installing SMRTtools 7 on MacOS error

Question

[Tatyana.sysoeva]

Hi! As an absolute novice in characterizing PacBio data, I am trying to install SMRTtools to check the data I received from PB sequel. My laptop is MacOS with Catalina 10.15.4. I downloaded SMRTlink 7 from PacBio website and I ran command in the terminal:

./smrtlink_7.0.1.66975.run --rootdir /Users/user1/smrttools/ smrtlink --smrttools-only
and get errors in 'readlink lines of the .run file:
readlink: illegal option -- f
usage: readlink [-n] [file ...]
smrtlink_7.0.1.66975.run: Error! Encountered unexpected error at 'line 372 ./smrtlink_7.0.1.66975.run', bailing out...
readlink: illegal option -- m
usage: readlink [-n] [file ...]
smrtlink_7.0.1.66975.run: Error! Encountered unexpected error at 'line 485 ./smrtlink_7.0.1.66975.run', bailing out...

I found that readlink may have some problem on MacOS and some workaround with brew install coreutils - but that did not seem to fix my problem..

I would really appreciate ideas on how to solve this, thank you! Tanya

[pristanna]

Hi Tanya, I also haven´t managed to install SMRTtools from SMRTlink. But I am successfully using PacBio tools distributed via Bioconda: https://github.com/PacificBiosciences/pbbioconda, if that could be of some help for you...