graphbin_SPAdes.py path and ModuleNotFoundError: No module named 'igraph' about graphbin

[anuradhawick]

@michaelwoodworth Thanks for your query. We have updated the code with the help of @alienzj that makes installation much easier for everybody including non-computer scientists.

With referencing to your cluster environment, one solution would be to install graphbin as user with pip3 install . --user. This is possible with our new release. However, if you still cannot install I have 2 workarounds that we use in our cluster NCI Australia.

1. Using conda environments.

This way you can install conda to a location on the cluster that you have permission and initialize in bash_rc. Go to Anaconda Website and download the installer. Then run sh ANACONDA_INSTALLER.sh. Afterwards, you can use conda command from your login node and install dependencies and run GraphBin code without having to run pip install. Make sure you install all dependencies to your conda environment before you run graphbin.

2. Using Linux modules and a python path in your project space in the cluster.

However, using conda might not help you in a cluster due to inode limitations. So you can follow the following steps. Assuming you have Linux modules in your cluster. Please run module avail python to ensure you have a python 3+ version in the cluster to load.

module load python/3.7
pip install -v --no-binary :all: --prefix=/short/your/directory/name .

Most likely when you import the python module pip3 will be aliased to pip in the cluster. This command will install graphbin in path /short/your/directory/name. Then in your job script please add the following.

module load python/3.7
export PYTHONPATH=$PYTHONPATH:/short/your/directory/name/lib/python3.7/site-packages
export PATH=$PATH:/short/your/directory/name/bin

Then you'll have access to graphbin program. This could be the most desired option considering the nature of file systems in clusters and inode limitation.

Please let us know if there are more issues popping. We are happy to help always.

I hope this helps you with your research work! Cheers. 👍

[alienzj]

mamba install -c conda-forge python-igraph

[Vini2]

Closing this issue after improving the code.