Modules failing to annotate

[tkmamidi]

I see that some modules are failing to annotate. Please see the example log below!

2023/07/26 17:04:35 cravat.cancer_genome_interpreter finished: Wed Jul 26 17:04:35 2023
2023/07/26 17:04:35 cravat.cancer_genome_interpreter runtime: 0.042s
2023/07/26 17:04:35 funseq2              No module named 'tabix'
2023/07/26 17:04:36 cravat.mutpred_indel started: Wed Jul 26 17:04:36 2023
2023/07/26 17:04:36 cravat.civic         finished: Wed Jul 26 17:04:36 2023
2023/07/26 17:04:36 cravat.civic         runtime: 0.030s
2023/07/26 17:04:36 cravat.phastcons     started: Wed Jul 26 17:04:36 2023
2023/07/26 17:04:36 cravat.gwas_catalog  finished: Wed Jul 26 17:04:36 2023
2023/07/26 17:04:36 cravat.gwas_catalog  runtime: 0.145s
2023/07/26 17:04:36 cadd                 No module named 'tabix'
2023/07/26 17:04:36 cravat.dbsnp         started: Wed Jul 26 17:04:36 2023
2023/07/26 17:04:36 cravat.metalr        started: Wed Jul 26 17:04:36 2023

Any help is appreciated! Thanks!

[tkmamidi]

Solved it by installing pytabix using the below command. I think this must be installed by default? several annotators are failing because of this!

pip3 install --user pytabix

Thank you for making this awesome tool!

[kmoad]

Some modules require pytabix. This is in the module READMEs when installing the GUI, but is not communicated to command-line users.

We don't install pytabix by default because it isn't supported on Windows.

We will work on installing it by default on Linux/Mac and making users more aware when it isn't installed.