generatemap script not included in conda install

[mheskett]

hi there. just trying to create the reference file for ichorCNA. i installed hmmcopy with conda and I do not see the util directory or generatemap.pl included anywhere.

[SPPearce]

I would also find this very useful

[marcjwilliams1]

I'm not familiar with ichorCNA but if it's the mappability and gc wig files you need, I've made a guide here. There's also a link to some precomputed ref files for both hg19 and hg38 at various bin sizes in the repo.

[SPPearce]

Hi Marc, Thanks, that is helpful. IchorCNA is basically hmmcopy with some tweaks, so requires the gc/map wig files. I am trying to package ichorCNA into a Nextflow module as a nf-core community resource. This needs a container with the required functionality. I've completed readCounter and gcCounter, but need a container that has the dependencies for the bigWig file that mapCounter takes.

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On Mon, 1 Nov 2021, 17:52 Marc Williams, ***@***.***> wrote: I'm not familiar with ichorCNA but if it's the mappability and gc wig files you need, I've made a guide here <https://github.com/shahcompbio/hmmcopy_refs>. There's also a link to some precomputed ref files for both hg19 and hg38 at various bin sizes in the repo. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF55TWM37B4TYD37VAKDSZDUJ3HWLANCNFSM5BHCKI7A> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub> .

[SPPearce]

If you can easily build a container that I can use that lets me call the generateMap.pl perl script with all its dependencies then that would save me a lot of time.

[marcjwilliams1]

That's outside of my wheelhouse I'm afraid. But I was able to run the generateMap.pl successfully within the conda environment defined here https://github.com/shahcompbio/hmmcopy_refs/tree/main/envs so that should get you most of the way there.

[SPPearce]

Yeah, thanks, that is a very useful starting point.

[Solenyalyl]

I couldnot find the generateMap.pl in https://github.com/shahcompbio/hmmcopy_refs/tree/main/envs after generate the environment either....where is it?

[SPPearce]

The bioconda recipe for hmmcopy has now been updated to include a working version of the generateMap.pl script (involved by generateMap.pl. This is then automatically pulled into a docker and a singularity version via the biocontainers framework.
I have used these to generate a hmmcopy module on the Nextflow community project nf-core .

I will point out that the generateMap.pl script is really slow and memory intensive for the human genome.