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make-based supertree pipeline

The initial thoughts for this are at https://github.com/OpenTreeOfLife/opentree/wiki/pseudo-code-supertree but that is likely to be a bit out-of-sync as this is a work in progress.

eventually...

The tree will be build-able by:

  1. downloading the files described in input/README.md
  2. and putting the otcetera tools on your path with something like: $ export PATH=$PATH:$PWD/../buildreleaseclang/installed/bin
  3. and then building with: $ make

Warning about the 2 Makefiles

Warning the 2 Makefiles (Makefile.exemplar and Makefile.synth-v3) here clash because they reuse the same set of temporary directories!. You choose the one you want (via adding a -f flag to make calls below to specify the Makefile or by renaming one to Makefile). If you change to the other one, you need to clean the temporaries!

Makefile.exemplar exemplifies taxa mapped to non-terminal taxa.

Makefile.synth-v3 is the version used to create the decompositions (on 29 Apr, 2014) for the 3rd version of the synthetic tree. That version of the decomposition does not replace higher taxa with exemplars. The subproblems from that run are posted at http://phylo.bio.ku.edu/ot/subproblems-v3.tar.gz for the time being. That archive was created by renaming step_7_scratch/export-sub-temp and then tar+gzipping it. The pruned taxonomy (copied from step_6/taxonomy.tre) is posted at http://phylo.bio.ku.edu/ot/synth-v3-pruned-taxonomy.tre

Warning about the fact that make will fail

The full pipeline is not working yet. In version 3 of the synthetic tree, treemachine is used for the analysis of each subproblem.

So, running make here will ultimately exit with an error, but it should run long enough to produce the decomposition into subproblems.

Usage

  1. Get the inputs Currently you can get inputs from Joseph Brown's repos of treemachine output. The instructions are in ./step_1/README.md and ./step_4/README.md

  2. put the otcetera tools on your PATH. I like to: 1. use the --prefix="$PWD/installed" as an argument to configure when I am building otcetera. 2. run make && make check && make install to put all of the tools in ./installed/bin. 3. cd ./installed/bin ; export PATH="${PATH}:${PWD}; cd -" to put the installed bin on my PATH.

  3. run make -fMakefile.synth-v3 from the supertree directory.

Expected outcome of Makefile.synth-v3

It should eventually crash with a message like:

python move-subproblems-if-differing.py step_7_scratch/checksummed-subproblem-ids.txt step_7_scratch/export-sub-temp step_7 step_8 step_9
Depends on some "bleeding edge" feature on the peyotl supertree branch
make: *** [step_7/subproblem-ids.txt] Error 1

If you put that branch on peyotl on your PYTHONPATH, then you'll get a little further (but none of the difficult subproblems will be solved). However, it should run long enough to produce:

  1. tree files in step_5. These should have the expanded tip version of each tree, so that there are no longer tips mapped to non terminal taxa. See step_5/README.md

  2. a pruned taxonomy in step_6/taxonomy.tre. See step_6/README.md

  3. the subproblems in step_7_scratch/export-sub-temp. See step_7_scratch/README.md

If you have the appropriate branch of peyotl installed, then you should get at least some of the subproblems moved from step_7_scratch/export-sub-temp to step_7, but that directory is likely to be incomplete if the move-subproblems-if-differing.py step did not succeed. Use step_7_scratch/export-sub-temp if you just want the subproblems!

Note about old version of the pipeline

There is some cruft from a previous stab at the pipeline (see here). I'm in the process of refactoring to agree with the pipeline described in the doc subdir: ../doc/summarizing-taxonomy-plus-trees.tex (also occasionally posted to this spot on the Holder lab site). Each of the steps in section 2 of that doc are mapped to step_# directories in this new system. So step_1 is described in section 2.1 of that doc; step_2 is section 2.2; etc.