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FROM nfcore/base:1.9
LABEL authors="Matthew McGowan" \
description="Docker image containing all software requirements for the nf-core/transcriptcorral pipeline"
# Install the conda environment
COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a
# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/nf-core-transcriptcorral-1.0dev/bin:$PATH
# Dump the details of the installed packages to a file for posterity
RUN conda env export --name nf-core-transcriptcorral-1.0dev > nf-core-transcriptcorral-1.0dev.yml
# Installing make
RUN apt-get --allow-releaseinfo-change --fix-missing -y update
RUN apt-get install -y make
RUN apt-get install -y g++
RUN apt-get install zlib1g-dev
# Installing TrimGalore
RUN wget https://github.com/FelixKrueger/TrimGalore/archive/0.6.6.tar.gz -O trim_galore.tar.gz \
&& tar -xvf trim_galore.tar.gz
ENV PATH "$PATH:/TrimGalore-0.6.6"
# Installing Jellyfish2 and RCorrector
RUN wget https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-2.3.0.tar.gz \
&& tar -xvf jellyfish-2.3.0.tar.gz
ENV PATH "$PATH:/jellyfish-2.3.0"
RUN git clone https://github.com/mourisl/rcorrector.git \
&& cd rcorrector \
&& make \
&& cd ..
ENV PATH "$PATH:/rcorrector"
# Get the non-redundant SILVA LSU databases and combine them
RUN mkdir SILVA_db \
&& cd SILVA_db \
&& wget https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/SILVA_138.1_LSURef_NR99_tax_silva.fasta.gz \
&& wget https://www.arb-silva.de/fileadmin/silva_databases/current/Exports/SILVA_138.1_SSURef_NR99_tax_silva.fasta.gz \
&& zcat *.fasta.gz > combined_silva.fasta \
&& sed '/^[^>]/s/U/T/g' combined_silva.fasta > combined_silva_Tfixed.fasta \
&& bowtie2-build combined_silva_Tfixed.fasta combined_silva_reference
WORKDIR /
# Getting scripts to handle corrected files from Harvard Informatics GitHub repository
RUN git clone https://github.com/harvardinformatics/TranscriptomeAssemblyTools
ENV PATH "$PATH:/TranscriptomeAssemblyTools"
# ----------------------------
# Aspera is not a conda module so we have to manually include it.
# Aspera can only be installed as a non-root user
RUN groupadd -g 61000 gemmaker \
&& useradd -g 61000 --no-log-init --create-home --shell /bin/bash -u 61000 gemmaker
USER gemmaker
WORKDIR /home/gemmaker
RUN wget -q https://download.asperasoft.com/download/sw/connect/3.8.1/ibm-aspera-connect-3.8.1.161274-linux-g2.12-64.tar.gz \
&& tar -xf ibm-aspera-connect-3.8.1.161274-linux-g2.12-64.tar.gz \
&& ./ibm-aspera-connect-3.8.1.161274-linux-g2.12-64.sh \
&& rm ibm-aspera-connect-3.8.1.161274-linux-g2.12-64.sh
USER root
WORKDIR /root
RUN mv /home/gemmaker/.aspera /opt/aspera
# Make sure the ascp command is in the path and to support future
# updates of aspera we'll add a new variable ASPERA_KEY that can be
# used in the GEMmaker bash code.
ENV PATH "$PATH:/opt/aspera/connect/bin"
ENV ASPERA_KEY "/opt/aspera/connect/etc/asperaweb_id_dsa.openssh"
WORKDIR /
# Installing Evidentialgenes and dependencies
RUN apt-get --allow-releaseinfo-change --fix-missing -y update \
&& apt-get install -y exonerate \
&& apt-get install -y cd-hit \
&& apt-get install -y ncbi-blast+ \
&& wget http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene20may20.tar \
&& tar -xvf evigene20may20.tar
ENV PATH "$PATH:/evigene/scripts"
ENV PATH "$PATH:/evigene/scripts/prot"
ENV PATH "$PATH:/evigene/scripts/rnaseq"
# Adding the BUSCO Docker image
COPY --from=ezlabgva/busco:v5.2.2_cv1 / /
# Adding the Trinity Docker image
COPY --from=trinityrnaseq/trinityrnaseq:2.13.2 / /
# Adding the TransAbyss Docker image
COPY --from=ss93/transabyss-2.0.1