rivera10
commented
2 years ago Hello @dbajpp0,
Yes, now TransPi will work differently for the creation of the environments. Before TransPi was creating a single environment for the entire pipeline. However, this was causing issues when updating a package or adding a new program. Thus, now each process will build a separate conda environment. This guarantees that no matter what program I add in the future or what version I used, this will not break the entire pipeline. Yes, this will create multiple environments but all of them are in the same directory. Once you are finished with the analysis the conda directory can be deleted. The directory is called condaEnv and is located in the directory where you are running TransPi. To save space just erase the old TransPi conda using conda env remove -n TransPi and then clean the packages downloaded with this directory using conda clean --all. Let me know if you have further questions.
Best, Ramón
Hi Ramon, Few days ago you updated TransPi.nf at github so now all programs (and specific versions) needed for the pipeline are installed by the script in a new environment is despite of some or all programs are alreay installed in the conda environment. However, this behaviour is performed for every analysis so the computer is populated with as many environments as analyses started. Could you change the behaviour of the script enclosed in TransPi.nf so the programs are installed just once at the original environment? Thanks a lot for making pipeline more user friendly at the installation level. Busco v4 is not well integrated in the older version since busco config file is not found by script and/or the path to programs are wrongly set by default. Cheers, Joan