From a84af6f9cfd9303b74b1ad3f443ed396d48be8cd Mon Sep 17 00:00:00 2001 From: Scott Cain Date: Sat, 7 Oct 2023 04:16:22 +0000 Subject: [PATCH 1/6] this shouldn't be necessary --- jbrowse2/config/track_configs/rnaseq_splice.json | 1 - 1 file changed, 1 deletion(-) delete mode 120000 jbrowse2/config/track_configs/rnaseq_splice.json diff --git a/jbrowse2/config/track_configs/rnaseq_splice.json b/jbrowse2/config/track_configs/rnaseq_splice.json deleted file mode 120000 index 6a567519..00000000 --- a/jbrowse2/config/track_configs/rnaseq_splice.json +++ /dev/null @@ -1 +0,0 @@ -c_elegans_PRJNA13758_rnaseq_splice.json \ No newline at end of file From 0f5bef633bc4ca7a38b1f6150e5d6de7df52b4da Mon Sep 17 00:00:00 2001 From: Scott Cain Date: Mon, 9 Oct 2023 11:31:09 -0700 Subject: [PATCH 2/6] adding sort/collapse to config --- jbrowse2/bin/make_global_config.pl | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/jbrowse2/bin/make_global_config.pl b/jbrowse2/bin/make_global_config.pl index 75da112a..9a68fa7d 100755 --- a/jbrowse2/bin/make_global_config.pl +++ b/jbrowse2/bin/make_global_config.pl @@ -126,6 +126,14 @@ # but darkened to improve contrast in some JB2 UI elements $$json{'configuration'}{'theme'}{'palette'}{'tertiary'}{'main'} = '#9da9b6'; +#add config for sorting/collapsing categories +$$json{'configuration'}{'sort'}{'trackNames'} = 'true'; +$$json{'configuration'}{'sort'}{'categories'} = 'true'; +$$json{'configuration'}{'defaultCollapsed'}{'subCategories'} = 'true'; +$$json{'configuration'}{'defaultCollapsed'}{'topLevelCategories'} = 'true'; + + + my $plugin; my $hex; $$hex{'name'} = "HexJexlPlugin"; From 57efe69ed795f450abbac38005e96f5dee848ec9 Mon Sep 17 00:00:00 2001 From: Scott Cain Date: Mon, 9 Oct 2023 11:50:44 -0700 Subject: [PATCH 3/6] adding WB help plugin --- jbrowse2/bin/make_global_config.pl | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/jbrowse2/bin/make_global_config.pl b/jbrowse2/bin/make_global_config.pl index 9a68fa7d..ca31ec7d 100755 --- a/jbrowse2/bin/make_global_config.pl +++ b/jbrowse2/bin/make_global_config.pl @@ -141,9 +141,13 @@ my $vColor; $$vColor{'name'} = "VariantColorPlugin"; $$vColor{'umdLoc'}{'uri'} = "variantColor_plugin.js"; -my @plugins = ($hex, $vColor); +my $help; +$$help{'name'} = "JBrowseSiteSpecificHelp"; +$$help{'umdLoc'}{'uri'}= "plugins/JBrowseSiteSpeci…help.umd.development.js"; +my @plugins = ($hex, $vColor, $help); $$json{'plugins'} = \@plugins; + #that might be all that's needed #I dont think we need several of the things that are empty arrays #in the existing config From 79a8e8d178317c2972e2d12282f71c58c26a0087 Mon Sep 17 00:00:00 2001 From: Scott Cain Date: Mon, 9 Oct 2023 19:00:13 +0000 Subject: [PATCH 4/6] maybe you should actually read what you're copy/pasting --- jbrowse2/bin/make_global_config.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/jbrowse2/bin/make_global_config.pl b/jbrowse2/bin/make_global_config.pl index ca31ec7d..9392cc7e 100755 --- a/jbrowse2/bin/make_global_config.pl +++ b/jbrowse2/bin/make_global_config.pl @@ -143,7 +143,7 @@ $$vColor{'umdLoc'}{'uri'} = "variantColor_plugin.js"; my $help; $$help{'name'} = "JBrowseSiteSpecificHelp"; -$$help{'umdLoc'}{'uri'}= "plugins/JBrowseSiteSpeci…help.umd.development.js"; +$$help{'umdLoc'}{'uri'}= "plugins/JBrowseSiteSpecificHelp/jbrowse-site-specific-help.umd.development.js"; my @plugins = ($hex, $vColor, $help); $$json{'plugins'} = \@plugins; From ae257a33bc3ea11b63085e6461cfe42784843725 Mon Sep 17 00:00:00 2001 From: Scott Cain Date: Mon, 9 Oct 2023 12:30:23 -0700 Subject: [PATCH 5/6] hopefully fixing the quoting of true --- jbrowse2/bin/make_global_config.pl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/jbrowse2/bin/make_global_config.pl b/jbrowse2/bin/make_global_config.pl index ca31ec7d..9f33e7d5 100755 --- a/jbrowse2/bin/make_global_config.pl +++ b/jbrowse2/bin/make_global_config.pl @@ -127,10 +127,10 @@ $$json{'configuration'}{'theme'}{'palette'}{'tertiary'}{'main'} = '#9da9b6'; #add config for sorting/collapsing categories -$$json{'configuration'}{'sort'}{'trackNames'} = 'true'; -$$json{'configuration'}{'sort'}{'categories'} = 'true'; -$$json{'configuration'}{'defaultCollapsed'}{'subCategories'} = 'true'; -$$json{'configuration'}{'defaultCollapsed'}{'topLevelCategories'} = 'true'; +$$json{'configuration'}{'sort'}{'trackNames'} = $JSON::true; +$$json{'configuration'}{'sort'}{'categories'} = $JSON::true; +$$json{'configuration'}{'defaultCollapsed'}{'subCategories'} = $JSON::true; +$$json{'configuration'}{'defaultCollapsed'}{'topLevelCategories'} = $JSON::true; From 7ca6d22ee5355ea727eb219d42cb7b4a8997da7a Mon Sep 17 00:00:00 2001 From: Scott Cain Date: Mon, 9 Oct 2023 12:56:30 -0700 Subject: [PATCH 6/6] helps if you get the json structure right --- jbrowse2/bin/make_global_config.pl | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/jbrowse2/bin/make_global_config.pl b/jbrowse2/bin/make_global_config.pl index 9ad36ac3..b311c742 100755 --- a/jbrowse2/bin/make_global_config.pl +++ b/jbrowse2/bin/make_global_config.pl @@ -127,10 +127,10 @@ $$json{'configuration'}{'theme'}{'palette'}{'tertiary'}{'main'} = '#9da9b6'; #add config for sorting/collapsing categories -$$json{'configuration'}{'sort'}{'trackNames'} = $JSON::true; -$$json{'configuration'}{'sort'}{'categories'} = $JSON::true; -$$json{'configuration'}{'defaultCollapsed'}{'subCategories'} = $JSON::true; -$$json{'configuration'}{'defaultCollapsed'}{'topLevelCategories'} = $JSON::true; +$$json{'configuration'}{'hierarchical'}{'sort'}{'trackNames'} = $JSON::true; +$$json{'configuration'}{'hierarchical'}{'sort'}{'categories'} = $JSON::true; +$$json{'configuration'}{'hierarchical'}{'defaultCollapsed'}{'subCategories'} = $JSON::true; +$$json{'configuration'}{'hierarchical'}{'defaultCollapsed'}{'topLevelCategories'} = $JSON::true;