Miniconda InvalidArchiveError when downloading FastQC

Question

[minifoog]

I am new to using miniconda and when I tried downloading FastQC, I keep getting this error:

InvalidArchiveError("Error with archive C:\\miniconda\\pkgs\\fastqc-0.11.9-hdfd78af_1.tar.bz2.  You probably need to delete and re-download or re-create this file.  Message from libarchive was:\n\nCan't create '\\\\?\\C:\\miniconda\\pkgs\\fastqc-0.11.9-hdfd78af_1\\bin\\fastqc'")

Any solution to this?

Answer 1

[GenoMax]

While conda is recommended for installing bioinformatics packages in this case it may be simple to download fastqc zip file for Windows directly from FastQC site (LINK). A Java Runtime is needed.

As for the error you are seeing, it may be due to Windows OS not being supported (as noted by dariober and/or windows not able to deal with bzip compressed files (You could try conda install -c anaconda bzip2 to fix that).

[minifoog]

I tried this and does not work. I'll just use the app provided by FastQC. Thanks for the response.

Answer 2

[Juke34]

Something went wrong when downloading the tar.bz2 archive. Just remove it re-launch your command

Answer 3

[dariober]

I don't know if this is related at all to your problem but fastQC comes from the bioconda repository and bioconda does not support Windows operating system (search for Windows on this page https://bioconda.github.io/contributor/guidelines.html), at least at the moment. From C:\miniconda\pkgs... I guess you are on Windows, right?

[minifoog]

I am on Windows, and you are right, FastQC is not supported by Windows as of right now. I'll just use the app as said by Geno.