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brentp / smoove

structural variant calling and genotyping with existing tools, but, smoothly.
Apache License 2.0
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libcrypto.so.1.0.0: cannot open shared object file error with biocontainers #193

Closed georgiesamaha closed 2 years ago

georgiesamaha commented 2 years ago

Hi,

Like previous users (#173, #147, #102, #13) I've run into the cannot find/open libcrypto error, this time while using Singularity and biocontainers (docker://quay.io/biocontainers/smoove:0.2.8--h9ee0642_0 and docker://quay.io/biocontainers/smoove:0.2.7--h9ee0642_0). I attempted to resolve the issue using the workarounds similar to that suggested by #173, but wasn't successful. Running both containers on two different systems I get the following error: 

[smoove] 2022/03/21 05:23:16 starting with version 0.2.8
[smoove] 2022/03/21 05:23:16 calculating bam stats for 1 bams
[smoove]: ([E]lumpy-filter) 2022/03/21 05:23:16 lumpy_filter: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

Cheers, Georgie

brentp commented 2 years ago

Hi, you can try, e.g.:

conda config --add channels bioconda
conda config --add channels conda-forge
conda install samtools==1.12
georgiesamaha commented 2 years ago

Hi Brent,

Thanks for getting back to me.

We are developing a portable structural variant calling pipeline with Singularity, biocontainers and nextflow. We were hoping to include Smoove as one of the tools. We hadn't planned to use conda. Is there another container source you recommend?

brentp commented 2 years ago

Hi, I do not maintain the biocontainers image. The docker image brentp/smoove should work find though.

georgiesamaha commented 2 years ago

ok thanks for your help

microtan0902 commented 2 years ago

Hi, you can try, e.g.:

conda config --add channels bioconda
conda config --add channels conda-forge
conda install samtools==1.12

If so, the following packages (especially for lumpy-sv) will be DOWNGRADED:

duphold 0.2.1-hec16e2b_3 --> 0.1.4-0 libdeflate 1.10-h7f98852_0 --> 1.7-h7f98852_5 lumpy-sv 0.3.0-ha52163a_3 --> 0.2.14a-hdfb72b2_2 pysam 0.19.0-py27hc2126ed_0 --> 0.17.0-py27hc729bab_0

rpetit3 commented 1 year ago

@brentp I'll update the bioconda package (might just need a rebuild). Do you by chance have any recommended pinnings, or should latest be fine?

brentp commented 1 year ago

I don't think there's any need to pin, but you could set to the latest versions. Thank you for debugging this!

rpetit3 commented 1 year ago

No problem! If you don't hear from me, consider all is well! Thanks for writing smoove.

Cheers

rpetit3 commented 1 year ago

@georgiesamaha should now be fixed on Biocontainer quay.io/biocontainers/smoove:0.2.8--h9ee0642_1

@brentp thanks as always, ended up having to pin lumpy-sv >=0.3