diff --git a/constants_phaeo.py b/constants_phaeo.py
index 10cdb8c2136bde0874803052fed285b3e44f1747..ace8d66dc798f42024d51515afc75967ac3005bd 100644
--- a/constants_phaeo.py
+++ b/constants_phaeo.py
@@ -9,7 +9,7 @@ import constants
WORKFLOWS_PATH = "workflows_phaeoexplorer/"
WF_LOAD_GFF_JB = "load_fasta_gff_jbrowse"
-WF_LOAD_GFF_JB_1_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v4.ga"
+WF_LOAD_GFF_JB_1_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v6.ga"
WF_LOAD_GFF_JB_1_ORG_INPUT_GENOME = "0"
WF_LOAD_GFF_JB_1_ORG_INPUT_GFF = "1"
WF_LOAD_GFF_JB_1_ORG_INPUT_PROTEINS = "2"
@@ -21,9 +21,9 @@ WF_LOAD_GFF_JB_1_ORG_STEP_FEATURE_SYNC = "7"
WF_LOAD_GFF_JB_1_ORG_STEP_POPULATE_VIEWS = "8"
WF_LOAD_GFF_JB_1_ORG_STEP_INDEX = "9"
-WF_LOAD_GFF_JB_2_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v4.ga"
-WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG1 = "0"
-WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG1 = "1"
+WF_LOAD_GFF_JB_2_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v6.ga"
+WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG1 = "0"
+WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG1 = "1"
WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG1 = "2"
WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG2 = "3"
WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG2 = "4"
diff --git a/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v6.ga b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v6.ga
new file mode 100644
index 0000000000000000000000000000000000000000..d9dae223daa8783f6dff89a5b1a7725b324613ed
--- /dev/null
+++ b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v6.ga
@@ -0,0 +1,519 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "chado_load_tripal_synchronize_jbrowse_1org_v6",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "genome"
+ }
+ ],
+ "label": "genome",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "bottom": 365.8000030517578,
+ "height": 61.80000305175781,
+ "left": 176.5,
+ "right": 376.5,
+ "top": 304,
+ "width": 200,
+ "x": 176.5,
+ "y": 304
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "40c1e307-2cc6-4914-aebc-76373131708d",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "42803cc3-a5cc-44e9-b6c8-2456472579cd"
+ }
+ ]
+ },
+ "1": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "annotations"
+ }
+ ],
+ "label": "annotations",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "bottom": 455.8000030517578,
+ "height": 61.80000305175781,
+ "left": 207.5,
+ "right": 407.5,
+ "top": 394,
+ "width": 200,
+ "x": 207.5,
+ "y": 394
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "ffb56c28-197b-4029-a678-2108ba95f21f",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "9aa9cb17-a004-4287-abf4-6ca2c2ad7b66"
+ }
+ ]
+ },
+ "2": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 2,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "proteins"
+ }
+ ],
+ "label": "proteins",
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "bottom": 544.8000030517578,
+ "height": 61.80000305175781,
+ "left": 229.5,
+ "right": 429.5,
+ "top": 483,
+ "width": 200,
+ "x": 229.5,
+ "y": 483
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "018cd90b-1f34-4d37-9919-7767c8c3026d",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "8623782b-77e2-4eea-bb20-0cf158a503ff"
+ }
+ ]
+ },
+ "3": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
+ "errors": null,
+ "id": 3,
+ "input_connections": {
+ "fasta": {
+ "id": 0,
+ "output_name": "output"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool Chado load fasta",
+ "name": "analysis_id"
+ },
+ {
+ "description": "runtime parameter for tool Chado load fasta",
+ "name": "organism"
+ },
+ {
+ "description": "runtime parameter for tool Chado load fasta",
+ "name": "wait_for"
+ }
+ ],
+ "label": null,
+ "name": "Chado load fasta",
+ "outputs": [
+ {
+ "name": "results",
+ "type": "json"
+ }
+ ],
+ "position": {
+ "bottom": 445,
+ "height": 144,
+ "left": 506.5,
+ "right": 706.5,
+ "top": 301,
+ "width": 200,
+ "x": 506.5,
+ "y": 301
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
+ "tool_shed_repository": {
+ "changeset_revision": "ba4d07fbaf47",
+ "name": "chado_feature_load_fasta",
+ "owner": "gga",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"do_update\": \"false\", \"ext_db\": {\"db\": \"\", \"re_db_accession\": \"\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"match_on_name\": \"false\", \"organism\": {\"__class__\": \"RuntimeValue\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"re_name\": \"\", \"re_uniquename\": \"\", \"relationships\": {\"rel_type\": \"none\", \"__current_case__\": 0}, \"sequence_type\": \"contig\", \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": null,
+ "type": "tool",
+ "uuid": "59bb1c33-b93f-49db-941d-66cbdaaf2cb5",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "results",
+ "uuid": "cff733d9-3e76-417e-95e2-7d4e2111ff59"
+ }
+ ]
+ },
+ "4": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0",
+ "errors": null,
+ "id": 4,
+ "input_connections": {
+ "reference_genome|genome": {
+ "id": 0,
+ "output_name": "output"
+ },
+ "track_groups_0|data_tracks_0|data_format|annotation": {
+ "id": 1,
+ "output_name": "output"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool JBrowse",
+ "name": "reference_genome"
+ }
+ ],
+ "label": null,
+ "name": "JBrowse",
+ "outputs": [
+ {
+ "name": "output",
+ "type": "html"
+ }
+ ],
+ "position": {
+ "bottom": 681.1999969482422,
+ "height": 205.1999969482422,
+ "left": 493.5,
+ "right": 693.5,
+ "top": 476,
+ "width": 200,
+ "x": 493.5,
+ "y": 476
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0",
+ "tool_shed_repository": {
+ "changeset_revision": "4542035c1075",
+ "name": "jbrowse",
+ "owner": "iuc",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"true\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"\"}}, \"jbstyle\": {\"style_classname\": \"transcript\", \"style_label\": \"product,name,id\", \"style_description\": \"ec32_ortholog_description,note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": [{\"__index__\": 0, \"menu_action\": \"iframeDialog\", \"menu_label\": \"View transcript report\", \"menu_title\": \"Transcript {id}\", \"menu_url\": \"__MENU_URL_ORG__\", \"menu_icon\": \"dijitIconBookmark\"}]}, \"track_visibility\": \"default_on\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": null,
+ "type": "tool",
+ "uuid": "212e883c-daeb-4b4f-9bed-c90f130da794",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "38052de9-61ed-4cdd-8a11-1b1d6dd8a8e6"
+ }
+ ]
+ },
+ "5": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.4+galaxy0",
+ "errors": null,
+ "id": 5,
+ "input_connections": {
+ "fasta": {
+ "id": 2,
+ "output_name": "output"
+ },
+ "gff": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "wait_for": {
+ "id": 3,
+ "output_name": "results"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool Chado load gff",
+ "name": "analysis_id"
+ },
+ {
+ "description": "runtime parameter for tool Chado load gff",
+ "name": "organism"
+ }
+ ],
+ "label": null,
+ "name": "Chado load gff",
+ "outputs": [
+ {
+ "name": "results",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "bottom": 472.3999938964844,
+ "height": 174.39999389648438,
+ "left": 783.5,
+ "right": 983.5,
+ "top": 298,
+ "width": 200,
+ "x": 783.5,
+ "y": 298
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.4+galaxy0",
+ "tool_shed_repository": {
+ "changeset_revision": "e9a6d7568817",
+ "name": "chado_feature_load_gff",
+ "owner": "gga",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"add_only\": \"false\", \"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"ConnectedValue\"}, \"gff\": {\"__class__\": \"ConnectedValue\"}, \"landmark_type\": \"contig\", \"no_seq_compute\": \"false\", \"organism\": {\"__class__\": \"RuntimeValue\"}, \"prot_naming\": {\"method\": \"regex\", \"__current_case__\": 1, \"re_protein_capture\": \"^mRNA(_.+)$\", \"re_protein\": \"prot\\\\1\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": null,
+ "type": "tool",
+ "uuid": "7b88e06e-9ab1-4201-a947-e12bb3d2b901",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "results",
+ "uuid": "d82c5b1c-323e-466e-b6af-8524f87c09ab"
+ }
+ ]
+ },
+ "6": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/jbrowse_to_container/jbrowse_to_container/0.5.1",
+ "errors": null,
+ "id": 6,
+ "input_connections": {
+ "organisms_0|jbrowse": {
+ "id": 4,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "Add organisms to JBrowse container",
+ "outputs": [
+ {
+ "name": "output",
+ "type": "html"
+ }
+ ],
+ "position": {
+ "bottom": 640,
+ "height": 134,
+ "left": 779.5,
+ "right": 979.5,
+ "top": 506,
+ "width": 200,
+ "x": 779.5,
+ "y": 506
+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/jbrowse_to_container/jbrowse_to_container/0.5.1",
+ "tool_shed_repository": {
+ "changeset_revision": "11033bdad2ca",
+ "name": "jbrowse_to_container",
+ "owner": "gga",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"organisms\": [{\"__index__\": 0, \"jbrowse\": {\"__class__\": \"ConnectedValue\"}, \"name\": \"__DISPLAY_NAME_ORG__\", \"advanced\": {\"unique_id\": \"__UNIQUE_ID_ORG__\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": null,
+ "type": "tool",
+ "uuid": "ff93af13-b389-44c7-9a37-e39f216f3619",
+ "workflow_outputs": [
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+ "output_name": "output",
+ "uuid": "97986774-449c-4019-9273-aae3f461ff0c"
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+ "7": {
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+ "errors": null,
+ "id": 7,
+ "input_connections": {
+ "wait_for": {
+ "id": 5,
+ "output_name": "results"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool Synchronize features",
+ "name": "organism_id"
+ }
+ ],
+ "label": null,
+ "name": "Synchronize features",
+ "outputs": [
+ {
+ "name": "results",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "bottom": 459.3999938964844,
+ "height": 154.39999389648438,
+ "left": 1065.5,
+ "right": 1265.5,
+ "top": 305,
+ "width": 200,
+ "x": 1065.5,
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+ },
+ "post_job_actions": {},
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_feature_sync/feature_sync/3.2.1.0",
+ "tool_shed_repository": {
+ "changeset_revision": "64e36c3f0dd6",
+ "name": "tripal_feature_sync",
+ "owner": "gga",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"repeat_ids\": [], \"repeat_types\": [{\"__index__\": 0, \"types\": \"mRNA\"}, {\"__index__\": 1, \"types\": \"polypeptide\"}], \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": null,
+ "type": "tool",
+ "uuid": "281d7aef-81e2-437b-8080-e9c451d67f5b",
+ "workflow_outputs": [
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+ "output_name": "results",
+ "uuid": "33bcb916-0427-475f-89d3-4928ae3c0708"
+ }
+ ]
+ },
+ "8": {
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+ "errors": null,
+ "id": 8,
+ "input_connections": {
+ "wait_for": {
+ "id": 7,
+ "output_name": "results"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "Populate materialized views",
+ "outputs": [
+ {
+ "name": "results",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "bottom": 458.3999938964844,
+ "height": 154.39999389648438,
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+ "changeset_revision": "3c08f32a3dc1",
+ "name": "tripal_db_populate_mviews",
+ "owner": "gga",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"mview\": \"\", \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": null,
+ "type": "tool",
+ "uuid": "cf37a05e-8125-491b-98be-d8f4df295e16",
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+ "output_name": "results",
+ "uuid": "3c0dbcb4-f832-4293-8c35-ce427b9ec28a"
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+ ]
+ },
+ "9": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_db_index/db_index/3.2.1.1",
+ "errors": null,
+ "id": 9,
+ "input_connections": {
+ "wait_for": {
+ "id": 8,
+ "output_name": "results"
+ }
+ },
+ "inputs": [],
+ "label": null,
+ "name": "Index Tripal data",
+ "outputs": [
+ {
+ "name": "results",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "bottom": 417.6000061035156,
+ "height": 113.60000610351562,
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+ "right": 1837.5,
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+ "changeset_revision": "d55a39f12dda",
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+ "tool_state": "{\"expose\": {\"do_expose\": \"no\", \"__current_case__\": 0}, \"queues\": \"10\", \"table\": {\"mode\": \"website\", \"__current_case__\": 0}, \"tokenizer\": \"standard\", \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": null,
+ "type": "tool",
+ "uuid": "ee3698f2-3c4e-456f-8c42-f1ad2aa4feb5",
+ "workflow_outputs": [
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+ "output_name": "results",
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+ }
+ ]
+ }
+ },
+ "tags": [],
+ "uuid": "167e6d35-4e56-41bc-a324-7f5abb56800f",
+ "version": 1
+}
\ No newline at end of file
diff --git a/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v6.ga b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v6.ga
new file mode 100644
index 0000000000000000000000000000000000000000..854b4b40bc14102c4bd5c488665867348bea5339
--- /dev/null
+++ b/workflows_phaeoexplorer/Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v6.ga
@@ -0,0 +1,887 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "chado_load_tripal_synchronize_jbrowse_2org_v6",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "content_id": null,
+ "errors": null,
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "genome org1"
+ }
+ ],
+ "label": "genome org1",
+ "name": "Input dataset",
+ "outputs": [],
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