Sergio Vargas

Hi Kátia, I don't think this is possible. The Trinity cmd line used by TransPi looks as follows: ``` Trinity --max_memory \${mem}G --seqType fq --left ${left} --right ${right} --CPU ${task.cpus}...

Hi Peter, this is a trinity problem I am not sure how to fix. It seems trinity gets caught in the salmon step and creates huge output files without ever...

Hi Chris, not an expert with the singularity stuff here but it seems as if the image is not being pulled because of some naming problem. We run TransPi with...

Good question, I think the way in which the conda environments are created now changed at some point and TransPi doesn't have one single environment anymore but many for the...

I found the .yml file can be found in the TransPi release. I am not sure, why the yml file was removed from the main repo and cannot test with...

Hi Chris, I checked the code. Specifically, the following line in the error message means that a different docker image is being used in this particular step. Why exactly busco...

Hi there, I think TransPi assumes signalP v4 is available. I think I have a patch to make it run with v5 but will need check. I face lots of...

Are u using conda? if the script was not found is because trinity cannot be located. The insilico normalization step is done using trinity scripts. cheers Sergio

Not really... the pipeline runs but breaks at normalization, correct? Sergio

Hi Ido, you can replace the old ulr with something looking like this: "https://legacy.uniprot.org/uniprot/?query=taxonomy:33208&format=fasta&compress=yes&include=no" changing the taxonomy ID accordingly, that should do the work. cheers Sergio