Install SATe locally

[Madza Y Farias-Virgens]

I'm on a cluster CentOS trying to install SATe locally.
Im not sudoer
cant do
sudo python setup.py develop
so I did 

python setup.py develop --user

but I'm getting the error

Traceback (most recent call last):

  File "run_sate.py", line 27, in <module>

    from sate.mainsate import sate_main

  File "/home/madzays/install/satesrc-v2.2.7-2013Feb15/sate-core/sate/mainsate.py", line 37, in <module>

    from sate.satejob import *

  File "/home/madzays/install/satesrc-v2.2.7-2013Feb15/sate-core/sate/satejob.py", line 34, in <module>

    from sate.treeholder import TreeHolder, resolve_polytomies

  File "/home/madzays/install/satesrc-v2.2.7-2013Feb15/sate-core/sate/treeholder.py", line 26, in <module>

    from sate.tree import PhylogeneticTree

  File "/home/madzays/install/satesrc-v2.2.7-2013Feb15/sate-core/sate/tree.py", line 25, in <module>

    from dendropy import convert_node_to_root_polytomy

ImportError: cannot import name convert_node_to_root_polytomy

I'm using python 2.7.13 loaded by anaconda2

Thanks!

[Mark Holder]

Hi,

My guess would be that there has been some refactoring in DendroPy has caused that function to be replaced by some other procedure.

In the best of all possible worlds, we could figure out how to fix the SATe code to use the latest version of DendroPy, but I suspect that it would be easier to install a version of DendroPy from the date that corresponds to the SATe version. 

I think that if you use git to download the full revision history of DendroPy from https://github.com/jeetsukumaran/DendroPy , then it should be possible to install the version that was available on 15 Feb, 2013. Just let me know if that does not work.

all the best,

Mark Holder

--
--
You received this message because you are subscribed to the Google Groups "SATe User" group.
To post to this group, send email to sate...@googlegroups.com
To unsubscribe from this group, send email to sate-user+unsubscribe@googlegroups.com
For more options, visit this group at http://groups.google.com/group/sate-user?hl=en

---
You received this message because you are subscribed to the Google Groups "SATe User" group.
To unsubscribe from this group and stop receiving emails from it, send an email to sate-user+unsubscribe@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

Mark Holder

mtho...@gmail.com

[Madza Y Farias-Virgens]

Hi Mark,

yes, it worked.

just 

git checkout 08e7ffb6e8640440f1ab36157b5696d481a92ff9

and then delete previous installation of DendroPy and reinstall that version.

Thanks!

To unsubscribe from this group, send email to sate-user+...@googlegroups.com

For more options, visit this group at http://groups.google.com/group/sate-user?hl=en

---
You received this message because you are subscribed to the Google Groups "SATe User" group.

To unsubscribe from this group and stop receiving emails from it, send an email to sate-user+...@googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

--

Mark Holder

mtho...@gmail.com