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Hopefully by now you have had enough experience installing packages via conda that it is second nature to think of going to https://anaconda.org/ searching for multiqc, finding https://anaconda.org/bioconda/multiqc, and using the information there to install the package. Instead, it is suggested that seeing that it recommends a command of conda install -c bioconda multiqc suggesting you can use this command and not worry about anything else. Instead, if you go to the multiqc homepage and see if they have any recommendations for installation. ← is a hint that there is something potentially unexpected recommended. Try to use this information to figure out what command you should use, and try what you think is best. Explanations follow the version check.
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| title | What versions of fastqc and multiqc does this install? |
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you might (or might not, it is not very visible disappointingly) that next to their conda installation instruction is a small warning icon which takes you to a page about setting up bioconda channels as a prerequisite to installing multiqc. Friday's class will go into detail about managing channels like this and it is not suggested that you follow the commands on that page.
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If you caught the trick from the multiqc homepage you should get returns of "FastQC v0.11.9" and "multiqc, version 1.12" respectively. | |||||||||
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| If the version number for multiqc is not matching up, I expect you will see something like this. You would expect this to return "0.12.1" and "1.14 respectively for the fastqc and multiqc versions, but instead you would see the following for multiqc:
First, the version lists "dev" in the tittle which typically means it is a temporary development version. Second, we get warnings about pyyaml loader being unsafe and depreciated likely as a matter of safety. Read through the next section which identifies the correct command before continuing as it is untested if this version of multiqc will work. | |||||||||
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| On the multiqc homepage the quick install section has a tab for conda which lists the following suggested installation block Based on this, this version is untested in the tutorial, but the real question is how do we get the versions we want and expect. |
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conda install -c bioconda -c conda-forge multiqc | ||
| Code Block | language | bash
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conda create -n GVA-ReadQC -c biocondaconda-forge -cconda-forge bioconda multiqc fastqcIf you did not get it the first time, go ahead and use the command above now (when prompted overwrite/replace the existing environment). While this is not the first time we have seen conda-forge be useful to the point of being required, stressing to look over the home page rather than just the anaconda page is done to try to instill a better practices. Sometimes, getting a program "working" is all you need, but more often you can save yourself some time by tracking down the installation instructions from the developer
conda activate GVA-RadQC |
The goal of presenting the "incorrect version" way is 3 fold:
- To suggest that there is actually minimal to no oversight or testing of the conda commands you may find.
- That different programs may have different expectations of what channels you have access to by default (anaconda seemingly expects access to conda-forge since it isn't listed in their command, while multiqc expects both conda-forge and bioconda by default as their command lists nothing but an obscure link to a page describing the defaults.
- To demonstrate how you can use error messages to figure out what might be going on.
Get some data and verify access to fastqc
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- Using information in the MultiQC report, modify the bash loop used to create the fastqc_commands file above to create a cutadapt_commands file that could modify all 544 files at once.
- Move over to the fasp tutorial and come back to trim all adapter sequences from all files and rerun fastqc/multiqc to see what a difference trimming makes on overall quality.
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