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Issues running bbmap tools (solved) #9

Closed rbtoscan closed 1 year ago

rbtoscan commented 1 year ago

Hi,

I had issues running bbmap tools, namely repair and tadpole, when those are installed as standalone executables (install instruction step 3).

The issue was related to java, or lack thereof. Even after installing java, the issues changed but did not vanish (something to do with not being able to find/load main class - similar error here).

The solve was to install bbmap via conda: conda install -c bioconda bbmap And to add the executables path (from condas bin folder) for both tadpole and repair to the configs/parameters.yaml.

So I guess bbmap should be added to the .yaml file to correctly setup the conda env. Attaching a working example. readqcc_conda-setup-example.yaml.zip

Thanks!

Best Rodolfo

katkopera commented 1 year ago

Hi, I only had part of the problem: "Java not found error". After installing Java, the module was completed successfully.

In the module's documentation, you could mention that Java is a prerequisite.

lauren-mak commented 1 year ago

The note about Java was added to the README, and the environment will be updated in the future. Thanks!