Comments (3)
TobyBaril
commented on June 1, 2024
Apologies for the delay on this, there is an issue with configuring Conda within the docker environment that seems to not be working anymore! I'm working on a fix and it should be live shortly, I am just testing now. Essentially, the workaround for the moment is to manually configure the Conda environment after starting the docker container and this seems to behave perfectly.
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TobyBaril
commented on June 1, 2024
I have developed a workaround for the moment. This involves the docker container running a different configure script, after which you have to configure the Conda environment manually. Instructions are on the README in the Docker directory. This has been tested with Dfam 3.7 without RepBase and works. If using an earlier version of RepBase the Dockerfile must be altered before building the container.
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TobyBaril
commented on June 1, 2024
Preconfigured docker container and build instructions updated, tested on different distributions and now stable, closing.
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Related Issues (20)
- Annotation accuracy HOT 1
- why so many 'unknown' sequences in generated TE lib HOT 2
- underprediction HOT 3
- Kimura expectations
- Runtime and Restarting HOT 1
- Error while using a custom library HOT 2
- Filtering overlapping repeats for chimers HOT 3
- Limiting Repeatmodeler rounds to 4/5 ?? HOT 3
- Variation in annotation within species/family HOT 2
- R step 12 "no"? HOT 1
- GFF attributes and wrong TE classification?? HOT 1
- Generate soft-masked genome without re-running? HOT 2
- Bug when using soft link to genome HOT 1
- Stuck at the "Cleaning Genome" phase HOT 7
- data for pie chart proportions HOT 8
- impact of initial ,masking by RM and usage of DFAM3.8 HOT 5
- RepeatModeler run successfully, but did not create *.classified file and *-families.fa, and so stopped the earlGrey. HOT 8
- Installation Errors following "Earl Grey Installation and Configuration (If you already have RepeatMasker and RepeatModeler)" HOT 2
- Question about error HOT 2
- annotations in gff file not shown in IGV
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