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dpryan79 / MethylDackel

A (mostly) universal methylation extractor for BS-seq experiments.
MIT License
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CURL_OPENSSL conflict with samtools #138

Open shraddhapai opened 2 years ago

shraddhapai commented 2 years ago

Hi, Thank you very much for writing MethylDackel. I'm running into a conflict of the libcurl version number on my setup. When running MethylDackel, I get 

MethylDackel: /usr/lib/x86_64-linux-gnu/libcurl.so.4: version `CURL_OPENSSL_4' not found (required by MethylDackel)

but if I install libcurl4 using apt-get install libcurl4-openssl-dev, I now have a conflict with samtools needing CURL_OPENSSL_3.

I realize this is not strictly a MethylDackel issue but was wondering if other users working with samtools and MethylDackel have run into this conflict and how they resolved it.

Thanks!

dpryan79 commented 2 years ago

How are you installing MethylDackel and samtools?

shraddhapai commented 2 years ago

I first attempted to install using conda and a Dockerfile, but ran into python package conflict errors. So I compiled MethylDackel from source. Had to add a couple linker flags in the Makefile for -lcrypto, -lssl, -llzma and -lbz2.

Also compiled samtools from source.

Right now in the painful hacky situation of having to swap out libcurl3 and libcurl4-openssl-dev using sudo apt-get install to run samtools or MethylDackel.

This is on a Ubuntu 18.04 system.

Any help would be great, thanks.

dpryan79 commented 2 years ago

Since you're familiar with conda already could you instead make a new conda environment with both samtools and MethylDackel? I've recently rebuilt both in Bioconda and can guarantee compatibility. Alternatively, you can use the premade docker containers for samtools and MethylDackel that we (Bioconda) provide to Biocontainers for hosting on quay.io (methyldackel here, samtools here).

I'm guessing that the root of your current headache was building MethylDackel in a container that had a different curl version inside compared to your system (against which samtools was compiled). Compiling tools yourself is a real pain, so I'd suggest sticking to just using conda or containers.