Dockerfile for SQANTI3/5.1.2 #227
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Hi @skchronicles -thank you for your contribution! We are going to release a new version of SQANTI3 in the next few days, but there shouldn't be major changes regarding dependencies. An update in the installation process of SQ3 is long overdue (e.g. see #180), so this will be extremely useful. |
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@aarzalluz That sounds good! I am going to test everything out today. If I find any issues, I will let you know. |
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@aarzalluz Okay, I have an update. I was able to successfully run the docker image ( Here is the final Dockerfile: # Base image for SQANTI3/v5.1.2,
# uses Ubuntu Jammy (LTS)
FROM ubuntu:22.04
# Depedencies of SQANTI:
# - https://github.com/ConesaLab/SQANTI3/wiki/Dependencies-and-installation
# - https://github.com/ConesaLab/SQANTI3/blob/master/SQANTI3.conda_env.yml
# Overview:
# -+ perl # apt-get, installs: 5.34.0-3
# -+ minimap2 # apt-get, installs: 2.24
# -+ kallisto # apt-get, installs: 0.46.2
# -+ samtools # apt-get, installs: 1.13-4
# -+ STAR # apt-get, installs: 2.7.10a
# -+ uLTRA # from pypi: installs: 0.1
# -+ deSALT # from github: https://github.com/ydLiu-HIT/deSALT
# -+ bedtools # apt-get, installs: 2.30.0
# -+ 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
# -+ python>3.7 # apt-get, installs: 3.10.12
# @requires: bx-python # pip install from pypi
# @requires: biopython # pip install from pypi
# @requires: bcbio-gff # pip install from pypi
# @requires: cDNA_Cupcake # pip install from github
# @requires: Cython # pip install from pypi
# @requires: numpy # pip install from pypi
# @requires: pysam # pip install from pypi
# @requires: pybedtools # pip install from pypi, needs bedtools
# @requires: psutil # pip install from pypi
# @requires: pandas # pip install from pypi
# @requires: scipy # pip install from pypi
LABEL maintainer="aarzalluz" \
base_image="ubuntu:22.04" \
version="v0.1.0" \
software="sqanti3/v5.1.2" \
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/" \
about.tags="Transcriptomics"
############### INIT ################
# Create Container filesystem specific
# working directory and opt directories
# to avoid collisions with the host's
# filesystem, i.e. /opt and /data
RUN mkdir -p /opt2 && mkdir -p /data2
WORKDIR /opt2
# Set time zone to US east coast
ENV TZ=America/New_York
RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime \
&& echo $TZ > /etc/timezone
############### SETUP ################
# This section installs system packages
# required for your project. If you need
# extra system packages add them here.
RUN apt-get update \
&& apt-get -y upgrade \
&& DEBIAN_FRONTEND=noninteractive apt-get install -y \
# bedtools/2.30.0
bedtools \
build-essential \
cmake \
cpanminus \
curl \
gawk \
# gffread/0.12.7
gffread \
git \
# gmap/2021-12-17
gmap \
gzip \
# kallisto/0.46.2
kallisto \
libcurl4-openssl-dev \
libssl-dev \
libxml2-dev \
locales \
# minimap2/2.24
minimap2 \
# perl/5.34.0-3
perl \
pkg-config \
# python/3.10.6
python3 \
python3-pip \
# R/4.1.2-1
r-base \
# STAR/2.7.10a
rna-star \
# samtools/1.13-4
samtools \
# seqtk/1.3-2
seqtk \
wget \
zlib1g-dev \
&& apt-get clean && apt-get purge \
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
# Set the locale
RUN localedef -i en_US -f UTF-8 en_US.UTF-8
# Perl fix issue
RUN cpanm FindBin Term::ReadLine
############### MANUAL ################
# Install tools from src manually,
# Installs deSALT/1.5.6 from GitHub:
# https://github.com/ydLiu-HIT/deSALT/releases/tag/v1.5.6
# This tool was created using an older
# version of GCC that allowed multiple
# definitions of global variables.
# We are using GCC/10, which does not
# allow multiple definitions. Adding
# -Wl,--allow-multiple-definition
# to the linker to fix this issue.
RUN mkdir -p /opt2/desalt/1.5.6/ \
&& wget https://github.com/ydLiu-HIT/deSALT/archive/refs/tags/v1.5.6.tar.gz -O /opt2/desalt/1.5.6/v1.5.6.tar.gz \
&& tar -zvxf /opt2/desalt/1.5.6/v1.5.6.tar.gz -C /opt2/desalt/1.5.6/ \
&& rm -f /opt2/desalt/1.5.6/v1.5.6.tar.gz \
&& cd /opt2/desalt/1.5.6/deSALT-1.5.6/src/deBGA-master/ \
&& make CFLAGS="-g -Wall -O2 -Wl,--allow-multiple-definition" \
&& cd .. \
&& make CFLAGS="-g -Wall -O3 -Wc++-compat -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-function -Wl,--allow-multiple-definition"
ENV PATH="${PATH}:/opt2/desalt/1.5.6/deSALT-1.5.6/src"
WORKDIR /opt2
# Installs namfinder, requirement of
# ultra-bioinformatics tool from pypi.
RUN mkdir -p /opt2/namfinder/0.1.3/ \
&& wget https://github.com/ksahlin/namfinder/archive/refs/tags/v0.1.3.tar.gz -O /opt2/namfinder/0.1.3/v0.1.3.tar.gz \
&& tar -zvxf /opt2/namfinder/0.1.3/v0.1.3.tar.gz -C /opt2/namfinder/0.1.3/ \
&& rm -f /opt2/namfinder/0.1.3/v0.1.3.tar.gz \
&& cd /opt2/namfinder/0.1.3/namfinder-0.1.3/ \
# Build to be compatiable with most
# Intel x86 CPUs, should work with
# old hardware, i.e. sandybridge
&& cmake -B build -DCMAKE_C_FLAGS="-msse4.2" -DCMAKE_CXX_FLAGS="-msse4.2" \
&& make -j -C build
ENV PATH="${PATH}:/opt2/namfinder/0.1.3/namfinder-0.1.3/build"
WORKDIR /opt2
############### INSTALL ################
# Install any bioinformatics packages
# available with pypi or CRAN/BioC
RUN ln -sf /usr/bin/python3 /usr/bin/python
RUN pip3 install --upgrade pip \
&& pip3 install Cython \
&& pip3 install bcbio-gff \
&& pip3 install biopython \
&& pip3 install bx-python \
&& pip3 install matplotlib \
&& pip3 install numpy \
&& pip3 install pandas \
&& pip3 install psutil \
&& pip3 install pybedtools \
&& pip3 install pysam \
&& pip3 install scipy \
&& pip3 install ultra-bioinformatics
# Installing the second to latest release
# of cDNA_cupcake (v28.0.0). The latest
# version of the tool has remove/depreciated
# some modules/scripts that overlap with
# PacBio's Iso-seq software. Using this
# version to ensure everything we may need
# will be installed.
RUN mkdir -p /opt2/cdna_cupcake/28.0.0/ \
&& wget https://github.com/Magdoll/cDNA_Cupcake/archive/refs/tags/v28.0.0.tar.gz -O /opt2/cdna_cupcake/28.0.0/v28.0.0.tar.gz \
&& tar -zvxf /opt2/cdna_cupcake/28.0.0/v28.0.0.tar.gz -C /opt2/cdna_cupcake/28.0.0/ \
&& rm -f /opt2/cdna_cupcake/28.0.0/v28.0.0.tar.gz \
&& cd /opt2/cdna_cupcake/28.0.0/cDNA_Cupcake-28.0.0 \
# Patch: some pyx files contain python2,
# need to specify the langauage_level as
# py2 otherwise it defaults to py3.
&& sed -i 's/cythonize(ext_modules)/cythonize(ext_modules, language_level = "2")/' setup.py \
# sklearn is depreciated, use scikit-learn instead
&& sed -i 's/sklearn/scikit-learn/' setup.py \
# numpy, np.int is depreciated, use np.int_ instead:
# https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
&& find /opt2/cdna_cupcake/28.0.0/cDNA_Cupcake-28.0.0 \
-type f -exec grep 'np\.int' {} /dev/null \; 2> /dev/null \
# Builds cmd: sed -i 's/np\.int\(\s\|$\)/np.int_/g' FILE_TO_FIX
| awk -F ':' -v q="'" -v b='\\' '{print "sed -i", q"s/np"b".int"b"("b"s"b"|$"b")/np.int_/g"q,$1}' \
| sort \
| uniq \
| bash \
&& python setup.py build \
&& python setup.py install
ENV PATH="${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
# 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 \
# 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 \
# Patch: adding absolute PATH to howToUse.png
# that gets embedded in the report. When running
# sqanti_qc.py within docker/singularity container,
# it fails at the report generation step because
# pandoc cannot find the png file (due to relative
# 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
ENV PATH="${PATH}:/opt2/sqanti3/5.1.2/SQANTI3-5.1.2:/opt2/sqanti3/5.1.2/SQANTI3-5.1.2/utilities"
WORKDIR /opt2
################ POST #################
# Add Dockerfile and export environment
# variables and update permissions
ADD Dockerfile /opt2/sqanti3_5-1-2.dockerfile
RUN chmod -R a+rX /opt2
ENV PATH="/opt2:$PATH"
# Hide deprecation warnings from sqanit
ENV PYTHONWARNINGS="ignore::DeprecationWarning"
WORKDIR /data2 |
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Thank you for your great contribution, @skchronicles! Yes, the RColorConesa package was recently accepted in CRAN -I have updated SQANTI3 to prevent installation from GitHub during the running of |
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Hi @skchronicles, I just wanted to let you know that there is a new SQANTI3 release, v5.2. We have updated the required versions for ggplot2, RColorConesa and R in the YML, in case you want to test your docker set up with the latest version. If it works, you are more than welcome to submit a PR including the dockerfile! Best, Ángeles |
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@aarzalluz Okay, that sounds good. I will test everything out next week. |
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Hello @aarzalluz, I just finished creating the new docker image, and I noticed one small thing in the new tagged release: Would it be possible to update the semantic version? Right now it is pointing to the previous release. With that being said, I just need to test the new docker image with some old data. I will let you know when everything is complete, and I will submit a PR with the final dockerfile. Have an awesome day, |
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Hi @skchronicles, thanks a lot for working on this, your dockerfile is awesome! I'm very sorry for the delayed answer. We have updated the semantic version now. Thanks for pointing it out! Best, |
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Hey all,
I have noticed a few issues related to installing sqanti via conda, and I decided to build a docker image for the latest version. Please feel free to use it or distribute it as you see fit. You can use this to build a docker image to push to Dockerhub. This will allow any user with docker or singularity/apptainer to run sqanti without much hassle. I installed most of the dependencies with apt. There were only a few I had to build from source.
Here is my Dockerfile (edit: if you are reading this use the Dockerfile at the bottom of this thread):
I hope this helps. If you have any questions, please let me know. I am going to test it out with my data tomorrow. If there are any issues, I will let you know.
Best regards,
@skchronicles
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