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Commit ac25f30a authored by Georgia Stuart's avatar Georgia Stuart
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Initial commit


Signed-off-by: default avatarGeorgia Stuart <gstuart@umass.edu>
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# Modified from https://docs.gitlab.com/ee/ci/docker/docker_layer_caching.html
default:
image: docker:24.0.7
services:
- docker:24.0.7-dind
before_script:
- docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
build:
stage: build
script:
- docker pull $CI_REGISTRY_IMAGE:latest || true
- docker build --cache-from $CI_REGISTRY_IMAGE:latest --tag $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA --tag $CI_REGISTRY_IMAGE:latest .
- docker push $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA
- docker push $CI_REGISTRY_IMAGE:latest
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FROM rocker/ml-verse:4
ARG HMMER_VERSION=3.4
ARG PRODIGAL_VERSION=2.6.3
ARG INFERNAL_VERSION=1.1.2
ARG TRNASCANSE_VERSION=2.0.12
ARG BEDTOOLS_VERSION=2.31.1
WORKDIR /build/hmmer_build
RUN wget http://eddylab.org/software/hmmer/hmmer-${HMMER_VERSION}.tar.gz -O hmmer.tar.gz \
&& tar zxf hmmer.tar.gz --strip-components=1 \
&& ./configure \
&& make && make install \
&& (cd easel; make install) \
&& rm -r ./*
WORKDIR /build/prodigal_build
RUN wget https://github.com/hyattpd/Prodigal/archive/refs/tags/v${PRODIGAL_VERSION}.tar.gz -O prodigal.tar.gz \
&& tar zxf prodigal.tar.gz --strip-components=1 \
&& make install \
&& rm -r ./*
WORKDIR /build/infernal_build
RUN wget http://eddylab.org/infernal/infernal-${INFERNAL_VERSION}.tar.gz -O infernal.tar.gz \
&& tar zxf infernal.tar.gz --strip-components=1 \
&& ./configure \
&& make && make install \
&& rm -r ./*
WORKDIR /build/trnascan-se_build
RUN wget https://github.com/UCSC-LoweLab/tRNAscan-SE/archive/refs/tags/v${TRNASCANSE_VERSION}.tar.gz -O trnascan-se.tar.gz \
&& tar zxf trnascan-se.tar.gz --strip-components=1 \
&& ./configure \
&& make && make install \
&& rm -r ./*
WORKDIR /build/bedtools_build
RUN wget https://github.com/arq5x/bedtools2/archive/refs/tags/v${BEDTOOLS_VERSION}.tar.gz -O bedtools.tar.gz \
&& tar zxf bedtools.tar.gz --strip-components=1 \
&& make \
&& cp bin/* /usr/local/bin \
&& rm -r ./*
WORKDIR /build
COPY microtrait_install.R /build/microtrait_install.R
RUN Rscript /build/microtrait_install.R
WORKDIR /data
RUN rm -r /build
ENTRYPOINT [ "R" ]
This diff is collapsed.
# MicroTrait container for Unity OnDemand
This provides the Dockerfile for a Unity OnDemand compatible
[MicroTrait](https://github.com/ukaraoz/microtrait) container.
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Bootstrap: docker
From: rocker/ml-verse:4
Stage: build
%arguments
HMMER_VERSION=3.4
PRODIGAL_VERSION=2.6.3
INFERNAL_VERSION=1.1.2
TRNASCANSE_VERSION=2.0.12
BEDTOOLS_VERSION=2.31.1
%post
mkdir build && cd build
# Install HMMER: http://hmmer.org/documentation.html
mkdir hmmer_build && cd hmmer_build
wget http://eddylab.org/software/hmmer/hmmer-{{ HMMER_VERSION }}.tar.gz -O hmmer.tar.gz
tar zxf hmmer.tar.gz --strip-components=1
./configure
make && make install
(cd easel; make install)
cd ..
# Install Prodigal
mkdir prodigal_build && cd prodigal_build
wget https://github.com/hyattpd/Prodigal/archive/refs/tags/v{{ PRODIGAL_VERSION }}.tar.gz -O prodigal.tar.gz
tar zxf prodigal.tar.gz --strip-components=1
make install
cd ..
# Install infernal
mkdir infernal_build && cd infernal_build
wget http://eddylab.org/infernal/infernal-{{ INFERNAL_VERSION }}.tar.gz -O infernal.tar.gz
tar zxf infernal.tar.gz --strip-components=1
./configure
make && make install
cd ..
# Install tRNAscan-SE
mkdir trnascan-se_build && cd trnascan-se_build
wget https://github.com/UCSC-LoweLab/tRNAscan-SE/archive/refs/tags/v{{ TRNASCANSE_VERSION }}.tar.gz -O trnascan-se.tar.gz
tar zxf trnascan-se.tar.gz --strip-components=1
./configure
make && make install
cd ..
# Install bedtools
mkdir bedtools_build && cd bedtools_build
wget https://github.com/arq5x/bedtools2/archive/refs/tags/v{{ BEDTOOLS_VERSION }}.tar.gz -O bedtools.tar.gz
tar zxf bedtools.tar.gz --strip-components=1
make
cp bin/* /usr/local/bin
cd ..
# Clean up dependency builds
cd ..
rm -r build
# Install microtrait
Rscript -e 'install.packages(c("R.utils", "RColorBrewer", "ape", "assertthat",
"checkmate", "coRdon", "corrplot", "doParallel", "dplyr", "futile.logger",
"grid", "gtools", "kmed", "lazyeval", "magrittr", "parallel", "pheatmap",
"readr", "stringr", "tibble", "tictoc", "tidyr", "BiocManager"))'
Rscript -e 'BiocManager::install("Biostrings")'
Rscript -e 'BiocManager::install("coRdon")'
Rscript -e 'BiocManager::install("ComplexHeatmap")'
Rscript -e 'devtools::install_github("jlw-ecoevo/gRodon")'
Rscript -e 'devtools::install_github("ukaraoz/microtrait")'
Rscript -e 'microtrait::prep.hmmmodels()'
install.packages(c("R.utils", "RColorBrewer", "ape", "assertthat",
"checkmate", "coRdon", "corrplot", "doParallel", "dplyr", "futile.logger",
"grid", "gtools", "kmed", "lazyeval", "magrittr", "parallel", "pheatmap",
"readr", "stringr", "tibble", "tictoc", "tidyr", "BiocManager"))
BiocManager::install("Biostrings")
BiocManager::install("coRdon")
BiocManager::install("ComplexHeatmap")
devtools::install_github("jlw-ecoevo/gRodon")
devtools::install_github("ukaraoz/microtrait")
microtrait::prep.hmmmodels()
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