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Feat: Adding dockerfile for latest version of sqanti3/v5.2.0
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@skchronicles
skchronicles committed Oct 12, 2023
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209 changes: 110 additions & 99 deletions docker/sqanti3/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Base image for SQANTI3/v5.1.2,
# Base image for SQANTI3/v5.2.0,
# uses Ubuntu Jammy (LTS)
FROM ubuntu:22.04

Expand All @@ -17,36 +17,36 @@ FROM ubuntu:22.04
# -+ gffread # apt-get, installs: 0.12.7-2
# -+ gmap # apt-get, installs: 2021-12-17+ds-1
# -+ seqtk # apt-get, installs: 1.3-2
# -+ R>=3.4 # apt-get, installs: 4.1.2-1
# @requires: noiseq # from Bioconductor
# @requires: busparse # from Bioconductor
# @requires: biocmanager # from CRAN
# @requires: caret # from CRAN
# @requires: dplyr # from CRAN
# @requires: dt # from CRAN
# @requires: devtools # from CRAN
# @requires: e1071 # from CRAN
# @requires: forcats # from CRAN
# @requires: ggplot2 # from CRAN
# @requires: ggplotify # from CRAN
# @requires: gridbase # from CRAN
# @requires: gridextra # from CRAN
# @requires: htmltools # from CRAN
# @requires: jsonlite # from CRAN
# @requires: optparse # from CRAN
# @requires: plotly # from CRAN
# @requires: plyr # from CRAN
# @requires: pROC # from CRAN
# @requires: purrr # from CRAN
# @requires: rmarkdown # from CRAN
# @requires: reshape # from CRAN
# @requires: readr # from CRAN
# @requires: randomForest # from CRAN
# @requires: scales # from CRAN
# @requires: stringi # from CRAN
# @requires: stringr # from CRAN
# @requires: tibble # from CRAN
# @requires: tidyr # from CRAN
# -+ R>=4.3.X # updated apt-get sources list, installs: 4.3.1
# @requires: noiseq # from Bioconductor
# @requires: busparse # from Bioconductor
# @requires: biocmanager # from CRAN
# @requires: caret # from CRAN
# @requires: dplyr # from CRAN
# @requires: dt # from CRAN
# @requires: devtools # from CRAN
# @requires: e1071 # from CRAN
# @requires: forcats # from CRAN
# @requires: ggplot2 # from CRAN
# @requires: ggplotify # from CRAN
# @requires: gridbase # from CRAN
# @requires: gridextra # from CRAN
# @requires: htmltools # from CRAN
# @requires: jsonlite # from CRAN
# @requires: optparse # from CRAN
# @requires: plotly # from CRAN
# @requires: plyr # from CRAN
# @requires: pROC # from CRAN
# @requires: purrr # from CRAN
# @requires: rmarkdown # from CRAN
# @requires: reshape # from CRAN
# @requires: readr # from CRAN
# @requires: randomForest # from CRAN
# @requires: scales # from CRAN
# @requires: stringi # from CRAN
# @requires: stringr # from CRAN
# @requires: tibble # from CRAN
# @requires: tidyr # from CRAN
# -+ python>3.7 # apt-get, installs: 3.10.12
# @requires: bx-python # pip install from pypi
# @requires: biopython # pip install from pypi
Expand All @@ -62,7 +62,7 @@ FROM ubuntu:22.04
LABEL maintainer="Skyler Kuhn <[email protected]>" \
base_image="ubuntu:22.04" \
version="v0.1.0" \
software="sqanti3/v5.1.2" \
software="sqanti3/v5.2.0" \
about.summary="SQANTI3: Tool for the Quality Control of Long-Read Defined Transcriptomes" \
about.home="https://github.com/ConesaLab/SQANTI3" \
about.documentation="https://github.com/ConesaLab/SQANTI3/wiki/" \
Expand Down Expand Up @@ -115,8 +115,10 @@ RUN apt-get update \
# python/3.10.6
python3 \
python3-pip \
# R/4.1.2-1
r-base \
# Requirements for installing latest R version:
# https://cran.r-project.org/bin/linux/ubuntu/
software-properties-common \
dirmngr \
# STAR/2.7.10a
rna-star \
# samtools/1.13-4
Expand All @@ -133,8 +135,19 @@ RUN localedef -i en_US -f UTF-8 en_US.UTF-8
# Perl fix issue
RUN cpanm FindBin Term::ReadLine


############### MANUAL ################
# Install tools from src manually,
# Installs R (4.3.X) and required packages
# For more information, check out:
# https://cran.r-project.org/bin/linux/ubuntu/
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
&& add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" \
&& apt-get -y install r-base r-base-dev r-recommended r-base-dev \
&& apt-get -y install libboost-dev \
# Update apt-get R package index
&& add-apt-repository ppa:c2d4u.team/c2d4u4.0+

# Build tools from src manually,
# Installs deSALT/1.5.6 from GitHub:
# https://github.com/ydLiu-HIT/deSALT/releases/tag/v1.5.6
# This tool was created using an older
Expand Down Expand Up @@ -174,7 +187,53 @@ WORKDIR /opt2

############### INSTALL ################
# Install any bioinformatics packages
# available with pypi or CRAN/BioC
# available with pypi or CRAN/BioC.
# Install required CRAN R packages via apt-get
RUN apt-get update \
&& apt-get -y upgrade \
&& DEBIAN_FRONTEND=noninteractive apt-get install -y \
# CRAN R packages
r-cran-caret \
r-cran-dplyr \
r-cran-dt \
r-cran-devtools \
r-cran-e1071 \
r-cran-forcats \
r-cran-ggplot2 \
r-cran-gridbase \
r-cran-gridextra \
r-cran-htmltools \
r-cran-jsonlite \
r-cran-optparse \
r-cran-plotly \
r-cran-plyr \
r-cran-proc \
r-cran-purrr \
r-cran-rmarkdown \
r-cran-reshape \
r-cran-readr \
r-cran-randomforest \
r-cran-scales \
r-cran-stringi \
r-cran-stringr \
r-cran-tibble \
r-cran-tidyr \
&& apt-get clean && apt-get purge \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Install remaining R packages manually,
# missing from apt-get sources list:
# - r-cran-biocmanager
# - r-cran-ggplotify
# - r-cran-rcolorconesa
# - r-bioc-busparse
# - r-bioc-noiseq
# Remaining CRAN packages
RUN Rscript -e 'install.packages(c("BiocManager","ggplotify", "RColorConesa"), repos="http://cran.r-project.org")'
# Remaining Bioconductor packages
RUN Rscript -e 'BiocManager::install(c("BUSpaRse", "NOISeq"), update = FALSE, Ncpus = 4)'

# Installs required python packages
RUN ln -sf /usr/bin/python3 /usr/bin/python
RUN pip3 install --upgrade pip \
&& pip3 install Cython \
Expand Down Expand Up @@ -224,70 +283,22 @@ ENV PATH="${PATH}:/opt2/cdna_cupcake/28.0.0/cDNA_Cupcake-28.0.0/sequence"
ENV PYTHONPATH="${PYTHONPATH}:/opt2/cdna_cupcake/28.0.0/cDNA_Cupcake-28.0.0/sequence"
WORKDIR /opt2

# Install R packages via apt
RUN apt-get update \
&& apt-get -y upgrade \
&& DEBIAN_FRONTEND=noninteractive apt-get install -y \
# CRAN R packages
r-cran-biocmanager \
r-cran-caret \
r-cran-dplyr \
r-cran-dt \
r-cran-devtools \
r-cran-e1071 \
r-cran-forcats \
r-cran-ggplot2 \
r-cran-gridbase \
r-cran-gridextra \
r-cran-htmltools \
r-cran-jsonlite \
r-cran-optparse \
r-cran-plotly \
r-cran-plyr \
r-cran-proc \
r-cran-purrr \
r-cran-rmarkdown \
r-cran-reshape \
r-cran-readr \
r-cran-randomforest \
r-cran-scales \
r-cran-stringi \
r-cran-stringr \
r-cran-tibble \
r-cran-tidyr \
# Bioconductor
r-bioc-noiseq \
&& apt-get clean && apt-get purge \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# Install R packages manually,
# missing from apt:
# - r-bioc-busparse
# - r-cran-ggplotify
# CRAN packages
RUN Rscript -e 'install.packages(c("ggplotify"), repos="http://cran.r-project.org")'
# Bioconductor packages
RUN Rscript -e 'BiocManager::install(c("BUSpaRse"), update = FALSE, Ncpus = 4)'
# Install missing packages,
# not listed in sqanti docs,
# noticed when running ML filter
RUN Rscript -e 'install.packages(c("RColorConesa"), repos="http://cran.r-project.org")'

########### SQANTI3/v5.1.2 ############
# Installs SQANTI3/v5.1.2, dependencies
########### SQANTI3/v5.2.0 ############
# Installs SQANTI3/v5.2.0, dependencies
# and requirements have already been
# satisfied, for more info see:
# https://github.com/ConesaLab/SQANTI3
RUN mkdir -p /opt2/sqanti3/5.1.2/ \
&& wget https://github.com/ConesaLab/SQANTI3/archive/refs/tags/v5.1.2.tar.gz -O /opt2/sqanti3/5.1.2/v5.1.2.tar.gz \
&& tar -zvxf /opt2/sqanti3/5.1.2/v5.1.2.tar.gz -C /opt2/sqanti3/5.1.2/ \
&& rm -f /opt2/sqanti3/5.1.2/v5.1.2.tar.gz \
RUN mkdir -p /opt2/sqanti3/5.2.0/ \
&& wget https://github.com/ConesaLab/SQANTI3/archive/refs/tags/v5.2.tar.gz -O /opt2/sqanti3/5.2.0/v5.2.tar.gz \
&& tar -zvxf /opt2/sqanti3/5.2.0/v5.2.tar.gz -C /opt2/sqanti3/5.2.0/ \
&& rm -f /opt2/sqanti3/5.2.0/v5.2.tar.gz \
# Removing exec bit for non-exec files
&& chmod -x \
/opt2/sqanti3/5.1.2/SQANTI3-5.1.2/LICENSE \
/opt2/sqanti3/5.1.2/SQANTI3-5.1.2/.gitignore \
/opt2/sqanti3/5.1.2/SQANTI3-5.1.2/*.md \
/opt2/sqanti3/5.1.2/SQANTI3-5.1.2/*.yml \
/opt2/sqanti3/5.2.0/SQANTI3-5.2/LICENSE \
/opt2/sqanti3/5.2.0/SQANTI3-5.2/.gitignore \
/opt2/sqanti3/5.2.0/SQANTI3-5.2/*.md \
/opt2/sqanti3/5.2.0/SQANTI3-5.2/*.yml \
# Patch: adding absolute PATH to howToUse.png
# that gets embedded in the report. When running
# sqanti_qc.py within docker/singularity container,
Expand All @@ -296,18 +307,18 @@ RUN mkdir -p /opt2/sqanti3/5.1.2/ \
# path). Converting relative path in Rmd files to
# an absolute path to avoid this issue altogether.
&& sed -i \
's@src="howToUse.png"@src="/opt2/sqanti3/5.1.2/SQANTI3-5.1.2/utilities/report_qc/howToUse.png"@g' \
/opt2/sqanti3/5.1.2/SQANTI3-5.1.2/utilities/report_qc/SQANTI3_report.Rmd \
/opt2/sqanti3/5.1.2/SQANTI3-5.1.2/utilities/report_pigeon/pigeon_report.Rmd
's@src="howToUse.png"@src="/opt2/sqanti3/5.2.0/SQANTI3-5.2/utilities/report_qc/howToUse.png"@g' \
/opt2/sqanti3/5.2.0/SQANTI3-5.2/utilities/report_qc/SQANTI3_report.Rmd \
/opt2/sqanti3/5.2.0/SQANTI3-5.2/utilities/report_pigeon/pigeon_report.Rmd

ENV PATH="${PATH}:/opt2/sqanti3/5.1.2/SQANTI3-5.1.2:/opt2/sqanti3/5.1.2/SQANTI3-5.1.2/utilities"
ENV PATH="${PATH}:/opt2/sqanti3/5.2.0/SQANTI3-5.2:/opt2/sqanti3/5.2.0/SQANTI3-5.2/utilities"
WORKDIR /opt2


################ POST #################
# Add Dockerfile and export environment
# variables and update permissions
ADD Dockerfile /opt2/sqanti3_5-1-2.dockerfile
ADD Dockerfile /opt2/sqanti3_5-2-0.dockerfile
RUN chmod -R a+rX /opt2
ENV PATH="/opt2:$PATH"
# Hide deprecation warnings from sqanit
Expand Down
12 changes: 6 additions & 6 deletions docker/sqanti3/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -7,20 +7,20 @@ Directly below are instructions for building an image using the provided Dockerf
docker image ls

# Build from Dockerfile
docker build --no-cache -f Dockerfile --tag=sqanti3:v0.1.0 .
docker build --no-cache -f Dockerfile --tag=sqanti3:v0.2.0 .

# Testing, take a peek inside
docker run -ti sqanti3:v0.1.0 /bin/bash
docker run -ti sqanti3:v0.2.0 /bin/bash

# Updating Tag before pushing to DockerHub
docker tag sqanti3:v0.1.0 skchronicles/sqanti3:v0.1.0
docker tag sqanti3:v0.1.0 skchronicles/sqanti3 # latest
docker tag sqanti3:v0.2.0 skchronicles/sqanti3:v0.2.0
docker tag sqanti3:v0.2.0 skchronicles/sqanti3 # latest

# Check out new tag(s)
docker image ls

# Push new tagged image to DockerHub
docker push skchronicles/sqanti3:v0.1.0
docker push skchronicles/sqanti3:v0.2.0
docker push skchronicles/sqanti3:latest
```

Expand All @@ -29,7 +29,7 @@ docker push skchronicles/sqanti3:latest
Scan your image for known vulnerabilities:

```bash
docker scan sqanti3:v0.1.0
docker scan sqanti3:v0.2.0
```

> **Please Note**: Any references to `skchronicles` should be replaced your username if you would also like to push the image to a non-org account.

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