MINTmap not found

[Ben7124]

Hello,

When I run the "XICRA config" command in the conda environment, it says ERROR: Software MINTmap could not be found. Below is the complete output. Any help is appreciated! ++++++++++++++++++++ External dependencies: ++++++++++++++++++++ Software: fastqc.........[ OK ] Software: cutadapt.........[ OK ] Software: multiqc.........[ OK ] Software: Rscript.........[ OK ] Software: java..........[ OK ] Software: python.........[ OK ] Software: perl..........[ OK ] Software: make..........[ OK ] Software: git...........[ OK ] Software: fastq-join.........[ OK ] Software: sRNAbench.jar.........[ OK ] Software: mirtop.........[ OK ] Software: optimir.........[ OK ] Software: miraligner.jar.........[ OK ] Software: STAR..........[ OK ] Software: featureCounts.........[ OK ]

**ERROR: Software MINTmap could not be found.

[JFsanchezherrero]

Hi there,

Thank you very much for your interest and giving a try to XICRA.

The error you are having here is a well-known issue due to the recent development of the tRNA module. We have just implemented a new version of MINTmap that arose a few weeks ago too. But MINTmap software is still under development and no release to conda has been generated yet.

We installed, tested and set MINTmap to work within XICRA by doing the following as I would show you here. So far, we recommend to install MINTmap following these instructions. We will work to include MINTmap in the XICRA environment and installation in following releases of XICRA.

You can do as follows, please be aware to have the XICRA conda environment activated and internet connection to donwload the MINTmap python code, v2 alpha release (https://github.com/TJU-CMC-Org/MINTmap).

# activate conda
conda activate XICRA_env

## get the MINTmap release
wget https://github.com/TJU-CMC-Org/MINTmap/releases/download/v2.0-alpha/MINTmap-2.0a0-py3-none-any.whl
## and install it
pip install MINTmap-2.0a0-py3-none-any.whl

## check XICRA configuration again
XICRA config

Then, if everything looks fine, you should be able to run the XICRA tRNA module.

If your concern here is not associated with tRNA analysis and you are only interested in XICRAfor the miRNA analysis, you might just skip all these steps to install MINTmapand follow the analysis as stated in the XICRAdocumentation: https://xicra.readthedocs.io/en/latest/user_guide/quickStart.html

Let me know if you manage to install and use tRNA module or if you need further assistance. Best regards,

[Ben7124]

Thank you for your help! I am only doing miRNA analysis so I guess I don't need to install MINTmap after all. If I need to, I will come back to these instructions. Thanks again!

[JFsanchezherrero]

Great!