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cbirdlab / dDocentHPC

hard fork of dDocent, edited to run without interactive user input
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dDocentHPC trimmomatic issue #17

Open ARW-UBT opened 8 months ago

ARW-UBT commented 8 months ago

Hello, I would like to try dDocentHPC on my Linux workstation and could not solve a trimmomatic issue.

dDocentHPC.bash is checking for the various dependencies. All but trimmomatic are marked as installed.

I installed trimmomatic into the same dDocent conda environment and added it to the path (although it is available without the PATH modification, though)

It is in the PATH: (ddocent) [bt140047@btbbx3 dD-Clara1]$ echo $PATH /home/bt140047/mambaforge/envs/ddocent/bin:/home/bt140047/mambaforge/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/home/bt140047/.local/bin:/home/bt140047/bin:/home/bt140047/mambaforge/envs/ddocent/bin/trimmomatic

It is available from the conda environment: (ddocent) [bt140047@btbbx3 dD-Clara1]$ which trimmomatic ~/mambaforge/envs/ddocent/bin/trimmomatic

It is installed in v0.39 (ddocent) [bt140047@btbbx3 dD-Clara1]$ trimmomatic -version 0.39

However, dDocentHPC stikk does not recognize trimmomatic. Does anybody have an advice to me how to get this issue solved? Best regards,

ARW-UBT commented 8 months ago

Update: Issue could be solved by installing trimmomatic outside ddocent conda environments. Was mislead by the same issue with bamtools, which could be resolved by adding bamtools to the ddocent conda environment.

Best regards,