TreeShrink

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run_treeshrink.py fails with python 3.10

6

FYK, After a recent local upgrade of my Ubuntu Linux OS --- which brought python to version 3.10.4 --- `run_treeshrink.py` no longer works. The reason seems to be an outdated...

nylander

Hi all, I am trying to use TreeShrink on my HPC account. I have downloaded TreeShrink via conda and via Git. When I try to check that everything is okay...

BioinfoAK

Failed with error in density.default

1

When launching treeshrink 1.3.9, the software died with the following error: Error in density.default(log(x), adjust = 1) : need at least 2 points to select a bandwidth automatically Calls: threshold...

mesti90

This pull request addresses the issue raised in [this issue](https://github.com/uym2/TreeShrink/issues/41)

AshtonPooley

Due to Windows using double backslash and the recursive list dir function assuming directories use a single forward slash the following exception is caused during installation `Traceback (most recent call...

AshtonPooley

removes taxa on short branches

3

Hi, Thanks for creating this program! I'm trying to use TreeShrink on 388 trees built for loci in my dataset, in order to detect and potentially remove taxa on long...

bmichanderson

Usage of collections.abc to provide MutableMapping to work with Python 3.10. It fixes https://github.com/uym2/TreeShrink/issues/33 (tested for installation using `python3.10 setup.py install --user`).

V-Z

Error in rank(x, ties.method = "min", na.last = "keep") : unimplemented type 'list' in 'greater'

6

Installed treeshrink using conda called it using `run_treeshrink.py -t min_marker_80_sub_hundred_RAxML_bestTree.sp_faa_refined.tre` but got this error ``` Launching TREESHRINK version 1.3.1 There are only 1 gene trees in the dataset. TreeShrink will...

adityabandla

Trying to install on Python3.9.2 CentOS: run_treeshrink -h bash: run_treeshrink: command not found run_treeshrink.py -h Traceback (most recent call last): File "/home/554/ta0341/.local/bin/run_treeshrink.py", line 4, in __import__('pkg_resources').run_script('TREESHRINK==1.3.9', 'run_treeshrink.py') File "/home/554/ta0341/.local/lib/python3.9/site-packages/pkg_resources/__init__.py", line...

theo-allnutt-bioinformatics

Error in running example dataset

3

Hi there, I seem to have the same problem as others but I'm not sure what the issue is. I've tried using different R versions (v3.5, v4.0) to double check...

FrancisNge