MetaWIBELE dependencies

Microbial community profiling MetaWIBELE
1

Hi bioBakery group,

Thank you for providing us with this tool. I am really interested in it but I am having trouble with the dependencies of MetaWIBELE.

  1. mspminer: I can’t install it. Can other users install it? From their paper “The binary is freely available for non-commercial users at Enterome” However, there is no settings.ini in it which is actually required.

  2. MaAsLin2: I installed MaAsLin2 thru Conda. Where can I find that Maaslin2.R if I want to run masslin2 in the command line? The location I tired: ls /projects/ohlab/ruoyun/data/database/conda/envs/mwgs_2022/lib/R/library/Maaslin2/R and it returned three files: Maaslin2 Maaslin2.rdb Maaslin2.rdx

Thank you!

Best,
Ruoyun

2

Hi Ruoyun,

Thanks for your interest in MetaWIBELE.

  1. Re. mspminer installation: It looks like this issue is specific to the latest version (v1.1.2). I tested v1.0.0 & v1.1.1, and both of them work well on my end. You might want to contact the MSPminer developer and see why settings.ini is missing in the latest version. Actually, MetaWIBELE has packed a default config file for MSPminer into the software package, which means you can well run MetaWIBELE for MSPminer-based processes without the settings.ini along with MSPminer. If you do want to customize MSPminer’s config file, you can use metawibele’s utility to download the MetaWIBELE packed MSPminer’config file (MSPminer_setting.cfg) by running the command like metawibele_download_config --config-type local. See more guidance here: GitHub - biobakery/metawibele: MetaWIBELE: Workflow to Identify novel Bioactive Elements in microbiome

  2. Re. MaAsLin2 installation: To install the command-line version of MaAsLin2, please follow the guidance in MaAsLin2’s manual: GitHub - biobakery/Maaslin2: MaAsLin2: Microbiome Multivariate Association with Linear Models In brief, you need to 1) install the MaAsLin2 dependencies, 2) download and decompress the MaAsLin2 package, 3) then you can run MaAsLin2 in the command line, e.g. /your/path/Maaslin2/R/Maaslin2.R, 4) Maaslin2.R can be treated as an executive file and can be added into you $PATH.

Thanks!
Yancong

1 Like
3

Hello Yanchong.

Could please teach me how to install the MSPminer after downloading the “binary” version in Enterome? I couldn’t find any tutorial for installing it.

I don’t know how to connect it with MetaWIBELE. Thanks a lot!

4

Hi there,

This “binary” version includes the executive file - mspminer, which means you don’t need to compile it on your end. To make it work:

  1. unzip MSPminer.zip
  2. chmod 755 mspminer (in the unzipped folder)
  3. You might need to add the executive file mspminer to your $PATH as it might not be included by default. You will know if it needs to be added if you see the following message “mspminer command not found” when trying to run mspminer.

Thanks!
Yancong

5

Thanks Yancong. it works!