UFCG dependency issues from AUGUSTUS and gsl issues

[Changwanseo]

What I did:

Installation

conda install -c conda-forge gsl
ufcg download -t full

Initial running

ufcg profile -i [input] -o [output] -t 32

ERROR! Following dependency binary remains unsolved : augustus

Re-run with AUGUSTUS path designation

ufcg profile -i ../101_assembly/nextdenovo/03.ctg_graph/nd.asm.fasta -s NUC -o ./UFCG_ITS -t 32 --augustus /home/genome/anaconda3/envs/ufcg/bin/augustus

java.nio.file.NotLinkException: /home/genome/anaconda3/envs/ufcg/bin/augustus
        at java.base/sun.nio.fs.UnixFileSystemProvider.readSymbolicLink(UnixFileSystemProvider.java:553)
        at java.base/java.nio.file.Files.readSymbolicLink(Files.java:1467)
        at envs.config.PathConfig.setAugustusPath(PathConfig.java:69)
        at module.ProfileModule.parseArgument(ProfileModule.java:160)
        at module.ProfileModule.run(ProfileModule.java:773)
        at pipeline.ModuleHandler.handle_profile(ModuleHandler.java:45)
        at pipeline.ModuleHandler.handle(ModuleHandler.java:83)
        at pipeline.UFCGMainPipeline.main(UFCGMainPipeline.java:301)
[AUG 27 19:04:26] UFCG  |:  ERROR! [AUG 27 19:04:26] UFCG  |:  ERROR! java.lang.NullPointerException: Cannot invoke "Object.getClass()" because "pipeline.ExceptionHandler.E" is null
[AUG 27 19:04:26] UFCG  |:      at pipeline.ExceptionHandler.printStackTrace(ExceptionHandler.java:66)
[AUG 27 19:04:26] UFCG  |:      at pipeline.ExceptionHandler.handle(ExceptionHandler.java:76)
[AUG 27 19:04:26] UFCG  |:      at envs.config.PathConfig.setAugustusPath(PathConfig.java:82)
[AUG 27 19:04:26] UFCG  |:      at module.ProfileModule.parseArgument(ProfileModule.java:160)
[AUG 27 19:04:26] UFCG  |:      at module.ProfileModule.run(ProfileModule.java:773)
[AUG 27 19:04:26] UFCG  |:      at pipeline.ModuleHandler.handle_profile(ModuleHandler.java:45)
[AUG 27 19:04:26] UFCG  |:      at pipeline.ModuleHandler.handle(ModuleHandler.java:83)
[AUG 27 19:04:26] UFCG  |:      at pipeline.UFCGMainPipeline.main(UFCGMainPipeline.java:301)

Run augustus:

augustus -h

augustus: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory

Install gsl==2.7.0 to solve dependency issues:

conda install gsl==2.7.0

Now augustus works

Rerun ufcg:

ufcg profile -i ../101_assembly/nextdenovo/03.ctg_graph/nd.asm.fasta -s NUC -o ./UFCG_ITS -t 32

Now it works

I think the problem is that AUGUSTUS has set default gsl option as gsl==2.7 or gsl>=2.7, which causes independency with gsl=2.7.1. Please set conda recipe more specific