Error Installing Nanopolish

[annamack]

Hello,

I am trying to install Nanopolish on a Linux computing cluster with a GCC compiler. Here is what I ran:

git clone --recursive https://github.com/jts/nanopolish.git cd nanopolish/ make

Here is the error I am getting: make: *** [Makefile:162: eigen/INSTALL] Error 4

Any help is appriciated!

[sbridgett]

I was also having difficulty installing Nanopolish, due to an issue with hdf5.

So instead of compiling Nanopolish from source, I have installed it using conda as follows:

(1) If conda isn't already installed, I installed miniconda from: https://docs.conda.io/en/latest/miniconda.html Then logout and login again to enable conda.

(2) Then set channels:

conda config --add channels bioconda

conda config --add channels conda-forge

(This 'conda-forge' channel is needed to install correct hdf5 version for Nanopolish 0.14.0, otherwise conda will install the earlier version 0.13.2 of Nanopolish.)

(3) Updated conda and installed mamba:

conda update -n base -c defaults conda

conda install mamba

(4) Installed Nanopolish 0.14.0:

conda create --name nanopolish
conda activate nanopolish

mamba install nanopolish

which installed the 0.14.0 version of nanopolish.

(5) Then to run Will need to activate the env:

conda activate nanopolish

Or in a script submitted to a compute cluster add:

source $(conda info --base)/etc/profile.d/conda.sh
conda activate nanopolish

I hope that helps.

[rdeborja]

@annamack It seems like a server issue with gitlab.com:

Resolving gitlab.com (gitlab.com)... failed: Temporary failure in name resolution.
wget: unable to resolve host address gitlab.com

I was able to manually retrieve the file:

wget https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.bz2;

I'm hoping it was a rare occurrence. Could you possibly try installing nanopolish again?

Although I personally agree with @sbridgett and use conda myself.

[annamack]

@rdeborja Yes, I was able to install using wget and the link you provided.

Thank you for your assistance!