Bioinformatics Training and Education Program

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efetch, bgzip, infoseq, seqkit, bioawk – commands not found. Do I need to install something?

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:


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

Answered on April 24th, 2020 by

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

Answered on April 30th, 2020 by