QuestionsCategory: BIOSTARefetch, bgzip, infoseq, seqkit, bioawk – commands not found. Do I need to install something?
mehtam5@nih.gov asked 6 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
stonelakeak@nih.gov Staff answered 6 months ago

Make sure the miniconda install goes as described – that should fix this problem. 
 

tillodc@nih.gov Staff answered 6 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.