search

Gabaldonlab / redundans

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.
GNU General Public License v3.0
129 stars 20 forks source link

Remove hardcoded path for SSPACE #15

Closed eburgueno closed 8 years ago

eburgueno commented 8 years ago

In https://github.com/lpryszcz/redundans/blob/master/redundans.py#L370 the assumption is that SSPACE will be installed under ~/src/SSPACE. This is the case when using the automated installed, but not when the user installs the dependencies manually.

While --spacebin can be used at invoke time, it would be better to treat SSPACE the same way other dependencies are treated. I.e.: if it's not in the PATH warn the user and exit.

lpryszcz commented 8 years ago

This is not going to change, simply because in many systems (including mine) the getopt.pl is missing. It can be installed system-wide with root priviledges or provided as file in SSPACE PATH (this is what is done by INSTALL.sh), but then the SSPACE has to be executed with full path.

Still, you can alter ./redundans.py and point SSPACEBIN to any path you wish by default.