Use of Cwd::abs_path breaks Galaxy wrapper by resolving symlinks

[pvanheus]

Shovill 1.0.9 switched to using Cwd::abs_path() instead of File::Spec->rel2abs() that was used previously. The Galaxy wrapper uses symbolic links to link the ".dat" files from the Galaxy data store to filenames used for shovill. One particular reason for this is that a number of bioinformatics tools use the file extension to "determine" if a file is compressed or not. One of these tools is kmc, used in shovill.

As detailed in this bug report, abs_path() resolves symbolic links whereas rel2abs() does not. This means that the kmc step is fed the path to the .dat filenames and fails.

I don't know the reasoning behind using abs_path (the change was made in this commit) but can it be reverted to avoid the behaviour described above?

Thanks, Peter