sepp
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smirarab
Ensemble of HMM methods (SEPP, TIPP, UPP)
Currently our merger code outputs .json files in old format. Convert it to the new format.
A new version of Dendropy was released a week ago and it is causing the SEPP conda build to break. Could you look into this and either update SEPP to...
Running UPP without arguments yields an `AttributeError` ``` $ run_upp.py [09:27:49] config.py (line 317): WARNING: Main configuration file was not found at: /home/mcdonadt/miniconda3/envs/qiime2-2023.5/share/sepp/sepp/upp.config Proceeding without the main configuration... [09:27:49] config.py...
re-activating the tests could help improving this software further.
Hey, would it be possible to release a conda recipe for Python 3.11? Thanks!
Traceback (most recent call last): File "/usr/local/bin/run_sepp.py", line 4, in __import__('pkg_resources').run_script('sepp==4.5.1', 'run_sepp.py') File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 656, in run_script self.require(requires)[0].run_script(script_name, ns) File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1453, in run_script exec(code, namespace, namespace) File...
Greetings! I have made a small change to setup.py to fix dendropy to the compatible version. This should close issue#125 "Dendropy v4.6.0 causing SEPP to break".
Hi there, I am trying to run UPP. I managed to get it installed and it responds correctly when I run the help (-h) option. When I try to build...
Hello, There are four places in the source code of sepp 4.5.1 (and also at the current tip of the master branch) where `open` is used with the "rU" speficier....
Hello, while looking at the code I noticed in `run-sep.sh` that some references files are not distributed. `gg_13_5_ssu_align_99_pfiltered.fasta` and `gg_13_5_ssu_align_99_pfiltered.fasta` are not available ``` # resort to the default reference...
