search

DerKevinRiehl / transposon_annotation_reasonaTE

Transposon annotation tool "resonaTE" (part of TransposonUltimate)
GNU General Public License v3.0
16 stars 1 forks source link

conda/ mamba version conflicts #1

Closed genio0815 closed 3 years ago

genio0815 commented 3 years ago

Hi,

when following the (conda style) installation procedure a lot of 

UnsatisfiableError: The following specifications were found to be incompatible with each other

pop up.

Even when changing the used version of python to python=3.9.2=hffdb5ce_0_cpython as found in the previously used transposon_annotation_reasonaTE.yml does not fix the issue.

Only easy (but untested) workaround is to stick to prior version and installation via mentioned yaml file

cheers

DerKevinRiehl commented 3 years ago

Hello genio0815, thank you very much for your suggestion.

Could you please explain me, if this happened with mamba as well? With conda, is was reported for some users, as conda struggles with environment solving sometimes. (even though its same OS and conda version)

Could you tell me, from a users perspective, why you did not chose the recommended way using mamba? Its completely doable using conda (as mamba is installed via conda).

Only easy (but untested) workaround is to stick to prior version and installation via mentioned yaml file Thats true, in the past I mentioned the installation procedure via yml file, but as I developed this github, I removed this option from the tutorial. Now its back there again.

Installation using yml file (works for Linux64)

wget https://raw.githubusercontent.com/DerKevinRiehl/transposon_annotation_reasonaTE/main/environment_yml/transposon_annotation_tools_env.yml
wget https://raw.githubusercontent.com/DerKevinRiehl/transposon_annotation_reasonaTE/main/environment_yml/transposon_annotation_reasonaTE.yml
conda env create -f transposon_annotation_tools_env.yml
conda env create -f transposon_annotation_reasonaTE.yml

Best regards and looking forward hearing back from you soon, Kevin

genio0815 commented 3 years ago

Hi,

I tried the mamba approach initially, but that failed with

Problem: nothing provides blast needed by transposon_annotation_tools_proteinncbicdd1000-1.0.0-1

and switched to the conda way, hoping that this pulls in blast from somewhere.

So, I guess adding a dependency on blast(as in the yml file; repeatmasker, repeatmodeler and genomictools I installed differently, but none of these depend on blast) and updating the installation instructions for python (it says python=2.7) could solve this.

cheers

DerKevinRiehl commented 3 years ago

Okay thank you very much.

As different users report different errors for different ways, we offer three ways now, I guess most of the people should manage installing the software now using one of these. Thank you for your report!

Best regards, Kevin