Developing-hcp structural pipeline installation

Dear fellow researchers,

We are having difficulties installing the dhcp-structural pipeline package https://github.com/BioMedIA/dhcp-structural-pipeline on our Linux server.

More specifically, we are running into compilation issues with VTK, where it seems downloads/tests during the VTK “make” are not working properly and it dies at around 40% complete (VTK cmake runs fine, btw). So far, workbench and ITK compile just fine. We have previously installed DRAWEM on its own, and VTK compiled fine…So we suspect that there is something wrong with this dhcp version and VTK.

Unfortunately, we cannot use docker on our cluster. Would it be possible for the developers to create a singularity image for us?

Many thanks in advance!
Fotis

Yes, it can be a beast to compile. A large number of software packages all have to line up correctly.

@Jianliang, sorry to ping you, I think you made a singularity image for our cluster, I don’t suppose you have a link to it?

Hi John,

No worries. I did only use the docker container image you built. I pulled the image using singularity pull and that converted the image to a new format recognizable by singularity. Then I ran the pipeline with singularity on cluster.

@Fotis hope above explanable with be helpful.
Best regards,
J

Hi Fotis,

Sorry for delayed reply. Please check below my reply to John. Any further questions please feel free to pin me.

Best regards,
J

Hi Jianliang,

Thank you for the tip! We have tried using the ‘pull’ option and it seemed to work better than compiling from scratch. I’m not sure yet whether it was fully installed as some colleagues are on holiday. I will find out soon, I hope, and let you know as well!

Kind Regards,
Fotis

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