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Update Braker3 #1091

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Jan 31, 2024
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24 changes: 12 additions & 12 deletions files/galaxy/tpv/tools.yml
Original file line number Diff line number Diff line change
Expand Up @@ -1060,21 +1060,21 @@ tools:
require:
- singularity

toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/3.0.6.*:
mem: 4
toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/.*:
cores: 6
env:
GENEMARK_PATH: "/usr/local/tools/_conda/envs/[email protected]/bin/genemark/bin/"
PROTHINT_PATH: "/usr/local/tools/_conda/envs/[email protected]/bin/genemark/bin/gmes/ProtHint/bin/"

toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/3.0.3.*:
mem: 4
cores: 6
params:
singularity_container_id_override: docker://quay.io/bgruening/braker3:v.1.0.4
scheduling:
require:
- singularity
singularity_enabled: true
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I think the +galaxy suffixes are needed for the tool versions here, right?
Looks like braker3 is not working at EMBO training

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rules:
- if: helpers.tool_version_eq(tool, '3.0.3')
execute: |
entity.params['singularity_container_id_override']="docker://teambraker/braker3:v.1.0.4"
- if: helpers.tool_version_eq(tool, '3.0.6')
execute: |
entity.params['singularity_container_id_override']="docker://teambraker/braker3:v1.0.6"
- if: helpers.tool_version_eq(tool, '3.0.7')
execute: |
entity.params['singularity_container_id_override']="docker://teambraker/braker3:v3.0.7.1"

# GeneMark is a pain and needs special casing
toolshed.g2.bx.psu.edu/repos/genouest/braker/braker/.*:
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