EDTA
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Published
20 hours ago •
oushujun
oushujun
dependencies not found in singularity install
I'm trying to use the latest image and singularity to run EDTA, it looks like EDTA can't find genometools, but I see it's installed on container. relevant info below:
[16:40:42] david.molik@ceres {/project/TE_annotations} $ singularity exec EDTA.sif EDTA.pl --check_dependencies
#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.2.0 #####
##### Shujun Ou ([email protected]) #####
#########################################################
Parameters: --check_dependencies
Tue Mar 12 16:43:45 CDT 2024 Dependency checking:
Error: gt is not found in the genometools path ./!
[16:43:45] david.molik@ceres {/project/TE_annotations} $ SINGULARITY_CACHEDIR=./
export SINGULARITY_CACHEDIR
[16:43:53] david.molik@ceres {/project/TE_annotations} $ singularity exec EDTA.sif EDTA.pl --check_dependencies
#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.2.0 #####
##### Shujun Ou ([email protected]) #####
#########################################################
Parameters: --check_dependencies
Tue Mar 12 16:43:57 CDT 2024 Dependency checking:
Error: gt is not found in the genometools path ./!
[16:43:57] david.molik@ceres {/project/TE_annotations} $ export PYTHONNOUSERSITE=1
[16:44:13] david.molik@ceres {/project/TE_annotations} $ singularity exec EDTA.sif EDTA.pl --check_dependencies
#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.2.0 #####
##### Shujun Ou ([email protected]) #####
#########################################################
Parameters: --check_dependencies
Tue Mar 12 16:44:16 CDT 2024 Dependency checking:
Error: gt is not found in the genometools path ./!
[16:44:16] david.molik@ceres {/project/TE_annotations} $ singularity --version
apptainer version 1.2.5
