kallisto - HDF5 brew issue // conda installation issue

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Olesia Ignatenko

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Apr 25, 2023, 9:24:48 PM4/25/23
to kallisto and applications
Hi everyone,

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:

  • kallisto'
iii) Finally, I tried to build kallisto from the source. The following ran OK:

$ 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


-----

Any help would be very much appreciated!! 

Best regards,

Oli


Pall Melsted

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Apr 26, 2023, 11:43:16 AM4/26/23
to kallisto and applications
Hi Oli

To fix this you need to install HDF5 (and autoconf probably) you can do this via conda/mamba

mamba install autoconf=2.69
mamba install hdf5

After this it should run fine, I've verified this on my M1 machine.

Since bioconda does not supply m1 binaries yet you can also set up a separate x86 environment as described in https://towardsdatascience.com/how-to-manage-conda-environments-on-an-apple-silicon-m1-mac-1e29cb3bad12 which is a bit easier 

- Pall


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