From 0d1afd463c9d8ce3f2ba85f7d36ddce9a3c02ee5 Mon Sep 17 00:00:00 2001 From: Anmol Kiran Date: Mon, 17 Jun 2024 16:49:28 +0100 Subject: [PATCH 1/4] Create riboseq.yml Beginning of riboseq.usegalaxy.eu --- files/galaxy/subdomains/riboseq/themes/riboseq.yml | 1 + 1 file changed, 1 insertion(+) create mode 100644 files/galaxy/subdomains/riboseq/themes/riboseq.yml diff --git a/files/galaxy/subdomains/riboseq/themes/riboseq.yml b/files/galaxy/subdomains/riboseq/themes/riboseq.yml new file mode 100644 index 000000000..8b1378917 --- /dev/null +++ b/files/galaxy/subdomains/riboseq/themes/riboseq.yml @@ -0,0 +1 @@ + From cc706c0fdb41cd9b456d8cfb8f2bb36716f89de3 Mon Sep 17 00:00:00 2001 From: codemeleon Date: Mon, 17 Jun 2024 17:26:34 +0100 Subject: [PATCH 2/4] Initial configurations for riboseq --- group_vars/sn06.yml | 7 +++---- templates/galaxy/config/global_host_filters.py.j2 | 1 + 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/group_vars/sn06.yml b/group_vars/sn06.yml index 58de5f569..681a16843 100644 --- a/group_vars/sn06.yml +++ b/group_vars/sn06.yml @@ -298,7 +298,6 @@ galaxy_virtualenv_command: "{{ conda_prefix }}/envs/_galaxy_/bin/python -m venv galaxy_nonrepro_tools: "{{ galaxy_root }}/custom-tools" galaxy_nonrepro_commit: master - # Custom override # Our galaxy_tool_dependency_dir is on NFS, and permissions are set in such a # way that they cannot be changed by the ansible connected user. @@ -373,7 +372,7 @@ galaxy_themes_subdomains: - name: cancer - name: aqua - name: eirene - + - name: riboseq galaxy_config_file_src_dir: files/galaxy galaxy_config_files: @@ -465,5 +464,5 @@ galaxy_config_templates: dest: "{{ galaxy_config['galaxy']['object_store_config_file'] }}" - src: "{{ galaxy_config_file_src_dir }}/tpv/destinations.yml.j2" dest: "{{ tpv_mutable_dir }}/destinations.yml" - - src: '{{ galaxy_config_template_src_dir }}/config/vault_conf.yml.j2' - dest: '{{ galaxy_config_dir }}/vault_conf.yml' + - src: "{{ galaxy_config_template_src_dir }}/config/vault_conf.yml.j2" + dest: "{{ galaxy_config_dir }}/vault_conf.yml" diff --git a/templates/galaxy/config/global_host_filters.py.j2 b/templates/galaxy/config/global_host_filters.py.j2 index c92073eb4..4972466d8 100644 --- a/templates/galaxy/config/global_host_filters.py.j2 +++ b/templates/galaxy/config/global_host_filters.py.j2 @@ -145,6 +145,7 @@ DOMAIN_SECTIONS = { "biodiversity_data_exploration" ], 'eirene': ['chemicaltoolbox','metabolomics','interactivetools'] + 'riboseq': ['transcriptomics','rna_seq','ribo_seq','rna_analysis', 'gene_regulation','interactivetools'] } From 11397751e65c10099ddd1d895c10ded2daa735fd Mon Sep 17 00:00:00 2001 From: codemeleon Date: Mon, 17 Jun 2024 17:27:57 +0100 Subject: [PATCH 3/4] correction --- templates/galaxy/config/global_host_filters.py.j2 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/galaxy/config/global_host_filters.py.j2 b/templates/galaxy/config/global_host_filters.py.j2 index 4972466d8..ebbf494a1 100644 --- a/templates/galaxy/config/global_host_filters.py.j2 +++ b/templates/galaxy/config/global_host_filters.py.j2 @@ -144,7 +144,7 @@ DOMAIN_SECTIONS = { "earth-system-section-interactivetools", "biodiversity_data_exploration" ], - 'eirene': ['chemicaltoolbox','metabolomics','interactivetools'] + 'eirene': ['chemicaltoolbox','metabolomics','interactivetools'], 'riboseq': ['transcriptomics','rna_seq','ribo_seq','rna_analysis', 'gene_regulation','interactivetools'] } From 4d8145f2586c6e26a9b9938e9728beb46cdb78b1 Mon Sep 17 00:00:00 2001 From: codemeleon Date: Tue, 18 Jun 2024 12:26:28 +0100 Subject: [PATCH 4/4] removed quoting changes --- group_vars/gxconfig.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/group_vars/gxconfig.yml b/group_vars/gxconfig.yml index 7c2dc94e7..a7bcd196a 100644 --- a/group_vars/gxconfig.yml +++ b/group_vars/gxconfig.yml @@ -1029,7 +1029,7 @@ base_app_main: &BASE_APP_MAIN 'cancer.usegalaxy.eu': Cancer 'aqua.usegalaxy.eu': Aqua 'eirene.usegalaxy.eu': EIRENE - + 'riboseq.usegalaxy.eu': RiboSeq # This option has been deprecated, use the `logo_src` instead to # change the default logo including the galaxy brand title.