Using the Homer suite with conda

Question

[rioualen]

Hello,

I'm getting my hands on Conda and I have an issue related to the Homer suite.

Using the chanel bioconda, I did conda install homer. The problem is, a lot of executables are missing compared to my local install. I have 35 executable instead of more than a hundred, and in particular the "makeTagDirectory" executable which is missing.

How to get a full install of Homer using Conda?

Thanks

Answer 1

[Devon Ryan]

You'd need to update the bioconda recipe to fix this.

As an aside, Homer is real mess to install and manage. I would encourage you to use something else if possible.

[rioualen]

Oh thanks, I'll look into that!

Eventually my point is to use many peak-calling tools, and that includes Homer... Besides, I wanted to use Macs2 but it raises conflict with python 2 and 3! I've also tried other peak-callers outside Conda but they're super annoying to install and they definitely aren't in Bioconda repositories. I guess my task is gonna be tough :-)

[CMosychuk]

@rioualen did you try setting up a namespace for the macs2 installation since it requires py2.7?

conda create --name macs python=2.7

source activate macs

conda install macs2

[rioualen]

I'm using python 3.5 cause I'm using snakemake, but I understand it is not possible to use both python versions in one environment?

[Devon Ryan]

macs2 doesn't have to be in the same environment. Have your shell command activate the appropriate one:

shell: """
    source activate my_macs2_env
    macs2 callpeak ...
    """

We do this all the time with environment modules.

[rioualen]

Thank you, that's the kind of plan I have for the future, but I have dozens of Snakemake rules and my workflows are available publicly, so it's gonna take a while until I do all of this properly. Like I said, I'm a total newbie with Conda and many of the software I'm using don't have Conda recipes.

Right now I need to write a little tutorial with a Snakemake demo, and I was hoping I could do that in one single environment. I'm gonna try to find another peak-caller that works out of the box with python3 for now :-)

[Devon Ryan]

"Installing software" is typically listed as one of the top annoyances in bioinformatics :(