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egaffo / circompara2

Improved bioinformatic pipeline to identify and quantify circRNA expression from RNA-seq data by combining multiple circRNA detection methods
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Quick installation fails #1

Closed sgmiriuka closed 3 years ago

sgmiriuka commented 3 years ago

hi @egaffo installation file (install_circompara) is missing. Found it in bash folder, though fail when run. thnks santiago

egaffo commented 3 years ago

Hi @sgmiriuka I fixed the path in the README. What is failing in your installation? Do you have any error message?

Before running the install script, you need to install the following packages:

Enrico

sgmiriuka commented 3 years ago

ok. A few things: -In the README the right path should read /circompara2/src/utils/bash -Din't realize it is in p2.7. After dealing with it, cannot run the test. I found a circompara file here --> /circompara2/src/utils/bash but not a circompara2. -I convert the raw files to python3. Looks that installation went find, not tested. Do you expect any problems, i.e., one of the 9 circ scripts running on 2.7?

egaffo commented 3 years ago

I updated the README with additional instructions. I hope now they are more clear. Yes, I had to stuck with Python2.7 as more than one of the integrated tools (now I do not remember exactly which ones) were not upgraded to Python3 from the original authors and some probably never will (e.g. TopHat2 has unmaintained code). I did try to convert all software to Python3 but it was a mess and I preferred to use a virtual environment. I put some instructions in the latest README. Using Python3 will eventually fail at some point. If you are struggling with the installation, please consider using the Docker image.