Problem while executing $ python2 run_sate.py incompatibility with current version of dendropy
Kibet Gilbert
I running on Ubuntu 18.04 lts on 64 bit desktop
Did as follows:
$ python2 run_sate.py
Traceback (most recent call last):
File "run_sate.py", line 27, in
from sate.mainsate import sate_main
File "/home/kibet/Downloads/satesrc-v2.2.7-2013Feb15/sate-core/sate/mainsate.py", line 37, in
from sate.satejob import *
File "/home/kibet/Downloads/satesrc-v2.2.7-2013Feb15/sate-core/sate/satejob.py", line 34, in
from sate.treeholder import TreeHolder, resolve_polytomies
File "/home/kibet/Downloads/satesrc-v2.2.7-2013Feb15/sate-core/sate/treeholder.py", line 26, in
from sate.tree import PhylogeneticTree
File "/home/kibet/Downloads/satesrc-v2.2.7-2013Feb15/sate-core/sate/tree.py", line 25, in
from dendropy import convert_node_to_root_polytomy
ImportError: cannot import name convert_node_to_root_polytomy
So I applied this fix on /satesrc-v2.2.7-2013Feb15/sate-core/sate/tree.py: Hacks to move to dendropy 4 #13
But got this error:
$ python2 run_sate.py
Traceback (most recent call last):
File "run_sate.py", line 27, in
from sate.mainsate import sate_main
File "/home/kibet/Downloads/satesrc-v2.2.7-2013Feb15/sate-core/sate/mainsate.py", line 37, in
from sate.satejob import *
File "/home/kibet/Downloads/satesrc-v2.2.7-2013Feb15/sate-core/sate/satejob.py", line 34, in
from sate.treeholder import TreeHolder, resolve_polytomies
File "/home/kibet/Downloads/satesrc-v2.2.7-2013Feb15/sate-core/sate/treeholder.py", line 35, in
from dendropy.treesplit import delete_outdegree_one
ImportError: No module named treesplit
my enviroment looks like:
$ conda list
# packages in environment at /home/kibet/bioinformatics/anaconda3/envs/sate_env:
#
# Name Version Build Channel
ca-certificates 2018.10.15 ha4d7672_0 conda-forge
certifi 2018.10.15 py27_1000 conda-forge
dendropy 3.12.3 py_1 bioconda
libffi 3.2.1 hfc679d8_5 conda-forge
libgcc-ng 7.2.0 hdf63c60_3 conda-forge
libstdcxx-ng 7.2.0 hdf63c60_3 conda-forge
ncurses 6.1 hfc679d8_1 conda-forge
openssl 1.0.2p h470a237_1 conda-forge
pip 18.1 py27_1000 conda-forge
python 2.7.15 h33da82c_4 conda-forge
readline 7.0 haf1bffa_1 conda-forge
setuptools 40.6.2 py27_0 conda-forge
sqlite 3.25.3 hb1c47c0_0 conda-forge
tk 8.6.8 ha92aebf_0 conda-forge
wheel 0.32.2 py27_0 conda-forge
zlib 1.2.11 h470a237_3 conda-forge
This looks like the only solution I can pursue is: Install SATe locally
that suggests i use an older version, probably Release 3.12.0 of 17 Jul 2012 in Releases
But I don't how to do this given that i am installing SATe from source code satesrc-v2.2.7-2013Feb15.tar.gz in Archived bundles of SATé
Can i install dendropy Release 3.12.0 in my conda environment sate_env? if so and how can i do this?
(Release 3.12.0 is not available in any anaconda channels.)
NB: I have other recent versions of Dendropy installed in different environments but are incompatible with SATe.
Eitherway, I need SATe and how else can i install it?
Kibet Gilbert
- SATé and PASTA software for co-estimating multiple sequence alignments and trees (PASTA is the improved version of SATé -- it is more accurate, and can analyze larger datasets). Publications: Liu, K., S. Raghavan, S. Nelesen, C. R. Linder, T. Warnow, 2009. "Rapid and accurate largescale coestimation of sequence alignments and phylogenetic trees." Science, vol. 324, no. 5934, pp. 1561-1564, 19 June 2009, doi: 10.1126/science.1171243 and (2) S. Mirarab, N. Nguyen, and T. Warnow. "PASTA: ultra-large multiple sequence alignment". Proceedings RECOMB 2014 (PDF). Supplementary materials at figshare -- (PDF).