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stringtie package

Are the files, PrepDE.py and PrepDE.py3 present in the stringtie package? if so, which archive?

Asked by Aaron Dickey

Are the files, PrepDE.py and PrepDE.py3 present in the stringtie package? if so, which archive?

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Ubuntu stringtie Edit question
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Manfred Hampl
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Best Manfred Hampl (m-hampl) said : 		#1

As far as I can see, none of the packages related to stringtie in Ubuntu contains PrepDE.py or PrepDE.py3.

The version numbers of stringtie in Ubuntu (e.g. 2.2.1+ds-2) do not contain the string "ubuntu". This means that the package was copied from Debian without Ubuntu-specific modification. As far as I can see also the Debian package does not contain these files either.

I suggest that you contact Debian to have these files included, and as soon as Debian has implemented that change, Ubuntu will follow suit for Ubuntu's development version.

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Aaron Dickey (phylloxera) said : 		#2

Thanks Manfred Hampl, that solved my question.

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Aaron Dickey (phylloxera) said : 		#5

It looks like Debian has uploaded. See https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1061576

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Manfred Hampl (m-hampl) said : 		#6

... and the updated package from Debian has already been copied into the repositories for Ubuntu 24.04 (noble, still in development). The Python3 script has been named /usr/bin/prepDE.py

Which Ubuntu release are you running?
You might consider trying to do a manual installation of the new package for noble onto your system and check whether it now works as desired.

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Aaron Dickey (phylloxera) said : 		#7

I'm building an apptainer container on noble to run 1-of-my pipelines. prepDE.py3 renamed prepDE.py may depend on pythonispython3, I'm not sure. But I'll let you know. my first bug report and my first time manually installing a package so, presumably lots of noob mistakes. ;)

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Aaron Dickey (phylloxera) said : 		#8

successful prepDE.py tests on my data using stringtie (2.2.1+ds-3) package inside both debian:sid and ubuntu:noble this morning!