kallisto bootstrap / condo installation problem

kallisto bootstrap / condo installation problem

0

I have used kallisto in the past, but am now struggling to get it to work on a new computer (MacBook M1).

  1. When I download kallisto using brew, and try to run kallisto quant, I get an error not generating bootstraps ‘Warning: kallisto was not compiled with HDF5 support so no bootstrapping will be performed. Run quant with –plaintext option or recompile with HDF5 support to obtain bootstrap estimates.’

% for file in *fastq.gz; do kallisto quant -i
kallisto_index_musmus.idx -o “$file.kallisto” -b 100 –single
–rf-stranded -l 260 -s 20 “$file”; done

[quant] fragment length distribution is truncated gaussian with mean =
260, sd = 20
Warning: kallisto was not compiled with HDF5 support so
no bootstrapping will be performed. Run quant with –plaintext option
or recompile with HDF5 support to obtain bootstrap estimates. [index]
k-mer length: 31 [index] number of targets: 118,489 [index] number of
k-mers: 100,614,952

  1. I have read that this might be an issue installing kallisto from brew. I installed conda and tried to install kallisto using condo, but
    get the following

      ~ % conda install kallisto
        Collecting package metadata (current_repodata.json): done
        Solving environment: failed with initial frozen solve. Retrying with flexible solve.
        Collecting package metadata (repodata.json): done
        Solving environment: failed with initial frozen solve. Retrying with flexible solve.
    

PackagesNotFoundError: The following packages are not available from
current channels:

Could you please help me to resolve this?


hfd5


kallisto


condo

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