# \`pip install kneaddata\` doesn't install dependencies

**URL:** <https://forum.biobakery.org/t/pip-install-kneaddata-doesnt-install-dependencies/2967>\
**Category:** KneadData\
**Created:** [January 3, 2022, 9:26pm UTC](https://forum.biobakery.org/t/pip-install-kneaddata-doesnt-install-dependencies/2967 "2022-01-03T21:26:41Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![crusher083](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/crusher083/32/1168_2.png) [@crusher083](https://forum.biobakery.org/u/crusher083)\
**Post date:** [January 3, 2022, 9:26pm UTC](https://forum.biobakery.org/t/pip-install-kneaddata-doesnt-install-dependencies/2967/1 "2022-01-03T21:26:41Z")

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When using `pip` dependencies such as `trimmomatic` or `bowtie2` aren’t installed.  
The docker [biobakery/Dockerfile at master · biobakery/biobakery · GitHub](https://github.com/biobakery/biobakery/blob/master/docker/kneaddata/Dockerfile) will not run kneaddata, as it fails to find trimmomatic and bowtie2 in `$PATH` .

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**Author:** ![rohit\_satyam](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/rohit_satyam/32/1689_2.png) [@rohit\_satyam](https://forum.biobakery.org/u/rohit_satyam)\
**Post date:** [September 30, 2022, 10:50pm UTC](https://forum.biobakery.org/t/pip-install-kneaddata-doesnt-install-dependencies/2967/2 "2022-09-30T22:50:40Z")

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Yes, even the conda recipe doesn’t install dependencies like `BMTagger` or `TRF` or `srprism` and `BMtools`. I am having a hard time using making hg48 indexes because of the inability to compile `Srprism` on HPC. Can these dependencies be included in conda package?

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**Author:** ![shrez28](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/shrez28/32/2773_2.png) [@shrez28](https://forum.biobakery.org/u/shrez28)\
**Post date:** [April 2, 2024, 8:14pm UTC](https://forum.biobakery.org/t/pip-install-kneaddata-doesnt-install-dependencies/2967/3 "2024-04-02T20:14:46Z")

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@sagunmaharjann

The pip install kneaddata did not install the dependencies (Trimmomatic, bowtie2, trf)

Is it due to any error or should we download/install the dependencies separately?

Thanks,  
Shrez