/idigphylo

Phylogenetic tree building based on gene sequences linked in iDigBio specimen records

Primary LanguageJupyter NotebookMIT LicenseMIT

idigphylotree

Phylogenetic tree building based on gene sequences linked in iDigBio specimen records

MrBayes Installation on Ubuntu 14.04

http://downloads.sourceforge.net/project/mrbayes/mrbayes/3.2.5/mrbayes-3.2.5.tar.gz?r=http%3A%2F%2Fmrbayes.sourceforge.net%2Fdownload.php&ts=1447378701&use_mirror=skylineservers

Do later when need parallel - git clone https://github.com/beagle-dev/beagle-lib.git

sudo apt-get install openmpi-bin openmpi-doc libopenmpi-dev cd src/ autoconf ./configure --with-beagle=no --enable-mpi=yes make mv mb ../bin/

And test with the first tutorial from the manual

FIXME: This still runs as one thread - might be compilation, might be libraries, might be model

Ref

http://sourceforge.net/p/mrbayes/mailman/message/34509537/ https://pascualanaya.wordpress.com/2014/09/08/compiling-and-working-with-mpi-version-of-mrbayes-3-2-2/

Good test case

  1. Sequence ID in iDigBio
  2. Search that returns the records w/ sequences
  3. Not too many sequences or a filterable amount
  4. Sequences types match and can be aligned
  5. Tree availible for comparision in treebase

Directory Structure

  1. seq/ - Spark code used for extracting GenBank sequence identifiers from iDigBio data dumps. Builds the uuid:seqid linking table used by the genbank worker
  2. workers/
  3. sequence/ - Celery worker that accepts iDigBio uuids and enqueues tasks for the align worker with sequences
  4. align/ - Celery worker that accepts sequences and aligns them and enqueues tasks for the tree worker
  5. tree/ - Celery workder that accepts aligned sequences and constructs trees that are then stored in Postgresql
  6. api/ - Python API code
  7. web/ - Web root of site (put on gh-pages branch?)

For ClustalOmega building

sudo apt-get install libargtable2-0 libargtable2-dev

iDigBio Python package pulled from github, fixes beta issue: git clone git@github.com:iDigBio/idigbio-python-client.git cd idigbio-python-client sudo python setup.py install

Api

pip install flask

tree/build

tree/view

Visualization apt-get install python-numpy python-qt4 python-lxml sudo pip install ete2

Need X server to render: etetoolkit/ete#101 sudo apt-get install xvfb then run xvfb-run python api_view_stub.py

Trouble parsing nexus files apt-get install bioperl