
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87-
85+
WORKDIR ${WORKDIR}

‎Dockerfile-fastqc

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Original file line numberDiff line numberDiff line change
@@ -19,7 +19,7 @@ ENV fastqc_version=${fastqc_version:-0.12.1}
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COPY ca.crt /root/ca.crt
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# Put certs in /etc/ssl/certs location
22-
RUN cat /root/ca.crt >> /etc/ssl/certs/ca-certificates.crt
22+
RUN cat /root/ca.crt >>/etc/ssl/certs/ca-certificates.crt
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2424
# Install system libraries of general use
2525
RUN apk update && apk add --no-cache \
@@ -29,9 +29,9 @@ RUN apk update && apk add --no-cache \
2929
bash \
3030
perl \
3131
unzip \
32-
vim \
33-
&& pip install --upgrade pip
34-
32+
vim &&
33+
pip install --upgrade pip
34+
3535
# Get package version
3636
ENV FASTQC_PKG="fastqc_v${fastqc_version}.zip"
3737

@@ -42,9 +42,9 @@ WORKDIR /usr/local
4242
ADD http://www.bioinformatics.babraham.ac.uk/projects/fastqc/${FASTQC_PKG} /tmp/
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# Download and install FastQC;
45-
RUN unzip /tmp/${FASTQC_PKG} \
46-
&& chmod 755 FastQC/fastqc \
47-
&& rm -rf /tmp/${FASTQC_PKG}
45+
RUN unzip /tmp/${FASTQC_PKG} &&
46+
chmod 755 FastQC/fastqc &&
47+
rm -rf /tmp/${FASTQC_PKG}
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4949
# Export program to PATH
5050
ENV PATH "$PATH:/usr/local/FastQC"
@@ -55,10 +55,10 @@ ENV PROJECT_DIR=/fastqc
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############# Fix vulnerablities pkgs ##################
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5757
# Copy all files to docker images
58-
COPY fixed_vulnerability_pkgs.txt ${PROJECT_DIR}/fixed_vulnerability_pkgs.txt
58+
COPY docker_files/fixed_vulnerability_pkgs.txt ${PROJECT_DIR}/fixed_vulnerability_pkgs.txt
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6060
# Copy all files to docker images
61-
COPY fixed_vulnerability_pkgs.sh ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
61+
COPY docker_files/fixed_vulnerability_pkgs.sh ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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6363
# Convert bash script from Windows style line endings to Unix-like control characters
6464
RUN dos2unix ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
@@ -67,15 +67,15 @@ RUN dos2unix ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
6767
RUN chmod a+x ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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6969
# Execute bash script to wget the file and tar the package
70-
RUN bash ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
70+
RUN bash ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
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7272
############# Remove vulnerability pkgs ##################
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7474
# Copy all files to docker images
75-
COPY remove_fastqc_vulnerability_pkgs.txt ${PROJECT_DIR}/remove_vulnerability_pkgs.txt
75+
COPY docker_files/remove_fastqc_vulnerability_pkgs.txt ${PROJECT_DIR}/remove_vulnerability_pkgs.txt
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7777
# Copy all files to docker images
78-
COPY remove_vulnerability_pkgs.sh ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
78+
COPY docker_files/remove_vulnerability_pkgs.sh ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
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# Convert bash script from Windows style line endings to Unix-like control characters
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RUN dos2unix ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
@@ -89,19 +89,18 @@ RUN bash ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
8989
############# Remove the vendor packages ##################
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9191
# Clean up and remove unwanted files
92-
RUN rm -rf /usr/local/lib/${python_version}/site-packages/pip/_vendor \
93-
&& rm -rf /usr/local/lib/${python_version}/site-packages/pipenv/patched/pip/_vendor \
94-
&& rm -rf /usr/local/lib/${python_version}/site-packages/examples \
95-
&& rm -rf /usr/local/FastQC/cisd-jhdf5.jar
92+
RUN rm -rf /usr/local/lib/${python_version}/site-packages/pip/_vendor &&
93+
rm -rf /usr/local/lib/${python_version}/site-packages/pipenv/patched/pip/_vendor &&
94+
rm -rf /usr/local/lib/${python_version}/site-packages/examples &&
95+
rm -rf /usr/local/FastQC/cisd-jhdf5.jar
9696

9797
############# Set up working directory ##################
9898

99-
# Create working directory variable
99+
# Create working directory variable
100100
ENV WORKDIR=/data
101101

102102
# Set up volume directory in docker
103103
VOLUME ${WORKDIR}
104104

105105
# Set up working directory in docker
106-
WORKDIR ${WORKDIR}
107-
106+
WORKDIR ${WORKDIR}

‎Dockerfile-multiqc

Lines changed: 14 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -19,26 +19,26 @@ ENV multiqc_version=${multiqc_version:-1.19}
1919
COPY ca.crt /root/ca.crt
2020

2121
# Put certs in /etc/ssl/certs location
22-
RUN cat /root/ca.crt >> /etc/ssl/certs/ca-certificates.crt
22+
RUN cat /root/ca.crt >>/etc/ssl/certs/ca-certificates.crt
2323

2424
# Install system libraries of general use
2525
RUN apk update && apk add --no-cache \
2626
openjdk21-jre=21.0.5_p11-r0 \
2727
bash \
28-
vim \
29-
&& pip install --upgrade pip \
30-
&& pip install --no-cache-dir multiqc==${multiqc_version}
28+
vim &&
29+
pip install --upgrade pip &&
30+
pip install --no-cache-dir multiqc==${multiqc_version}
3131

3232
# Set up project directory
3333
ENV PROJECT_DIR=/multiqc
3434

3535
############# Fix vulnerablities pkgs ##################
3636

3737
# Copy all files to docker images
38-
COPY fixed_vulnerability_pkgs.txt ${PROJECT_DIR}/fixed_vulnerability_pkgs.txt
38+
COPY docker_files/fixed_vulnerability_pkgs.txt ${PROJECT_DIR}/fixed_vulnerability_pkgs.txt
3939

4040
# Copy all files to docker images
41-
COPY fixed_vulnerability_pkgs.sh ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
41+
COPY docker_files/fixed_vulnerability_pkgs.sh ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
4242

4343
# Convert bash script from Windows style line endings to Unix-like control characters
4444
RUN dos2unix ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
@@ -47,15 +47,15 @@ RUN dos2unix ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
4747
RUN chmod a+x ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
4848

4949
# Execute bash script to wget the file and tar the package
50-
RUN bash ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
50+
RUN bash ${PROJECT_DIR}/fixed_vulnerability_pkgs.sh
5151

5252
############# Remove vulnerability pkgs ##################
5353

5454
# Copy all files to docker images
55-
COPY remove_multiqc_vulnerability_pkgs.txt ${PROJECT_DIR}/remove_vulnerability_pkgs.txt
55+
COPY docker_files/remove_multiqc_vulnerability_pkgs.txt ${PROJECT_DIR}/remove_vulnerability_pkgs.txt
5656

5757
# Copy all files to docker images
58-
COPY remove_vulnerability_pkgs.sh ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
58+
COPY docker_files/remove_vulnerability_pkgs.sh ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
5959

6060
# Convert bash script from Windows style line endings to Unix-like control characters
6161
RUN dos2unix ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
@@ -69,10 +69,10 @@ RUN bash ${PROJECT_DIR}/remove_vulnerability_pkgs.sh
6969
############# Remove the vendor packages ##################
7070

7171
# Clean up and remove unwanted files
72-
RUN rm -rf /usr/local/lib/${python_version}/site-packages/pip/_vendor \
73-
&& rm -rf /usr/local/lib/${python_version}/site-packages/pipenv/patched/pip/_vendor \
74-
&& rm -rf /usr/local/lib/${python_version}/site-packages/examples
75-
72+
RUN rm -rf /usr/local/lib/${python_version}/site-packages/pip/_vendor &&
73+
rm -rf /usr/local/lib/${python_version}/site-packages/pipenv/patched/pip/_vendor &&
74+
rm -rf /usr/local/lib/${python_version}/site-packages/examples
75+
7676
############# Set up working directory ##################
7777

7878
# Create working directory variable
@@ -82,5 +82,4 @@ ENV WORKDIR=/data
8282
VOLUME ${WORKDIR}
8383

8484
# Set up working directory in docker
85-
WORKDIR ${WORKDIR}
86-
85+
WORKDIR ${WORKDIR}

‎bbtools/BBMap_39.01.tar.gz renamed to ‎docker_files/bbtools/BBMap_39.01.tar.gz

File renamed without changes.

‎bbtools/bbtools_file.txt renamed to ‎docker_files/bbtools/bbtools_file.txt

File renamed without changes.

‎bbtools/bbtools_file_clean.txt renamed to ‎docker_files/bbtools/bbtools_file_clean.txt

File renamed without changes.

‎bbtools/install_bbtools.sh renamed to ‎docker_files/bbtools/install_bbtools.sh

File renamed without changes.

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