Install Dependencies Error about atac-seq-pipeline HOT 9 CLOSED

This is Conda's issue. conda/conda#4088
Full path for Conda's installation should not be long (~80). Try installing Conda on your home (e.g. /home/your_username, whose path is much shorter than /ifs/scratch/columbia/CSCI/Passegue/Paul_Dellorusso/miniconda3).

Or try with SGE + singularity method.

from atac-seq-pipeline.

Thanks for the quick reply.

My home directory on the cluster is: /ifs/scratch/columbia/CSCI/Passegue/Paul_Dellorusso/

Is there any way around this using Conda? I would prefer it over singularity if possible. Otherwise I will try singularity if there is nothing to do about it

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There might be an workaround but I am not sure. In my experience, I could increase maximum path ($CONDA_PREFIX) length to 255 from 80. But It's long long time ago so I don't remember how I fixed it.

Please install the latest Conda and read through similar issues on Conda (like conda/conda-build#1484).

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Closing this.

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I've been trying to make this work as I can't get singularity installed on my cluster (working on this issue in a parallel).

I've searched through the similar issues but I can't follow along with what the suggested workarounds are. If you happen to know a specific set of commands that will make this work I would appreciate it. I'm not sure if I need to directly edit the install dependencies script to do so?

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This will be fixed in the next release v1.1.5. That limit will increase to 255 from 80. You may need to uninstall (conda/uninstall_dependencies.sh)/re-install(conda/install_dependencies.sh) Conda dependencies.

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great thanks a lot, I will try again when v1.1.5 is released

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https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/conda/requirements_py3.txt#L11

You can actually fix it by commenting out version information in line 11 of requirements_py3.txt.
matplotlib ==1.5.1 -> matplotlib #==1.5.1. Please uninstall (bash/uninstall_dependencies.sh)/reinstalling(bash/install_dependencies.sh) dependencies after this.

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this worked! thank you!

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