installation issue in Orfeo for freebayes depedencies (vcflib)
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I am experiencing some installation troubles while I am installing freebayes into the cluster (ORFEO). Frebayees is useful to generate the input .vcf file to pass to WhatsHap. The problem rises when I tried to install some of the dependencies, in particular vcflib.
The easiest way to dot his:
conda install -c bioconda vcflib
but of course, it fails. I am doing so inside a conda env I created. the error I have is the following:
ERROR conda.core.link:_execute(740): An error occurred while installing package 'conda-forge::zlib-1.2.13-hd590300_5'.
Rolling back transaction: done
[Errno 2] No such file or directory: '/orfeo/opt/programs/intel/fedora37/conda/23.3.1/pkgs/zlib-1.2.13-hd590300_5/lib/libz.so'
()
I already tried to export the path of the library, but it didn't work. I try to update conda into the cluster since is not the latest version, but sadly nothing changed. I tried other way to install vcf, but all of them bring me at the same error or didn't work
You can try to use Singularity image Frebayees without installation it into cluster. I also experienced fist time similar issues with packages dependencies installation and now I use the Singularity containers whenever possible.