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Issue tracker for the Biostar Handbook
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Issues loading programs #158

Closed theokirkland closed 3 years ago

theokirkland commented 3 years ago

I have previously used the programs from this book without issues. When I purchased an update problems developed. I am running these programs on a Mac

The errors were CondaVerificationError: The package for emboss located at /Users/theoneal/miniconda3/pkgs/emboss-6.6.0-h6debe1e_0 appears to be corrupted. The path 'share/EMBOSS/data/TAXONOMY/names.dmp' specified in the package manifest cannot be found. ClobberError: This transaction has incompatible packages due to a shared path. packages: bioconda/osx-64::perl-compress-raw-bzip2-2.087-pl526h6de7cb9_0, bioconda/osx-64::perl-extutils-makemaker-7.36-pl526_1, bioconda/osx-64::perl-io-zlib-1.10-pl526_2, bioconda/osx-64::perl-json-4.02-pl526_0 path: 'lib/5.26.2/darwin-thread-multi-2level/perllocal.pod' ClobberError: This transaction has incompatible packages due to a shared path. packages: conda-forge/osx-64::openjdk-11.0.9.1-hcf210ce_1, conda-forge/osx-64::freetype-2.10.4-h4cff582_1 path: 'lib/libfreetype.dylib'

When I run doctor.py bwa, fastqc, seqret, subread-align, featureCounts, efetch, esearch, fastq-dump are missing. I went through the doctor.py --fixme routine without fixing the problem.

Thanks for any help.

ialbert commented 3 years ago

I think you need to reinstall everything,

delete the miniconda3 directory

rm -rf ~/miniconda3

then start from the beginning. It looks like your conda got damaged big time, harder to fix than starting new

theokirkland commented 3 years ago

Thanks for your quick response. That fixed the problems.

Theo

On Nov 5, 2021, at 2:35 PM, Istvan Albert @.***> wrote:

I think you need to reinstall everything,

delete the miniconda3 directory

rm -rf ~/miniconda3

then start from the beginning. It looks like your conda got damaged big time, harder to fix than starting new

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ialbert commented 3 years ago

great to hear