Installation issues

[Mrudhula Komanduri]

Hi team,

I am trying to install q2-metaphlan2 in qiime2 (in conda) on Ubuntu 18.10. I have followed the installation instructions as in https://library.qiime2.org/plugins/q2-metaphlan2/12/. However, after the commands

conda install q2-metaphlan2 -c fasnicar -c bioconda
wget https://bitbucket.org/biobakery/metaphlan2/downloads/SRS019033.fastq
echo -e "sample-id, absolute-filepath,direction\nSRS019033.fastq, $pwd/SRS019033.fastq,forward" > SRS019033.manifest
qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path SRS019033.manifest --output-path SRS019033.qza --input-format SingleEndFastqManifestPhred33

the error message

Command 'qiime' not found, but can be installed with:

sudo apt install qiime

is coming up.

I have tried reinstalling qiime as well. But of no use. Could you please help me with this.

Thank you.

Regards,
Mrudhula

[Francesco Asnicar]

Hi Mrudhula,

q2-metaphlan2 is the plugin of MetaPhlAn2 for QIIME2. After having installed QIIME2, have you activated it?

Here some documentation: https://docs.qiime2.org/2019.1/install/

However, if you're not gonna run MetaPhlAn2 within the QIIME2 environment you can install form bioconda the stand-alone version (https://bioconda.github.io/recipes/metaphlan2/README.html):

$ conda install metaphlan2 -c bioconda

Many thanks,

Francesco

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[Jorge Eduardo]

Hi Franceso,

I'm experiencing the same problem. After installing qiime2 with the instructions I found here https://docs.qiime2.org/2019.4/install/native/ I've tried to install the q2-metaphlan2 plugin after activating the environment as

conda activate qiime2-2019.4

conda install q2-metaphlan2 -c fasnicar -c bioconda

and from outside the environment as

conda install q2-metaphlan2 -c fasnicar -c bioconda -n qiim2-2019.4

and in both cases, conda removes qiime2 and all the other plugins which is why the "qiime command not found" error appears after running

qiime tools import --type 'SampleData[SequencesWithQuality]' --input-path SRS019033.manifest --output-path SRS019033.qza --input-format SingleEndFastqManifestPhred33

Regards,
Jorge

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