Cannot initialize GLFW3

[pwh124]

Describe the bug A clear and concise description of what the bug is.

When trying to run gw, GLFW3 cannot be initialized.

To Reproduce Steps to reproduce the behavior:

Installation

mamba create -n gw
mamba activate gw
mamba install -c bioconda -c conda-forge gw

Running

gw
# then entered 0 for ce11 genome

Expected behavior A clear and concise description of what you expected to happen.

gw runs

Screenshots If applicable, add screenshots to help explain your problem.

System (please complete the following information):

• GW version: 1.0.1
• OS: Ubuntu 22.04

Additional context Add any other context about the problem here.

Two other people in my lab can run this (installed from conda) on the same remote server

[kcleal]

Hi @pwh124, The conda recipie has just been updated, would you mind trying the install again just to double check if the latest change has resolved it? Also, Ive noticed that the order of conda channels can sometimes resolve install issues:

mamba install -c condo-forge -c bioconda gw

The previous conda recipe was not including the "core dependency tree" libraries, so for minimal installations (miniforge) this lead to missing libraries. I have updated the recipe, but I have not had a chance to test it yet.

Alternatively, if the conda package is not yet fixed, building from source should work:

mamba install -c conda-forge -c bioconda htslib glfw
git clone https://github.com/kcleal/gw && cd gw
make prep
CONDA_PREFIX=/pathTo/mamba make -j4

[kcleal]

Hi @pwh124, I believe v1.0.2 fixes this issue. Let me know if this is not the case and I will re-open!

[pwh124]

Apologies for not checking up on this sooner.

I have reinstalled gw v1.0.2 on a fresh server in a fresh mamba environment.

I receive the same error:

GLFW Error: Failed to detect any supported platform
ERROR: could not initialize GLFW3
terminate called without an active exception
Aborted (core dumped)

[kcleal]

OK thanks @pwh124.

I will add some more debugging code to try and help resolve this. Thanks for your patience

[pwh124]

No worries! Happy to try to help run stuff to see if it works.

[kcleal]

Hi @pwh124, v1.0.3 has been released might help debug the issue. Ive added some details in issue #38

Your issue is slightly different though and occurs when creating a window. GLFW3 library indicates that it cannot detect any supported platform. I suspect this is because the correct X11 lib cannot be found, or perhaps you may be running a Wayland session?

Happy to provide more details if needs be.