problems with report generation

[Khabibullin543]

Hello! Could you tell me, please, are there any workarounds to generate the html-report, without using the pipeline? None of posted solutions worked for me.

Best, Nikita

[biobrad]

Hi Nikita,

Assuming you have already run the pipeline once and it didn't generate the report, try the following:

activate your tormes environment

conda activate tormes-1.3.0

then install bionconductor-ggtree=2.0.0 using this command:

conda install -c bioconda bioconductor-ggtree=2.0.0

then go into your tormes results from the pipeline analysis and decompress the report_files.tgz file.

tar -xvzf report_files.tgz

then go into the folder and run the render_report script

cd report_files/
./render_report.sh

let me know how you go!

[Khabibullin543]

In the end fresh install with https://github.com/biobrad/Tormes-Meta-Create/blob/main/tormes-1.3.0.yml has worked for me. Thank you very much!

[biobrad]

Great news! That saves me some testing @Narciso Martín Quijada @.***> 🙂

On Tue, 7 Mar 2023, 4:22 pm Khabibullin543, @.***> wrote:

In the end fresh install with https://github.com/biobrad/Tormes-Meta-Create/blob/main/tormes-1.3.0.yml has worked for me. Thank you very much!

— Reply to this email directly, view it on GitHub https://github.com/nmquijada/tormes/issues/63#issuecomment-1457582379, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANITBGROZW2FQFT4TLYYGR3W23EKPANCNFSM6AAAAAAVOGIE4A . You are receiving this because you commented.Message ID: @.***>

[nmquijada]

Hi all,

Thank you very much @Khabibullin543 for the feedback and @biobrad for the new yaml! I will update the solution in the main repo page!

Best, Narciso