Installations, builds, and tests Q&A - oushujun/EDTA GitHub Wiki

This is a collection of issues people trying to get EDTA ready for use. Hopefully, it can provide helps for future users.

1. Error: The RMblast engine is not installed in RepeatMasker #250
   This error means RepeatMasker is not correctly installed/configured. If you installed EDTA using conda with EDTA.yml and still received this error, it could be caused by RepeatMasker configuration RepeatMasker error: mdb_env_open: Cannot allocate memory, which sometimes occurred when the software tries to build the index for the input fasta file.

   Solution by JiyangChang: Adding the following line in the job script may solve this issue:
   export BLASTDB_LMDB_MAP_SIZE=100000000

2. gt is not found in the genometools path ./! #309
   EDTA looks for dependencies from $ENV. You may want to check if gt is available through $ENV. If you installed EDTA through conda and still have this error, you may want to check your $PATH in the ~/.bashrc file and see if anything supersedes the default conda $ENV.

3. TIR_Learner error: Python 3.6 in the conda environment is mocked by a previously installed python outside of conda. #14
   It could be solved by using: export PYTHONNOUSERSITE=True

   Solution was found here: https://stackoverflow.com/questions/55089352/anaconda-does-not-use-package-from-activated-environment
   Similar problem and explanation: https://github.com/conda/conda/issues/6018