ggTree installation error - part 2

[biobrad]

Hi Narciso,

Unfortunately the solution for ggtree didn't work for me, but I found another way around it. It has a few more steps but it works nicely.

1. Create a new environment in conda using the attached txt file. You will have to change it to a .yml file though. (change the txt to yml). Call the new environment tormes_report. conda env create -n tormes_report --file tormes_report.yml
2. After it has been created, activate your new environment and run the following command (NOTE: change the path to your newly created conda 'tormes_report' install path) Rscript -e 'library(BiocManager); BiocManager::install("ggtree", ask = FALSE, lib.loc=YOUR/CONDA/INSTALLS/PATH/miniconda3/envs/tormes_report/lib/R/library/")'
3. Go the tormes folder where you ran the pipeline and which has your results.
4. Untar/unzip the reports file: tar -xzf report_files.tgz
5. run the following command: Rscript -e 'library(rmarkdown); rmarkdown::render("tormes_report.Rmd", "html_document", encoding="UTF-8")'
6. Your Tormes report should build and you will now have a file in your folder called 'tormes-report.html.
7. PROFIT. tormes_report.txt

[nmquijada]

Thanks for sharing the conda environment configuration that worked for your report generation Brad!

Your point "2." is the same ggtree installation as included in tormes-setup script: https://github.com/nmquijada/tormes/blob/f5a547020f4d6cf562930f327799070bcf42cedc/bin/version-1.3.0/tormes-setup#L36

So, it is definitely an issue of some dependencies missing for some set-ups in the original .yaml file. Although it does not run into errors in every system...

For step 5 you can also run the command ./render_report.sh that is included inside the uncompressed report_files directory (https://github.com/nmquijada/tormes#rendering-customized-reports)

Thanks for posting and additional solution for the installation of ggtree. We must dig into this issue for the next release ;)

[biobrad]

Man... R is painful sometimes. Thanks for running your eye over it. Just one thing though which you may have noticed, doesn't matter which way you fix the issue it still mangles the core genome comparison horizontal gene presence absence plot.

On Fri, 8 Apr 2022, 6:37 pm Narciso Martin Quijada, < @.***> wrote:

Thanks for sharing the conda environment configuration that worked for you Brad! If users are using your yaml file instead of the tormes original one for creating the conda environment, they must also run tormes-setup so all the databases and the missing dependencies are also installed.

Your point "2." is the same ggtree installation as included in tormes-setup script:

https://github.com/nmquijada/tormes/blob/f5a547020f4d6cf562930f327799070bcf42cedc/bin/version-1.3.0/tormes-setup#L36

So, it is definitely an issue of some dependencies missing for some set-ups in the original .yaml file. Although it does not run into errors in every system...

For step 5 you can also run the command ./render_report.sh that is included inside the uncompressed report_files directory ( https://github.com/nmquijada/tormes#rendering-customized-reports)

Thanks for posting and additional solution for the installation of ggtree. We must dig into this issue for the next release ;)

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