s-andrews / FastQC

A quality control analysis tool for high throughput sequencing data
GNU General Public License v3.0
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Add FindBin Perl module install guide for Linux #131

Closed harriebird closed 9 months ago

harriebird commented 11 months ago

When installing FastQC on Fedora, the fastqc can't run due to a missing FindBin Perl module. To solve this, it more more appropriate to add a guide on how to install the FindBin module and run the fastqc command smoothly on Linux.

s-andrews commented 10 months ago

This would seem to be a bug in Fedora. The FindBin module is a core Perl module (https://perldoc.perl.org/modules) which means that it should be installed anywhere where there is a perl installation.

From a quick look it seems the Fedora team had packaged perl into multiple packages, but that this broke things, so they reverted to a single package which included all core modules, which should include FindBin as of Fedora release 27 (https://docs.fedoraproject.org/uz/fedora/f27/release-notes/developers/Development_Perl/).

If this is a fixed issue in a limited release of one linux distro then I'm not sure it requires specific documentation in FastQC - although a search for the issue will probably now find this patch which might point the affected people to the correct solution.

harriebird commented 9 months ago

Hi @s-andrews, we can just put it for the meantime and remove it once the perl FindBIn issue on Fedora is already fixed.

s-andrews commented 9 months ago

Adding to this - I just built a server with RHEL9 and perl wasn't installed at all, which came as a surprise, so we should add that as an explicit dependency. The FindBin was a packaging bug (now fixed) but we should state the overall dependency on perl and we can mention the module at the same time.

s-andrews commented 9 months ago

I've updated the install instructions with a note that perl is also required in 1faeea0

harriebird commented 9 months ago

That's cool @s-andrews! I guess there is no need for this PR to be approved and merged.

s-andrews commented 9 months ago

Equivalent update provided in 1faeea0