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Commit b9d17f94 authored by Arthur Le Bars's avatar Arthur Le Bars
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Fix missing runtime parameters for blast workflow

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2 merge requests!11Workflow v2,!9Release 2.0 (merge dev to master)
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README.md
+ 1
− 1
View file @ b9d17f94
......@@ -75,7 +75,7 @@ $ python3 /path/to/repo/gga_load_data.py input_file.yml -c/--config config_file
```bash
$ python3 /path/to/repo/gga_load_data.py input_file.yml -c/--config config_file --workflow workflow_type [-v/--verbose] [OPTIONS]
--workflow (Valid options: "chado_load_fasta_gff_jbrowse", "blast", "intepro", a couple of preset workflows are available in the workflows_phaeoexplorer directory in this repository)
--workflow (Valid options: "chado_load_fasta_gff_jbrowse", "blast", "interpro", a couple of preset workflows are available in the workflows_phaeoexplorer directory in this repository)
--main-directory $PATH (Path where to access stacks; default=current directory)
```
......
workflows_phaeoexplorer/Galaxy-Workflow-load_blast_results_2org_v1.ga
+ 124
− 103
View file @ b9d17f94
......@@ -20,14 +20,14 @@
"name": "Input dataset",
"outputs": [],
"position": {
"bottom": 356.1999969482422,
"height": 82.19999694824219,
"left": 168,
"right": 368,
"top": 274,
"bottom": 230.39999389648438,
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"width": 200,
"x": 168,
"y": 274
"x": 97.5,
"y": 169.1999969482422
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
......@@ -38,7 +38,7 @@
{
"label": null,
"output_name": "output",
"uuid": "8c6e3cd8-d0a0-403f-a882-f5206c8627f9"
"uuid": "72006174-6297-4777-95bd-ca427b9ea729"
}
]
},
......@@ -58,14 +58,14 @@
"name": "Input dataset",
"outputs": [],
"position": {
"bottom": 467.1999969482422,
"height": 82.19999694824219,
"left": 200,
"right": 400,
"top": 385,
"bottom": 341.40000915527344,
"height": 61.19999694824219,
"left": 129.5,
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"width": 200,
"x": 200,
"y": 385
"x": 129.5,
"y": 280.20001220703125
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
......@@ -76,7 +76,7 @@
{
"label": null,
"output_name": "output",
"uuid": "8d7cef33-5fdc-481b-a0fd-542c42c6d032"
"uuid": "45971e82-4e85-4993-a9cb-9a4608e9def7"
}
]
},
......@@ -96,10 +96,6 @@
"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"
......@@ -118,14 +114,14 @@
}
],
"position": {
"bottom": 361.3999938964844,
"height": 164.39999389648438,
"left": 528,
"right": 728,
"top": 197,
"bottom": 255.8000030517578,
"height": 163.60000610351562,
"left": 457.5,
"right": 657.5,
"top": 92.19999694824219,
"width": 200,
"x": 528,
"y": 197
"x": 457.5,
"y": 92.19999694824219
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_blast/load_blast/2.3.4+galaxy0",
......@@ -135,7 +131,7 @@
"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_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"blastdb_id\": \"21\", \"input\": {\"__class__\": \"ConnectedValue\"}, \"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": "595f6e1f-955a-42be-b03b-1269d1f7d189",
......@@ -143,33 +139,33 @@
{
"label": null,
"output_name": "results",
"uuid": "c0ad63b8-045e-4a7c-97ba-8bc45862550b"
"uuid": "cb238779-29f4-4f22-b6f3-6a8cc84857d1"
}
]
},
"3": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_blast/load_blast/2.3.4+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
"errors": null,
"id": 3,
"input_connections": {
"input": {
"id": 1,
"output_name": "output"
"wait_for": {
"id": 2,
"output_name": "results"
}
},
"inputs": [
{
"description": "runtime parameter for tool Chado load Blast results",
"name": "input"
"description": "runtime parameter for tool Synchronize an analysis",
"name": "analysis_id"
},
{
"description": "runtime parameter for tool Chado load Blast results",
"description": "runtime parameter for tool Synchronize an analysis",
"name": "wait_for"
}
],
"label": "load blast results org2",
"name": "Chado load Blast results",
"label": "sync blast analysis org1",
"name": "Synchronize an analysis",
"outputs": [
{
"name": "results",
......@@ -177,54 +173,70 @@
}
],
"position": {
"bottom": 545.3999938964844,
"height": 164.39999389648438,
"left": 591,
"right": 791,
"top": 381,
"bottom": 254.8000030517578,
"height": 153.60000610351562,
"left": 787.5,
"right": 987.5,
"top": 101.19999694824219,
"width": 200,
"x": 591,
"y": 381
"x": 787.5,
"y": 101.19999694824219
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_blast/load_blast/2.3.4+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
"tool_shed_repository": {
"changeset_revision": "08ae8b27b193",
"name": "chado_load_blast",
"changeset_revision": "f487ff676088",
"name": "tripal_analysis_sync",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"analysis_id\": \"1\", \"blastdb_id\": \"1\", \"input\": {\"__class__\": \"RuntimeValue\"}, \"match_on_name\": \"false\", \"organism_id\": \"2\", \"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",
"tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.0",
"type": "tool",
"uuid": "5d08ed84-681b-431c-92c9-3b2fd5f32176",
"uuid": "c98dedf6-8857-4d23-be94-fe6630f245d7",
"workflow_outputs": [
{
"label": null,
"label": "Synchronize Analysis into Tripal",
"output_name": "results",
"uuid": "6ed0a7c4-5b78-4016-8c21-0aaa992acd11"
"uuid": "1ff4b1db-b6bf-4c48-a0ab-0a8513683999"
}
]
},
"4": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
"content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_blast/load_blast/2.3.4+galaxy0",
"errors": null,
"id": 4,
"input_connections": {
"input": {
"id": 1,
"output_name": "output"
},
"wait_for": {
"id": 2,
"id": 3,
"output_name": "results"
}
},
"inputs": [
{
"description": "runtime parameter for tool Synchronize an analysis",
"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": "sync blast analysis org1",
"name": "Synchronize an analysis",
"label": "load blast results org2",
"name": "Chado load Blast results",
"outputs": [
{
"name": "results",
......@@ -232,32 +244,32 @@
}
],
"position": {
"bottom": 360.3999938964844,
"height": 154.39999389648438,
"left": 858,
"right": 1058,
"top": 206,
"bottom": 439.8000183105469,
"height": 163.60000610351562,
"left": 520.5,
"right": 720.5,
"top": 276.20001220703125,
"width": 200,
"x": 858,
"y": 206
"x": 520.5,
"y": 276.20001220703125
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_load_blast/load_blast/2.3.4+galaxy0",
"tool_shed_repository": {
"changeset_revision": "f487ff676088",
"name": "tripal_analysis_sync",
"changeset_revision": "08ae8b27b193",
"name": "chado_load_blast",
"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",
"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": "99e7496d-ac32-467d-8c09-2efd48d0231a",
"uuid": "a7ec5c91-7cef-4b9f-95a0-ed5542b8e142",
"workflow_outputs": [
{
"label": "Synchronize Analysis into Tripal",
"label": null,
"output_name": "results",
"uuid": "9792ea7a-0b4d-4355-9ce6-db2ba1ed36e9"
"uuid": "119f219e-3d80-4b42-bb38-d07d4583048c"
}
]
},
......@@ -268,11 +280,20 @@
"id": 5,
"input_connections": {
"wait_for": {
"id": 3,
"id": 4,
"output_name": "results"
}
},
"inputs": [],
"inputs": [
{
"description": "runtime parameter for tool Synchronize an analysis",
"name": "analysis_id"
},
{
"description": "runtime parameter for tool Synchronize an analysis",
"name": "wait_for"
}
],
"label": "sync blast analysis org2",
"name": "Synchronize an analysis",
"outputs": [
......@@ -282,14 +303,14 @@
}
],
"position": {
"bottom": 545.3999938964844,
"height": 154.39999389648438,
"left": 899,
"right": 1099,
"top": 391,
"bottom": 440.8000183105469,
"height": 153.60000610351562,
"left": 828.5,
"right": 1028.5,
"top": 287.20001220703125,
"width": 200,
"x": 899,
"y": 391
"x": 828.5,
"y": 287.20001220703125
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_analysis_sync/analysis_sync/3.2.1.0",
......@@ -299,15 +320,15 @@
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"analysis_id\": \"1\", \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "3.2.1.0",
"type": "tool",
"uuid": "99f68436-37c7-409a-bcf0-70bde40a9a8e",
"uuid": "2fff7637-7904-46ff-87e1-ce2721727e75",
"workflow_outputs": [
{
"label": "Synchronize Analysis into Tripal",
"output_name": "results",
"uuid": "ce2c98b7-17f2-4646-a3bf-784af0103f4e"
"uuid": "924991f3-6dd4-4752-9ce2-3832d72dff57"
}
]
},
......@@ -332,14 +353,14 @@
}
],
"position": {
"bottom": 474.3999938964844,
"height": 154.39999389648438,
"left": 1174,
"right": 1374,
"top": 320,
"bottom": 368.8000030517578,
"height": 153.60000610351562,
"left": 1103.5,
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"top": 215.1999969482422,
"width": 200,
"x": 1174,
"y": 320
"x": 1103.5,
"y": 215.1999969482422
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_db_populate_mviews/db_populate_mviews/3.2.1.0",
......@@ -357,7 +378,7 @@
{
"label": "Populate Tripal materialized view(s)",
"output_name": "results",
"uuid": "31970b1e-e567-4994-b05e-31d3406ebdf3"
"uuid": "dc519305-8c27-4c53-9150-7dd37b5090cd"
}
]
},
......@@ -382,14 +403,14 @@
}
],
"position": {
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"height": 113.60000610351562,
"left": 1444,
"right": 1644,
"top": 341,
"bottom": 349,
"height": 112.80000305175781,
"left": 1373.5,
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"width": 200,
"x": 1444,
"y": 341
"x": 1373.5,
"y": 236.1999969482422
},
"post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_db_index/db_index/3.2.1.1",
......@@ -407,12 +428,12 @@
{
"label": "Index Tripal data",
"output_name": "results",
"uuid": "c4398cf0-10ca-45c7-ab62-9854b7519ecb"
"uuid": "e2911922-2412-4618-97fe-bcc783bb0865"
}
]
}
},
"tags": [],
"uuid": "1219fcfa-e57c-437e-ac5e-4d803e3dafd9",
"version": 5
"uuid": "ffae97b5-698a-41a5-8561-470300594544",
"version": 6
}
\ No newline at end of file
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