TIPP2 doesn't work with SEPP bioconda recipe

[nick-youngblut]

The TIPP2 readme states that SEPP must be installed to run TIPP2 (but doesn't list SEPP in the requirements). I installed SEPP via bioconda (it's the best approach, given that the user can easily maintain/isolate software versions), but it appears that TIPP2 doesn't work with the SEPP bioconda recipe:

$ python setup.py tipp
running tipp

Creating main TIPP config file at /ebio/abt3/nyoungblut/.sepp/tipp.config and tools at /ebio/abt3/nyoungblut/.sepp
error: [Errno 2] No such file or directory: '/ebio/abt3/nyoungblut/.sepp/bundled-v4.3.21/tippJsonMerger.jar'

[nick-youngblut]

Also, just curious: why bundle pplacer, hmmer, etc as part of TIPP2 instead of just including them as dependencies, since they are all available via bioconda?

[shahnidhi]

Hi Nick, I haven't tested TIPP2 with Bioconda installation of SEPP. I will test that and get back to you. My guess is pplacer and hmmer were bundled so it is easier for installation. Siavash may know better, though.

[sjanssen2]

I think the reason was that the specific version of pplacer/guppy was not available through conda for OSX and I - as of today - still fail to compile these programs from OCML sources :-/

[nick-youngblut]

Just to check: is TIPP2 in the master branch or just in the TIPP2 branch? The documentation isn't very clear (eg., the main README states "TIPP", not "TIPPv1" or "TIPPv2")

[nick-youngblut]

Even in the tipp2 branch, the SEPP readme states:

If you use Bioconda, you can try installing SEPP using https://anaconda.org/bioconda/sepp

...but the SEPP bioconda recipe doesn't seem work with TIPP(2). The documentation is very confusing.

[nick-youngblut]

I think the reason was that the specific version of pplacer/guppy was not available through conda for OSX and I - as of today - still fail to compile these programs from OCML sources :-/

Dropping the odd config setup with the path specification for hmmbuild, hmmsearch, pplacer, etc., would make the setup substantially easier and result in less AssertionError: path for hmmbuild does not exist errors. Instead you can just check for the existence of the required executable dependencies (installed via bioconda) at the start of the script with distutils.spawn.find_executable.

Since the config is mainly for setting the paths of these executables, you could completely get rid of the config, so that there are no issues about creating/finding the config (eg., no config in the home directory, which could cause problems with multiple installs for 1 user).