QuestionsCategory: BIOSTARefetch, bgzip, infoseq, seqkit, bioawk – commands not found. Do I need to install something? asked 12 months ago

Update: found the problem – I had not activated bioinfo in the new terminal window! Its all working now. 🙂

Leaving this question here in case anybody else is facing the same issue.

Original question – Most of the commands described in the data compression and subsequent chapters are not working – On trying commands like efetch, bgzip, infoseq, seqkit, bioawk etc, I get ‘command not found’. Is there any additional the needs to be installed for these?

2 Answers Staff answered 12 months ago

Make sure the miniconda install goes as described – that should fix this problem. Staff answered 12 months ago

Always run the command “conda activate bioinfo” in your terminal window before working on any of the exercises described in the textbook or  class.