**Software Installation on UBC ARC Sockeye - Info for Learners**
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---
Section 1: Use software installed in Sockeye
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1.1 To check whether the software is installed:
which python
module spider python
---
1.2 To load software as a module
module load python
or
module load python/3.8.10
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1.3 manage the module loaded
module list
module avail
---
Section 2: Download the binary
-----------------------------
cd $HOME
mkdir cowsay
cd cowsay
wget https://github.com/Code-Hex/Neo-cowsay/releases/download/v1.0.3/cowsay_1.0.3_Linux_x86_64.tar.gz
tar -xf cowsay_1.0.3_Linux_x86_64.tar.gz
$HOME/cowsay/cowsay Hello
export PATH=$HOME/cowsay:$PATH
cowsay Hello
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Section 3: Compile from the source code
---------------------------------------
module load gcc
module load git
module load cmake
git clone https://github.com/jameskbride/cmake-hello-world
cd cmake-hello-world/
# First attempt: install based on its instruction
mkdir build
cd build/
cmake ..
make
make install
# Second attempt: install in local directory
cmake .. -DCMAKE_INSTALL_PREFIX=$PWD
make
make install
# Test run
$PWD/bin/CMakeHelloWorld
CMakeHelloWorld
# make the system know it is
export PATH=$PWD/bin:$PATH
CMakeHelloWorld
---
Section 4: Install tools in a virtual environment
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# Download Miniconda3
mkdir /arc/project/<allocation_code>/training/bootcamp2023
cd /arc/project/<allocation_code>/training/bootcamp2023
mkdir downloads
cd downloads
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
# Install Miniconda3
bash Miniconda3-latest-Linux-x86_64.sh
# create a Conda environment and install the tool "cowpy"
conda create -n env1
conda activate env1
conda install -c conda-forge cowpy
# copy the the environment
conda env export > env1.yml
conda create -n env2 -f env1.yml
# display the packages installed
conda activate env2
conda list
# arvhive the old environment
conda env export > env1_backup.yml
conda remove -n env1 --all
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Section 5: Use the software through Singularity/Apptainer container
-------------------------------------------------------------------
# load apptainer in Sockeye and pull the pre-built container from DockerHub
module load apptainer
apptainer pull docker://ubuntu
# use the tool in the container
apptainer exec ubuntu_latest.sif perl -v
# enter the container
apptainer shell ubuntu_latest.sif
# Use case - R
cd /arc/project/<allocation_code>/shared/Miniconda3/envs/shared_env
mkdir bioconductor
cd bioconductor
apptainer pull docker://bioconductor/bioconductor_docker
apptainer exec bioconductor_docker_latest.sif Rscript test.r
# install R packages - Option 1
apptainer shell bioconductor_docker_latest.sif
mkdir Rlibs
.libPaths('$PWD/Rlibs')
install.packages("ggplot2")
# install R packages - Option 2
apptainer build --fakeroot --sandbox bioconductor_docker_latest.sandbox
apptainer shell -c --fakeroot --writable bioconductor_docker_latest.sandbox
R
install.packages("ggplot2")
q()
exit
apptainer build --fakeroot bioconductor_docker_latest.modified.sif bioconductor_docker_latest.sandbox
apptainer exec bioconductor_docker_latest.modified.sif Rscript test1.r
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