From e7ceec686c3f068bb256490ae4055847527f7483 Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Tue, 23 Jun 2026 15:16:09 +0000 Subject: [PATCH 1/4] Add new tool configurations for aoptk recetox tools --- templates/galaxy/config/tpv_rules_meta.yml.j2 | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/templates/galaxy/config/tpv_rules_meta.yml.j2 b/templates/galaxy/config/tpv_rules_meta.yml.j2 index 39601ac..877820a 100644 --- a/templates/galaxy/config/tpv_rules_meta.yml.j2 +++ b/templates/galaxy/config/tpv_rules_meta.yml.j2 @@ -259,6 +259,15 @@ tools: inherits: local_running_tools env: LITELLM_CONFIG_FILE: "{{ galaxy_config_dir }}/llm_hub_config.yaml" + toolshed.g2.bx.psu.edu/repos/recetox/aoptk_find_relationships_chemicals/aoptk_find_relationships_chemicals/.* + inherits: local_running_tools + env: + LITELLM_CONFIG_FILE: "{{ galaxy_config_dir }}/llm_hub_config.yaml" +toolshed.g2.bx.psu.edu/repos/recetox/aoptk_parse_pdf/aoptk_parse_pdf/.*: + inherits: toolshed.g2.bx.psu.edu/repos/recetox/aoptk_find_relationships_chemicals/aoptk_find_relationships_chemicals/.* +toolshed.g2.bx.psu.edu/repos/recetox/aoptk_normalize_chemicals/aoptk_normalize_chemicals/.*: + inherits: toolshed.g2.bx.psu.edu/repos/recetox/aoptk_find_relationships_chemicals/aoptk_find_relationships_chemicals/.* + roles: From f9d57365b35e1cad2c10401bac510d45c4434ec2 Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Tue, 23 Jun 2026 15:17:10 +0000 Subject: [PATCH 2/4] Update inheritance for aoptk_parse_pdf and aoptk_normalize_chemicals --- templates/galaxy/config/tpv_rules_meta.yml.j2 | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/templates/galaxy/config/tpv_rules_meta.yml.j2 b/templates/galaxy/config/tpv_rules_meta.yml.j2 index 877820a..e75c6e5 100644 --- a/templates/galaxy/config/tpv_rules_meta.yml.j2 +++ b/templates/galaxy/config/tpv_rules_meta.yml.j2 @@ -263,10 +263,10 @@ tools: inherits: local_running_tools env: LITELLM_CONFIG_FILE: "{{ galaxy_config_dir }}/llm_hub_config.yaml" -toolshed.g2.bx.psu.edu/repos/recetox/aoptk_parse_pdf/aoptk_parse_pdf/.*: - inherits: toolshed.g2.bx.psu.edu/repos/recetox/aoptk_find_relationships_chemicals/aoptk_find_relationships_chemicals/.* -toolshed.g2.bx.psu.edu/repos/recetox/aoptk_normalize_chemicals/aoptk_normalize_chemicals/.*: - inherits: toolshed.g2.bx.psu.edu/repos/recetox/aoptk_find_relationships_chemicals/aoptk_find_relationships_chemicals/.* + toolshed.g2.bx.psu.edu/repos/recetox/aoptk_parse_pdf/aoptk_parse_pdf/.*: + inherits: toolshed.g2.bx.psu.edu/repos/recetox/aoptk_find_relationships_chemicals/aoptk_find_relationships_chemicals/.* + toolshed.g2.bx.psu.edu/repos/recetox/aoptk_normalize_chemicals/aoptk_normalize_chemicals/.*: + inherits: toolshed.g2.bx.psu.edu/repos/recetox/aoptk_find_relationships_chemicals/aoptk_find_relationships_chemicals/.* From 14952a5d45f2237c850cf20bf74b27efb26f9190 Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Tue, 23 Jun 2026 15:22:17 +0000 Subject: [PATCH 3/4] Refactor tpv_rules_meta.yml.j2 for aoptk tools Removed unnecessary inherits for aoptk tools and added docker and singularity environment variables for LITELLM_CONFIG_FILE. --- templates/galaxy/config/tpv_rules_meta.yml.j2 | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/templates/galaxy/config/tpv_rules_meta.yml.j2 b/templates/galaxy/config/tpv_rules_meta.yml.j2 index e75c6e5..6a7c5a9 100644 --- a/templates/galaxy/config/tpv_rules_meta.yml.j2 +++ b/templates/galaxy/config/tpv_rules_meta.yml.j2 @@ -259,16 +259,12 @@ tools: inherits: local_running_tools env: LITELLM_CONFIG_FILE: "{{ galaxy_config_dir }}/llm_hub_config.yaml" - toolshed.g2.bx.psu.edu/repos/recetox/aoptk_find_relationships_chemicals/aoptk_find_relationships_chemicals/.* + toolshed.g2.bx.psu.edu/repos/recetox/aoptk_.*: inherits: local_running_tools env: LITELLM_CONFIG_FILE: "{{ galaxy_config_dir }}/llm_hub_config.yaml" - toolshed.g2.bx.psu.edu/repos/recetox/aoptk_parse_pdf/aoptk_parse_pdf/.*: - inherits: toolshed.g2.bx.psu.edu/repos/recetox/aoptk_find_relationships_chemicals/aoptk_find_relationships_chemicals/.* - toolshed.g2.bx.psu.edu/repos/recetox/aoptk_normalize_chemicals/aoptk_normalize_chemicals/.*: - inherits: toolshed.g2.bx.psu.edu/repos/recetox/aoptk_find_relationships_chemicals/aoptk_find_relationships_chemicals/.* - - + docker_env_LITELLM_CONFIG_FILE: "{{ galaxy_config_dir }}/llm_hub_config.yaml" + SINGULARITYENV_LITELLM_CONFIG_FILE: "{{ galaxy_config_dir }}/llm_hub_config.yaml" roles: training.*: From 57cef5ff5ede2c7f6593ac82c53b3879ca28dc5c Mon Sep 17 00:00:00 2001 From: Helge Hecht Date: Wed, 24 Jun 2026 06:59:00 +0000 Subject: [PATCH 4/4] Change inherits from local_running_tools to local_sing_running_tools --- templates/galaxy/config/tpv_rules_meta.yml.j2 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/galaxy/config/tpv_rules_meta.yml.j2 b/templates/galaxy/config/tpv_rules_meta.yml.j2 index 6a7c5a9..40e4883 100644 --- a/templates/galaxy/config/tpv_rules_meta.yml.j2 +++ b/templates/galaxy/config/tpv_rules_meta.yml.j2 @@ -260,7 +260,7 @@ tools: env: LITELLM_CONFIG_FILE: "{{ galaxy_config_dir }}/llm_hub_config.yaml" toolshed.g2.bx.psu.edu/repos/recetox/aoptk_.*: - inherits: local_running_tools + inherits: local_sing_running_tools env: LITELLM_CONFIG_FILE: "{{ galaxy_config_dir }}/llm_hub_config.yaml" docker_env_LITELLM_CONFIG_FILE: "{{ galaxy_config_dir }}/llm_hub_config.yaml"