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# run Trinity via docker
% docker run --rm -v `pwd`:`pwd` trinityrnaseq/trinityrnaseq Trinity \
--seqType fq \
--left `pwd`/test_data/reads.left.fq.gz \
--right `pwd`/test_data/reads.right.fq.gz \
--max_memory 1G --CPU 4 --output `pwd`/trinity_out_dir
# If you need to install Singularity on linux
sudo apt-get update && \
sudo apt-get install -y build-essential \
libseccomp-dev pkg-config squashfs-tools cryptsetup
sudo rm -r /usr/local/go
export VERSION=1.13.15 OS=linux ARCH=amd64 # change this as you need
wget -O /tmp/go${VERSION}.${OS}-${ARCH}.tar.gz https://dl.google.com/go/go${VERSION}.${OS}-${ARCH}.tar.gz && \
sudo tar -C /usr/local -xzf /tmp/go${VERSION}.${OS}-${ARCH}.tar.gz
echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \
echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc && \
source ~/.bashrc
curl -sfL https://install.goreleaser.com/github.com/golangci/golangci-lint.sh |
sh -s -- -b $(go env GOPATH)/bin v1.21.0
mkdir -p ${GOPATH}/src/github.com/sylabs && \
cd ${GOPATH}/src/github.com/sylabs && \
git clone https://github.com/sylabs/singularity.git && \
cd singularity
git checkout v3.6.3
cd ${GOPATH}/src/github.com/sylabs/singularity && \
./mconfig && \
cd ./builddir && \
make && \
sudo make install
singularity version
# as per: https://github.com/apptainer/singularity/issues/5099#issuecomment-1286798317
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