NextPolish, SSPACE-LongRead and backmap.pl

IFB Core Cluster Demande de logiciel ou de banque de données
1

Hi,

I would like to test out these three programs, but I am not being able to compile them. I think because I don't know very well how to install perl programs and set the right paths. Anyway, it would be easier if these three programs would be in the cluster:
NextPolish - GitHub - Nextomics/NextPolish: Fast and accurately polish the genome generated by long reads.
SSPACE-LongRead - GitHub - Runsheng/sspace_longread: The modified version of sspac_longread.pl, add compatibility with blasr5.x
backmap.pl - GitHub - schellt/backmap: Wrapper for short and long read mapping, creation of quality report(s) and estimation of genome size

Thank you for your help
Cheers,
Ana

2

Hi,
I figured out that to compile NextPolish curses.h is missing (NextPolish Installation · Issue #52 · Nextomics/NextPolish · GitHub) but I can't install this without sudo. Could you install it? sudo yum install ncurses-devel ncurses

Thanks,
Ana

3

Hello,

Sorry, we do not install package from linux distribution (with yum or apt)

We use conda or singularity to make software available on the cluster.

As it look like those 3 tools are not in conda, we will need a singularity image definition to install them.

If you can provide those singularity image definition file we can add them quickly.

If not we will try to do it as soon as possible.

Here are some example of singularity file we use for perl software:

4

Hi thanks for your reply, I still don't understand singularity enough to try to build an image file to provide to you so I just decided to try other approaches.
Thanks for you help
Ana

5

Hello,

I have find some time to create a singularity image for NextPolish.
You may want to have a look at it:

But I don't know if we can install it on the cluster, as there is no precise information about the LICENSE of this software.

The only mention I have seen is on the doc:
image

Which I think is not enough precise to allow us or not to made it available for every user.