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I tied to install genometools with anaconda:

conda install -c bioconda genometools

Though, after running that successfully the command gt is not available in my conda environment.

The program 'gt' is currently not installed. You can install it by typing: sudo apt install genometools

While conda tells me the program is installed. Are there multiple packages called genometools? What is the difference and can I install the package providing gt with anaconda at all? There is also a package called genometools-genometools, but it only has two downloads. So, I am not sure that is what I need.

Soerendip
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2 Answers2

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genometools-genometools seem to be the current version. By installing the genometools package I received the same error like you. I guess it's because the binary isn't copy to bin during installation.

genometools-genometools seems to work fine. And it has 2k (2000) and not 2 :)

finswimmer
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genometools-genometools worked for me, while 2 other options (genometools and -c leylabmpi genometools) did not.

Sara Oppenheim
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  • Hi thanks Sara could you clarify your installation code please? it appears you are designating channnels within Anaconda – M__ Jul 26 '20 at 07:34
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    Hi Michael, the example with the channel specified was a "fix" that was suggested elsewhere. What worked for me was "conda install -n GT genometools-genometools" where I specified the environment I wanted to install in (GT) but not the channel to use. – Sara Oppenheim Jul 27 '20 at 18:20