I have used kallisto in the past, but now am struggling to get bootstrapping to work on a new computer (MacBook M1). I have searched through the issues that others encountered and tried three different methods of installation, but still no luck. Could you please help or direct me to what I may be doing wrong? Thank you so much in advance!!
i) When I downloaded kallisto using brew, and ran kallisto quant, I get the following error (and no 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.'
ii) I then installed conda and tried installing using 'conda install kallisto' or 'conda install -c conda-forge -c bioconda kallisto', but get an error: 'PackagesNotFoundError: The following packages are not available from current channels:
$ git clone https://github.com/pachterlab/kallisto.git
$ cd kallisto/
$ mkdir build
$ cd build
$ cmake .. -DUSE_HDF5=ON
But then I get the following error:
make
[ 3%] Creating directories for 'htslib'
[ 6%] No download step for 'htslib'
[ 10%] No update step for 'htslib'
[ 13%] No patch step for 'htslib'
[ 17%] Performing configure step for 'htslib'
configure: error: cannot find required auxiliary files: config.guess config.sub
make[2]: *** [/Users/ignatenk/kallisto/ext/htslib/src/htslib-stamp/htslib-configure] Error 1
make[1]: *** [CMakeFiles/htslib.dir/all] Error 2
make: *** [all] Error 2
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Any help would be very much appreciated!!
Best regards,
Oli
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