Closed Drosofriends closed 1 year ago
sjroth
commented
1 year ago Hi,
If you are not able to use the conda environment, I recommend trying to install the individual software tools with the correct version so they do not clash. I cannot help with software incompatibilities as I do not have access to your system.
Drosofriends
commented
1 year ago I created a new empty enviroment and than I install python version 3.6 and than i run the following command: conda install -c bioconda bedops=2.4. bioconductor-deseq2=1.20. bx-python=0.8. homer=4.9. networkx=2. numpy=1.16. pandas=0.24. pybigwig rpy2=2.9. rseqc=3.0.* samtools=1.9 But i had a lot of conflicts and only bedops installed.
sjroth
commented
1 year ago Again, without access to your machine, it’s hard for me to help. You are probably using a newer version of conda, which is known to have conflicts with R packages. I would try installing packages one at a time.
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From: Drosofriends @.> Sent: Friday, January 27, 2023 8:38:32 AM To: sjroth/ARTDeco @.> Cc: Samuel Roth @.>; Comment @.> Subject: Re: [sjroth/ARTDeco] problem in installing ARTDeco (Issue #16)
I created a new empty enviroment and than I install python version 3.6 and than i run the following command: conda install -c bioconda bedops=2.4. bioconductor-deseq2=1.20. bx-python=0.8. homer=4.9. networkx=2. numpy=1.16. pandas=0.24. pybigwig rpy2=2.9. rseqc=3.0.* samtools=1.9 But i had a lot of conflicts and only bedops installed.
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Drosofriends
commented
1 year ago I solved the problem by using mamba and the .yml file for the installation. Thank you for the help. I close this issue!
Hi, I'm trying to install artdeco but I have many problems in doing it. When I launch python setup.py install this error occured: canceled (core dump created). What kind of problem is this? Moreover, I'm not able to download the required packages because the conda env create -f environment.yml does not work. So I manually downloaded the packages but beacuse of conflicts I have many problems in terms of versions. Any help? thanks for the support!