Downloading Multiqc Error

Question

[smithkthedale]

For my university, the way to download multiqc is: singularity exec --cleanenv /n/singularity_images/informatics/multiqc/multiqc_1.9.sif multiqc

Singularity is installed. When I type this into my command line, I'm getting Error: Missing argument '<analysis directory>'.

Can someone please help me rewrite the scirpt, so that multiqc can be installed?

Answer 1

[Phil Ewels]

It sounds like it basically is working already, you just need to provide some arguments.

With a normal installation, you would do:

multiqc <path/to/files>

(where the path is often "." - the current working directory).

In your case, you need to do:

singularity exec --cleanenv /n/singularity_images/informatics/multiqc/multiqc_1.9.sif multiqc <path/to/files>

You might find it easier to make a bash alias in your .bashrc file:

alias multiqc="singularity exec --cleanenv /n/singularity_images/informatics/multiqc/multiqc_1.9.sif multiqc"

Then you can run multiqc commands as you'd normally see in the documentation (and my first example above).

[smithkthedale]

Phil Ewels Can you explain what you mean/give an example of <path/to/files>. I am new to coding and am now getting a -bash: singularity: command not found error

[ATpoint]

Probably you have to load some module first, no?

[GenoMax]

<path/to/files> is the directory which has the result files you are trying to summarize with multiqc. Provide actual path on your server. If you are running this from the directory where the files are then simply add a . (period) to indicate that.

[Phil Ewels]

Yup - see docs here: https://multiqc.info/docs/

MultiQC doesn't run other tools for you - it's designed to be placed at the end of analysis pipelines or to be run manually when you've finished running your tools. When you launch MultiQC, it recursively searches through any provided file paths and finds files that it recognises.

..just go to your analysis directory and run multiqc, followed by a list of directories to search. At it's simplest, this can just be . (the current working directory). MultiQC will scan the specified directories and produce a report based on details found in any log files that it recognises.

[smithkthedale]

singularity exec --cleanenv /n/singularity_images/informatics/multiqc/multiqc_1.9.sif multiqc .

does not work...still can't download.

[GenoMax]

does not work...still can't download.

That does not give us much to work with.

singularity exec --cleanenv /n/singularity_images/informatics/multiqc/multiqc_1.9.sif multiqc . will ONLY work, if you are in the directory where the result files are. There is nothing to "download" at this point.

Do you see "in-line" help if you run:

singularity exec --cleanenv /n/singularity_images/informatics/multiqc/multiqc_1.9.sif multiqc -h

You should see a long thing that starts with

Usage: multiqc [OPTIONS] <analysis directory>

  MultiQC aggregates results from bioinformatics analyses across many
  samples into a single report.