Release 2.0 (merge dev to master)

General

• Reorganize repository
• Fix verbosity mode
• Fix logs details
• Update README.md
• Update the "help" option in the scripts
• Update examples
• Factorize and optimize code
• Create file constants.py containing the constant variables

Input organisms.yml file

• Change root structure (a list instead of a dictionary, the name parameter is added to the species dictionary sp_dict)
• Add parameter main_species. Useful when there are multiple strains for the same species: set to yes to define the strain used as home for JBrowse
• Parameters species, genus, strain, sex, common will be sanitized (removing " ", "-", "(", ")", "'")
• Add jinja2 template

Input config file

• Change root structure (one-level dictionary)
• Add parameters authelia_secrets_env_path and authelia_db_postgres_password required for Authelia
• Change the name of some parameters (galaxy_persist_data, tripal_banner_path, jbrowse_menu_url)
• Remove unused apollo parameters (webapollo_user, webapollo_password)

Step "init"

• Update templates files
• Fix the copy of the specified banner
• Write galaxy_nginx.conf only if needed

Step "get data"

• Prefix data filenames with g_species_s
• Add the last modification date of the source file to the gff filename

Step "load data"

• Use Bioblend function upload_from_galaxy_fs() instead of upload_from_local() (to enable symlink, instead of copy)

Step "run workflow Phaeoexplorer"

• Development of a workflow loading fasta and gff files to Chado, Tripal and JBrowse, for one or two organisms of the same species

workflows_phaeoexplorer/Galaxy-Workflow-load_blast_results_1org_v1.ga

+{
+    "a_galaxy_workflow": "true",
+    "annotation": "",
+    "format-version": "0.1",
+    "name": "load_blast_results_1org_v1",
+    "steps": {
+        "0": {
+            "annotation": "",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "blast file xml org1"
+                }
+            ],
+            "label": "blast file xml org1",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "bottom": 416.1999969482422,
+                "height": 82.19999694824219,
+                "left": 410,
+                "right": 610,
+                "top": 334,
+                "width": 200,
+                "x": 410,
+                "y": 334
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "b1c63d94-61a7-4bf1-8b5d-e08fb34c0357",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "f602d234-8cea-4db9-ab77-678cdc0d2101"
+                }
+            ]
+        },
+        "1": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_blast/load_blast/2.3.4+galaxy0",
+            "errors": null,
+            "id": 1,
+            "input_connections": {
+                "input": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Chado load Blast results",
+                    "name": "analysis_id"
+                },
+                {
+                    "description": "runtime parameter for tool Chado load Blast results",
+                    "name": "input"
+                },
+                {
+                    "description": "runtime parameter for tool Chado load Blast results",
+                    "name": "organism_id"
+                },
+                {
+                    "description": "runtime parameter for tool Chado load Blast results",
+                    "name": "wait_for"
+                }
+            ],
+            "label": "load blast results org1",
+            "name": "Chado load Blast results",
+            "outputs": [
+                {
+                    "name": "results",
+                    "type": "json"
+                }
+            ],
+            "position": {
+                "bottom": 457.3999938964844,
+                "height": 164.39999389648438,
+                "left": 711,
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+                "top": 293,
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+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_blast/load_blast/2.3.4+galaxy0",
+            "tool_shed_repository": {
+                "changeset_revision": "08ae8b27b193",
+                "name": "chado_load_blast",
+                "owner": "gga",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"blastdb_id\": \"21\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"match_on_name\": \"false\", \"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"query_type\": \"polypeptide\", \"re_name\": \"\", \"skip_missing\": \"false\", \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "2.3.4+galaxy0",
+            "type": "tool",
+            "uuid": "10144cf8-f121-45f3-ba64-9f4d66bf1e56",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "results",
+                    "uuid": "95708895-8439-4257-bff6-96e4c51a0725"
+                }
+            ]
+        },
+        "2": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
+            "errors": null,
+            "id": 2,
+            "input_connections": {
+                "wait_for": {
+                    "id": 1,
+                    "output_name": "results"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Synchronize an analysis",
+                    "name": "analysis_id"
+                }
+            ],
+            "label": "sync blast analysis org1",
+            "name": "Synchronize an analysis",
+            "outputs": [
+                {
+                    "name": "results",
+                    "type": "json"
+                }
+            ],
+            "position": {
+                "bottom": 451.3999938964844,
+                "height": 154.39999389648438,
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+                "top": 297,
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+            "post_job_actions": {},
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
+            "tool_shed_repository": {
+                "changeset_revision": "f487ff676088",
+                "name": "tripal_analysis_sync",
+                "owner": "gga",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "3.2.1.0",
+            "type": "tool",
+            "uuid": "99e7496d-ac32-467d-8c09-2efd48d0231a",
+            "workflow_outputs": [
+                {
+                    "label": "Synchronize Analysis into Tripal",
+                    "output_name": "results",
+                    "uuid": "1fb6db92-90a2-4e33-beec-f2f974e369e9"
+                }
+            ]
+        },
+        "3": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_db_populate_mviews/db_populate_mviews/3.2.1.0",
+            "errors": null,
+            "id": 3,
+            "input_connections": {
+                "wait_for": {
+                    "id": 2,
+                    "output_name": "results"
+                }
+            },
+            "inputs": [],
+            "label": "populate mat views",
+            "name": "Populate materialized views",
+            "outputs": [
+                {
+                    "name": "results",
+                    "type": "txt"
+                }
+            ],
+            "position": {
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+                "height": 154.39999389648438,
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+            "post_job_actions": {},
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+            "tool_shed_repository": {
+                "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": "3.2.1.0",
+            "type": "tool",
+            "uuid": "5c947dd5-89df-4146-9ab8-9e1d6de42360",
+            "workflow_outputs": [
+                {
+                    "label": "Populate Tripal materialized view(s)",
+                    "output_name": "results",
+                    "uuid": "0a0c9fa7-3a3c-459d-b5c7-b7a5a11459f3"
+                }
+            ]
+        },
+        "4": {
+            "annotation": "",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_db_index/db_index/3.2.1.1",
+            "errors": null,
+            "id": 4,
+            "input_connections": {
+                "wait_for": {
+                    "id": 3,
+                    "output_name": "results"
+                }
+            },
+            "inputs": [],
+            "label": "index tripal data",
+            "name": "Index Tripal data",
+            "outputs": [
+                {
+                    "name": "results",
+                    "type": "txt"
+                }
+            ],
+            "position": {
+                "bottom": 433.6000061035156,
+                "height": 113.60000610351562,
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+                "name": "tripal_db_index",
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+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "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}",
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+            "uuid": "5ecc30b0-07ab-4f9b-81f0-31310358c221",
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+    },
+    "tags": [],
+    "uuid": "80e32784-e39e-48ce-a6e3-7627de734ca6",
+    "version": 4
+}
\ No newline at end of file