From 36012d51be3b91db2e06b8447c152412ba4ef011 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 3 Feb 2020 08:52:54 +0100 Subject: [PATCH 1/5] Add build_sites_config_file option to config_schema We need this for the default value. Without the defaults many external display applications won't load. --- lib/galaxy/webapps/galaxy/config_schema.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml index efc23f9d1f8..fe8d4ed6b71 100644 --- a/lib/galaxy/webapps/galaxy/config_schema.yml +++ b/lib/galaxy/webapps/galaxy/config_schema.yml @@ -553,6 +553,14 @@ mapping: will use a less efficient monitoring scheme that may work in wider range of scenarios than the watchdog default. + build_sites_config_file: + type: str + default: config/build_sites.yml.sample + required: false + desc: | + File that defines the builds (dbkeys) available at sites used by display applications + and the URL to those sites. + builds_file_path: type: str default: tool-data/shared/ucsc/builds.txt From 6c100551a645e1b13d5e6954ae394b20ec2dd77f Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 3 Feb 2020 08:56:18 +0100 Subject: [PATCH 2/5] Run make config-rebuild --- doc/source/admin/galaxy_options.rst | 11 +++++++++++ lib/galaxy/config/sample/galaxy.yml.sample | 4 ++++ 2 files changed, 15 insertions(+) diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst index 7c576240ef9..e5420a52692 100644 --- a/doc/source/admin/galaxy_options.rst +++ b/doc/source/admin/galaxy_options.rst @@ -732,6 +732,17 @@ :Type: str +~~~~~~~~~~~~~~~~~~~~~~~~~~~ +``build_sites_config_file`` +~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +:Description: + File that defines the builds (dbkeys) available at sites used by + display applications and the URL to those sites. +:Default: ``config/build_sites.yml.sample`` +:Type: str + + ~~~~~~~~~~~~~~~~~~~~ ``builds_file_path`` ~~~~~~~~~~~~~~~~~~~~ diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample index 3e359311296..b3fbdf40c6c 100644 --- a/lib/galaxy/config/sample/galaxy.yml.sample +++ b/lib/galaxy/config/sample/galaxy.yml.sample @@ -441,6 +441,10 @@ galaxy: # scenarios than the watchdog default. #watch_tool_data_dir: 'false' + # File that defines the builds (dbkeys) available at sites used by + # display applications and the URL to those sites. + #build_sites_config_file: config/build_sites.yml.sample + # File containing old-style genome builds #builds_file_path: tool-data/shared/ucsc/builds.txt From dd0f1d73809704ff6ea9bd576021d9bd50771971 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 5 Feb 2020 16:26:25 +0100 Subject: [PATCH 3/5] Move sam_pileup to GALAXY_LIB_TOOLS_VERSIONED Will be fixed in https://github.com/galaxyproject/tools-devteam/pull/545 --- lib/galaxy/tools/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index ed52ad0a33f..706e5326656 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -163,7 +163,6 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [ "lastz_paired_reads_wrapper", "subRate1", "substitutions1", - "sam_pileup", "find_diag_hits", "cufflinks", # Tools improperly migrated to the tool shed (iuc) @@ -188,6 +187,7 @@ GALAXY_LIB_TOOLS_VERSIONED = { "lastz_wrapper_2": packaging.version.parse("1.3"), "PEsortedSAM2readprofile": packaging.version.parse("1.1.1"), "sam_to_bam": packaging.version.parse("1.1.3"), + "sam_pileup": packaging.version.parse("1.1.2"), } From a384c6c393d2a5844ab1eaf8bb637f099e291e79 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Fri, 7 Feb 2020 18:26:10 +0100 Subject: [PATCH 4/5] Fix app reference in guess_shed_config --- lib/galaxy/model/tool_shed_install/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py index c010e4cc361..48e9430148e 100644 --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -137,7 +137,7 @@ class ToolShedRepository(object): self.shed_config_filename = shed_tool_conf_dict['config_filename'] return shed_tool_conf_dict # Very last resort, get default shed_tool_config file for this instance - shed_tool_conf_dict = self.app.toolbox.default_shed_tool_conf_dict() + shed_tool_conf_dict = app.toolbox.default_shed_tool_conf_dict() self.shed_config_filename = shed_tool_conf_dict['config_filename'] return shed_tool_conf_dict From b7c6f4eb44a2bc4503eba6362ed0178378a859ff Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 11 Feb 2020 02:55:04 +0000 Subject: [PATCH 5/5] Fix version in which ``sam_pileup`` was fixed xref. https://github.com/galaxyproject/galaxy/pull/9320/files#r376192439 --- lib/galaxy/tools/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 706e5326656..922c6f42357 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -187,7 +187,7 @@ GALAXY_LIB_TOOLS_VERSIONED = { "lastz_wrapper_2": packaging.version.parse("1.3"), "PEsortedSAM2readprofile": packaging.version.parse("1.1.1"), "sam_to_bam": packaging.version.parse("1.1.3"), - "sam_pileup": packaging.version.parse("1.1.2"), + "sam_pileup": packaging.version.parse("1.1.3"), }