# Metaphlan install error with pip

**URL:** <https://forum.biobakery.org/t/metaphlan-install-error-with-pip/2832>\
**Category:** MetaPhlAn\
**Created:** [November 24, 2021, 10:15pm UTC](https://forum.biobakery.org/t/metaphlan-install-error-with-pip/2832 "2021-11-24T22:15:36Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![ll2021](https://avatars.discourse-cdn.com/v4/letter/l/f17d59/32.png) [@ll2021](https://forum.biobakery.org/u/ll2021)\
**Post date:** [November 24, 2021, 10:15pm UTC](https://forum.biobakery.org/t/metaphlan-install-error-with-pip/2832/1 "2021-11-24T22:15:36Z")

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I am trying to follow the biobakery workflow tutorial and am running into errors trying to install the workflows with pip. I successfully installed kneaddata and humann, but metaphlan is giving me trouble.  
Specifically, I am stuck here:  
$ metaphlan --install --nproc 2

This returns an error related to bowtie2:  
FileNotFoundError: [Errno 2] No such file or directory: ‘bowtie2-build’: ‘bowtie2-build’

How can I fix this?

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<div class="post-metadata">

**Author:** ![w\_ceasea](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/w_ceasea/32/1127_2.png) [@w\_ceasea](https://forum.biobakery.org/u/w_ceasea)\
**Post date:** [November 25, 2021, 8:33am UTC](https://forum.biobakery.org/t/metaphlan-install-error-with-pip/2832/2 "2021-11-25T08:33:52Z")

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Hi,

You could download bowtie2 directly from [Bowtie - Browse /bowtie2/2.4.4 at SourceForge.net](https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.4/)

After decompress, add that path to the $PATH

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<div class="post-metadata">

**Author:** ![Heba\_Allah\_Mohamed\_H](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/heba_allah_mohamed_h/32/1733_2.png) [@Heba\_Allah\_Mohamed\_H](https://forum.biobakery.org/u/Heba_Allah_Mohamed_H)\
**Post date:** [December 1, 2022, 4:52pm UTC](https://forum.biobakery.org/t/metaphlan-install-error-with-pip/2832/3 "2022-12-01T16:52:28Z")

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Can u explain this more plz:

```auto
After decompress, add that path to the $PATH

```

what does this mean? I need to put it in metaphlan folder of repo I installed?

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I installed metaphlan using lines below

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/e/e0f11ef0c89dfb4bea039bf9732b45be211236dc.png)

and then everything was going smoothly till this error appeared below

 ![image](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/e/edd87fb667d10243c7baa2418f1a2bc123d10048.png)

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<div class="post-metadata">

**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [December 6, 2022, 8:20am UTC](https://forum.biobakery.org/t/metaphlan-install-error-with-pip/2832/4 "2022-12-06T08:20:33Z")

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Hi all, installing metaphlan with pip will NOT install all the libraries and dependencies necessary to run the tool (and they should be installed manually), I suggest you instead to install it using conda