tigmint-make ignores $PATH and is supposed to be run from unpacked source tree instead about tigmint HOT 3 CLOSED

The parent script calling tigmint could just export for example:

SCRATCH=/scratch/mmokrejs/job_3024668.foo
TMPDIR=/scratch/mmokrejs/job_3024668.foo
SORT_OPTS='-S 2G'

Please note that sort uses /tmp by default.

from tigmint.

Hi @mmokrejs,

Yes, the current organization of the Tigmint code uses paths relative to the installation location. If you don't wish to use the path to the github repo for running Tigmint, I recommend using bioconda or brew - we maintain Tigmint in both of those package managers.
While I do appreciate the feedback and suggestions in changing the installation of Tigmint, this isn't a priority for our developers. Changing the installation would also require updates to the package manager formulae, and we have a lot of other projects with more pressing work.

For your second comment, that seems more related to your issue #60 and PR #64 so perhaps we can discuss there.

Thanks,
Lauren

from tigmint.

Hi @lcoombe ,
although I am trying to understand what you say, practically. The first three installation procesdures I not relevant to meant as I want the binaries self-compile and tuned. The section Install Tigmint from the source code in the README simply lacks the installation step. I thought it was by mistake but it is as I see it now not. So we can conclude one cannot install tigmint and one is supposed to run it directly from the compiled source tree dirrectly. I imagine how many package maintainers had to come over thsi repeatedly to only later realzie the hardcoded paths in the files and to be edited by sed as well. I find it frustrating work. Please contact some package maintainers at e.g. Debian and Scientific Linux and some maintainers of you cluster environment. And the setup.py is I think also incomplete.

So the whole report can be solved by documenting that one cannot install tigmint with make install which would also call python's setup.py. Just a simple change to the README.md.

from tigmint.