From 1d0a9b5cd644aad3962b4d5e6a1a05053664eced Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Thu, 21 Jan 2021 17:28:55 +0100
Subject: [PATCH] Fixed toolshed version issue (now using 2.3.3 GMOD tools),
added new Jbrowse workflow
---
gga_init.py | 6 +-
gga_load_data.py | 2 +-
run_workflow_phaeoexplorer.py | 183 ++++----
workflows/Chado_load_Tripal_synchronize.ga | 174 +++++---
.../Chado_load_Tripal_synchronize.ga.bak | 413 ++++++++++++++++++
workflows/Demo.ga | 91 ----
workflows/Jbrowse.ga | 163 ++++++-
7 files changed, 782 insertions(+), 250 deletions(-)
create mode 100644 workflows/Chado_load_Tripal_synchronize.ga.bak
delete mode 100644 workflows/Demo.ga
diff --git a/gga_init.py b/gga_init.py
index b77251c..5a7b47d 100644
--- a/gga_init.py
+++ b/gga_init.py
@@ -11,6 +11,7 @@ import yaml
import shutil
from pathlib import Path
+from jinja2 import Template
import utilities
import speciesData
@@ -19,7 +20,7 @@ import speciesData
"""
gga_init.py
-Usage: $ python3 gga_init.py -i example.yml [OPTIONS]
+Usage: $ python3 gga_init.py -i input_example.yml [OPTIONS]
"""
@@ -56,11 +57,12 @@ class DeploySpeciesStack(speciesData.SpeciesData):
# Copy the custom banner to the species dir (banner used in tripal pages)
if not self.config["custom_banner"] or not self.config["custom_banner"] == "/path/to/banner" or not self.config["custom_banner"] == "":
try:
+ logging.debug("Custom banner path: %s" % self.config["custom_banner"])
if os.path.isfile(os.path.abspath(self.config["custom_banner"])):
shutil.copy(os.path.abspath(self.config["custom_banner"]), "%s/banner.png" % self.species_dir)
except FileNotFoundError:
- logging.warning("Custom banner (%s), skipping" % self.config["custom_banner"])
+ logging.warning("Specified banner not found (%s), skipping" % self.config["custom_banner"])
# Copy nginx conf
try:
diff --git a/gga_load_data.py b/gga_load_data.py
index 945d85d..25b8a65 100644
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -23,7 +23,7 @@ from bioblend import galaxy
"""
gga_load_data.py
-Usage: $ python3 gga_init.py -i example.yml [OPTIONS]
+Usage: $ python3 gga_init.py -i input_example.yml [OPTIONS]
Do not call this script before the galaxy container is ready
"""
diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py
index 984c00f..c28a769 100644
--- a/run_workflow_phaeoexplorer.py
+++ b/run_workflow_phaeoexplorer.py
@@ -18,7 +18,7 @@ from bioblend import galaxy
"""
gga_init.py
-Usage: $ python3 gga_init.py -i example.yml [OPTIONS]
+Usage: $ python3 gga_init.py -i input_example.yml [OPTIONS]
"""
@@ -446,86 +446,101 @@ if __name__ == "__main__":
else:
workflow = os.path.abspath(args.workflow)
- # Starting
- logging.info("run_workflow.py called for %s" % run_workflow_for_current_organism.full_name)
-
- # Setting some of the instance attributes
- run_workflow_for_current_organism.main_dir = args.main_directory
- run_workflow_for_current_organism.species_dir = os.path.join(run_workflow_for_current_organism.main_dir,
- run_workflow_for_current_organism.genus_species +
- "/")
-
- # Parse the config yaml file
- run_workflow_for_current_organism.config = utilities.parse_config(args.config)
- # Set the instance url attribute
- for env_variable, value in run_workflow_for_current_organism.config.items():
- if env_variable == "custom_host":
- run_workflow_for_current_organism.instance_url = "http://{0}:8888/sp/{1}_{2}/galaxy/".format(
- value, run_workflow_for_current_organism.genus_lowercase, run_workflow_for_current_organism.species)
- break
- else:
- run_workflow_for_current_organism.instance_url = "http://localhost:8888/sp/{0}_{1}/galaxy/".format(
- run_workflow_for_current_organism.genus_lowercase,
- run_workflow_for_current_organism.species)
-
- run_workflow_for_current_organism.connect_to_instance()
- run_workflow_for_current_organism.set_get_history()
- # run_workflow_for_current_organism.get_species_history_id()
-
- # Prepare the instance+history for the current organism (add organism and analyses in Chado) TODO: add argument "setup"
- # (althought it should pose no problem as the "Chado add" refuses to duplicate an analysis/organism anyway)
- run_workflow_for_current_organism.prepare_history()
-
- # Get the attributes of the instance and project data files
- run_workflow_for_current_organism.get_instance_attributes()
- run_workflow_for_current_organism.get_organism_and_analyses_ids()
-
- # Import datasets into history TODO: put this only for the chado load tripal sync workflow?
- run_workflow_for_current_organism.import_datasets_into_history()
-
- # Explicit workflow parameter names
- # TODO: Create distinct methods to call different pre-set workflows using CL arguments/config options (i.e load-chado, jbrowse, functional-annotation, orthology, ...)
-
- workflow_parameters = dict()
-
- GENOME_FASTA_FILE = "0"
- GFF_FILE = "1"
- PROTEINS_FASTA_FILE = "2"
- TRANSCRIPTS_FASTA_FILE = "3"
-
-
- LOAD_FASTA_IN_CHADO = "4"
- LOAD_GFF_IN_CHADO = "5"
- SYNC_ORGANISM_INTO_TRIPAL = "6"
- SYNC_GENOME_ANALYSIS_INTO_TRIPAL = "7"
- SYNC_OGS_ANALYSIS_INTO_TRIPAL = "8"
- SYNC_FEATURES_INTO_TRIPAL = "9"
-
- workflow_parameters[GENOME_FASTA_FILE] = {}
- workflow_parameters[GFF_FILE] = {}
- workflow_parameters[PROTEINS_FASTA_FILE] = {}
- workflow_parameters[TRANSCRIPTS_FASTA_FILE] = {}
- workflow_parameters[LOAD_FASTA_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
- "analysis_id": run_workflow_for_current_organism.genome_analysis_id,
- "do_update": "true"}
- # Change "do_update": "true" to "do_update": "false" in above parameters to prevent appending to the fasta file in chado
- # WARNING: It is safer to never update it and just change the genome/ogs versions in the config
- workflow_parameters[LOAD_GFF_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
- "analysis_id": run_workflow_for_current_organism.ogs_analysis_id}
- workflow_parameters[SYNC_ORGANISM_INTO_TRIPAL] = {"organism_id": run_workflow_for_current_organism.org_id}
- workflow_parameters[SYNC_GENOME_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.ogs_analysis_id}
- workflow_parameters[SYNC_OGS_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.genome_analysis_id}
- workflow_parameters[SYNC_FEATURES_INTO_TRIPAL] = {"organism_id": run_workflow_for_current_organism.org_id}
-
- # Datamap for input datasets - dataset source (type): ldda (LibraryDatasetDatasetAssociation)
- run_workflow_for_current_organism.datamap = dict()
- run_workflow_for_current_organism.datamap[GENOME_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["genome_file"]}
- run_workflow_for_current_organism.datamap[GFF_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["gff_file"]}
- run_workflow_for_current_organism.datamap[PROTEINS_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["proteins_file"]}
- run_workflow_for_current_organism.datamap[TRANSCRIPTS_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["transcripts_file"]}
-
- # Run the Chado load Tripal sync workflow with the parameters set above
- run_workflow_for_current_organism.run_workflow(workflow_path=workflow,
- workflow_parameters=workflow_parameters,
- datamap=run_workflow_for_current_organism.datamap,
- workflow_name="Chado load Tripal synchronize")
+ # Verifying the galaxy container is running
+ if utilities.check_galaxy_state(genus_lowercase=run_workflow_for_current_organism.genus_lowercase,
+ species=run_workflow_for_current_organism.species,
+ script_dir=run_workflow_for_current_organism.script_dir):
+
+ # Starting
+ logging.info("run_workflow.py called for %s" % run_workflow_for_current_organism.full_name)
+
+ # Setting some of the instance attributes
+ run_workflow_for_current_organism.main_dir = args.main_directory
+ run_workflow_for_current_organism.species_dir = os.path.join(run_workflow_for_current_organism.main_dir,
+ run_workflow_for_current_organism.genus_species +
+ "/")
+
+ # Parse the config yaml file
+ run_workflow_for_current_organism.config = utilities.parse_config(args.config)
+ # Set the instance url attribute
+ for env_variable, value in run_workflow_for_current_organism.config.items():
+ if env_variable == "custom_host":
+ run_workflow_for_current_organism.instance_url = "http://{0}:8888/sp/{1}_{2}/galaxy/".format(
+ value, run_workflow_for_current_organism.genus_lowercase, run_workflow_for_current_organism.species)
+ break
+ else:
+ run_workflow_for_current_organism.instance_url = "http://localhost:8888/sp/{0}_{1}/galaxy/".format(
+ run_workflow_for_current_organism.genus_lowercase,
+ run_workflow_for_current_organism.species)
+
+ run_workflow_for_current_organism.connect_to_instance()
+ run_workflow_for_current_organism.set_get_history()
+ # run_workflow_for_current_organism.get_species_history_id()
+
+ # Prepare the instance+history for the current organism (add organism and analyses in Chado) TODO: add argument "setup"
+ # (althought it should pose no problem as the "Chado add" refuses to duplicate an analysis/organism anyway)
+ run_workflow_for_current_organism.prepare_history()
+
+ # Get the attributes of the instance and project data files
+ run_workflow_for_current_organism.get_instance_attributes()
+ run_workflow_for_current_organism.get_organism_and_analyses_ids()
+
+ # Import datasets into history
+ # TODO: put this only for the chado load tripal sync workflow?
+ # TODO: it seems it is not required anymore since using "ldda" option for datasets in the workflow datamap doesn't need the files
+ run_workflow_for_current_organism.import_datasets_into_history()
+
+ # Explicit workflow parameter names
+ # TODO: Create distinct methods to call different pre-set workflows using CL arguments/config options (i.e load-chado, jbrowse, functional-annotation, orthology, ...)
+
+ # Chado load and Tripal synchronize workflow
+ workflow_parameters = {}
+
+ GENOME_FASTA_FILE = "0"
+ GFF_FILE = "1"
+ PROTEINS_FASTA_FILE = "2"
+ TRANSCRIPTS_FASTA_FILE = "3"
+
+
+ LOAD_FASTA_IN_CHADO = "4"
+ LOAD_GFF_IN_CHADO = "5"
+ SYNC_ORGANISM_INTO_TRIPAL = "6"
+ SYNC_GENOME_ANALYSIS_INTO_TRIPAL = "7"
+ SYNC_OGS_ANALYSIS_INTO_TRIPAL = "8"
+ SYNC_FEATURES_INTO_TRIPAL = "9"
+
+ workflow_parameters[GENOME_FASTA_FILE] = {}
+ workflow_parameters[GFF_FILE] = {}
+ workflow_parameters[PROTEINS_FASTA_FILE] = {}
+ workflow_parameters[TRANSCRIPTS_FASTA_FILE] = {}
+ workflow_parameters[LOAD_FASTA_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
+ "analysis_id": run_workflow_for_current_organism.genome_analysis_id,
+ "do_update": "true"}
+ # Change "do_update": "true" to "do_update": "false" in above parameters to prevent appending/updates to the fasta file in chado
+ # WARNING: It is safer to never update it and just change the genome/ogs versions in the config
+ workflow_parameters[LOAD_GFF_IN_CHADO] = {"organism": run_workflow_for_current_organism.org_id,
+ "analysis_id": run_workflow_for_current_organism.ogs_analysis_id}
+ workflow_parameters[SYNC_ORGANISM_INTO_TRIPAL] = {"organism_id": run_workflow_for_current_organism.org_id}
+ workflow_parameters[SYNC_GENOME_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.ogs_analysis_id}
+ workflow_parameters[SYNC_OGS_ANALYSIS_INTO_TRIPAL] = {"analysis_id": run_workflow_for_current_organism.genome_analysis_id}
+ workflow_parameters[SYNC_FEATURES_INTO_TRIPAL] = {"organism_id": run_workflow_for_current_organism.org_id}
+
+ # Datamap for input datasets - dataset source (type): ldda (LibraryDatasetDatasetAssociation)
+ run_workflow_for_current_organism.datamap = {}
+ run_workflow_for_current_organism.datamap[GENOME_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["genome_file"]}
+ run_workflow_for_current_organism.datamap[GFF_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["gff_file"]}
+ run_workflow_for_current_organism.datamap[PROTEINS_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["proteins_file"]}
+ run_workflow_for_current_organism.datamap[TRANSCRIPTS_FASTA_FILE] = {"src": "ldda", "id": run_workflow_for_current_organism.datasets["transcripts_file"]}
+
+ # Run the Chado load Tripal sync workflow with the parameters set above
+ run_workflow_for_current_organism.run_workflow(workflow_path=workflow,
+ workflow_parameters=workflow_parameters,
+ datamap=run_workflow_for_current_organism.datamap,
+ workflow_name="Chado load Tripal synchronize")
+
+ # Jbrowse creation workflow
+
+ workflow_parameters = {}
+
+ else:
+ logging.critical("The galaxy container for %s is not ready yet!" % run_workflow_for_current_organism.full_name)
diff --git a/workflows/Chado_load_Tripal_synchronize.ga b/workflows/Chado_load_Tripal_synchronize.ga
index a194b03..c8ce7a4 100644
--- a/workflows/Chado_load_Tripal_synchronize.ga
+++ b/workflows/Chado_load_Tripal_synchronize.ga
@@ -16,14 +16,20 @@
"outputs": [],
"position": {
"left": 200,
- "top": 200
+ "top": 227
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "89e7487e-004d-4db1-b5eb-1676b98aebde",
- "workflow_outputs": []
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "08f77326-1435-4fad-a610-e56f06a0ced5"
+ }
+ ]
},
"1": {
"annotation": "",
@@ -37,14 +43,20 @@
"outputs": [],
"position": {
"left": 200,
- "top": 290
+ "top": 317
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "1d25f54c-7575-4c8d-be55-73dd7e58613f",
- "workflow_outputs": []
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "e8f16746-c91f-4147-b460-f1052650e699"
+ }
+ ]
},
"2": {
"annotation": "",
@@ -58,14 +70,20 @@
"outputs": [],
"position": {
"left": 200,
- "top": 380
+ "top": 407
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "6c1a20fa-828a-404c-b107-76fb8ddf3954",
- "workflow_outputs": []
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "98ade546-95a4-477c-bd19-38d278849b98"
+ }
+ ]
},
"3": {
"annotation": "",
@@ -79,38 +97,44 @@
"outputs": [],
"position": {
"left": 200,
- "top": 470
+ "top": 497
},
"tool_id": null,
"tool_state": "{\"optional\": false}",
"tool_version": null,
"type": "data_input",
"uuid": "74f22d9b-e764-45e4-b0eb-579c9b647ea0",
- "workflow_outputs": []
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "output",
+ "uuid": "41417aad-64e5-4480-9c36-842d0dda1c6d"
+ }
+ ]
},
"4": {
"annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.3",
"errors": null,
"id": 4,
"input_connections": {
"fasta": {
- "id": 3,
+ "id": 0,
"output_name": "output"
},
"wait_for": {
- "id": 3,
+ "id": 0,
"output_name": "output"
}
},
"inputs": [
{
"description": "runtime parameter for tool Chado load fasta",
- "name": "fasta"
+ "name": "analysis_id"
},
{
"description": "runtime parameter for tool Chado load fasta",
- "name": "wait_for"
+ "name": "organism"
}
],
"label": null,
@@ -123,31 +147,31 @@
],
"position": {
"left": 486,
- "top": 200
+ "top": 227
},
"post_job_actions": {},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.3",
"tool_shed_repository": {
- "changeset_revision": "ba4d07fbaf47",
+ "changeset_revision": "a7ab30ded37d",
"name": "chado_feature_load_fasta",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"analysis_id\": \"1\", \"do_update\": \"false\", \"ext_db\": {\"db\": \"\", \"re_db_accession\": \"\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"match_on_name\": \"false\", \"organism\": \"2\", \"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": "2.3.4+galaxy0",
+ "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__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "2.3.3",
"type": "tool",
- "uuid": "ed72bf37-aa81-4b25-8ab4-dccb54bc68d9",
+ "uuid": "f7a44182-3620-4a19-9e67-94fe584d4206",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
- "uuid": "c617e0d3-a44c-4fb1-b831-22a487a6be6a"
+ "uuid": "24ed7255-b4a6-4000-b82b-c18d81822262"
}
]
},
"5": {
"annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.4+galaxy0",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.3",
"errors": null,
"id": 5,
"input_connections": {
@@ -165,6 +189,10 @@
}
},
"inputs": [
+ {
+ "description": "runtime parameter for tool Chado load gff",
+ "name": "analysis_id"
+ },
{
"description": "runtime parameter for tool Chado load gff",
"name": "fasta"
@@ -173,6 +201,10 @@
"description": "runtime parameter for tool Chado load gff",
"name": "gff"
},
+ {
+ "description": "runtime parameter for tool Chado load gff",
+ "name": "organism"
+ },
{
"description": "runtime parameter for tool Chado load gff",
"name": "wait_for"
@@ -188,25 +220,25 @@
],
"position": {
"left": 772,
- "top": 200
+ "top": 227
},
"post_job_actions": {},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.4+galaxy0",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.3",
"tool_shed_repository": {
- "changeset_revision": "e9a6d7568817",
+ "changeset_revision": "6fdfbf0caa8c",
"name": "chado_feature_load_gff",
"owner": "gga",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
- "tool_state": "{\"add_only\": \"false\", \"analysis_id\": \"1\", \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"gff\": {\"__class__\": \"RuntimeValue\"}, \"landmark_type\": \"\", \"no_seq_compute\": \"false\", \"organism\": \"2\", \"prot_naming\": {\"method\": \"auto\", \"__current_case__\": 0}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "2.3.4+galaxy0",
+ "tool_state": "{\"add_only\": \"false\", \"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"gff\": {\"__class__\": \"RuntimeValue\"}, \"landmark_type\": \"contig\", \"no_seq_compute\": \"false\", \"organism\": {\"__class__\": \"RuntimeValue\"}, \"prot_naming\": {\"method\": \"regex\", \"__current_case__\": 1, \"re_protein_capture\": \"^mRNA(\\\\..+)$\", \"re_protein\": \"protein\\\\1\"}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "2.3.3",
"type": "tool",
- "uuid": "0b5746d7-952d-4aff-b688-4666c13cab8a",
+ "uuid": "b100a055-0dab-4f2f-8c46-573713ed3fff",
"workflow_outputs": [
{
"label": null,
"output_name": "results",
- "uuid": "5da80c86-c510-425a-b8e1-475ab26436f3"
+ "uuid": "d0ce6d85-fb8b-4509-9784-a8ded1aeae05"
}
]
},
@@ -237,15 +269,9 @@
],
"position": {
"left": 1058,
- "top": 200
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- "post_job_actions": {
- "HideDatasetActionresults": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "results"
- }
+ "top": 227
},
+ "post_job_actions": {},
"tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_organism_sync/organism_sync/3.2.1.0",
"tool_shed_repository": {
"changeset_revision": "afd5d92745fb",
@@ -256,8 +282,14 @@
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"tool_version": "3.2.1.0",
"type": "tool",
- "uuid": "05314408-41fa-4a2f-8aae-3988e2d899f6",
- "workflow_outputs": []
+ "uuid": "040183a5-1aba-4bf6-9669-c6e93cfff3ea",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "results",
+ "uuid": "f1f2dc7a-37e2-4bd3-b997-8f1e3eed11aa"
+ }
+ ]
},
"7": {
"annotation": "",
@@ -286,15 +318,9 @@
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- "top": 200
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- "post_job_actions": {
- "HideDatasetActionresults": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "results"
- }
+ "top": 227
},
+ "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",
@@ -305,8 +331,14 @@
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"tool_version": "3.2.1.0",
"type": "tool",
- "uuid": "44c7cc7c-0848-47a7-872c-351f057803c1",
- "workflow_outputs": []
+ "uuid": "6096e174-c85d-4e50-916f-a396d58a909b",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "results",
+ "uuid": "a309f4e4-3402-4eb5-8b70-1acfa1f26bb4"
+ }
+ ]
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"8": {
"annotation": "",
@@ -335,15 +367,9 @@
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"position": {
"left": 1630,
- "top": 200
- },
- "post_job_actions": {
- "HideDatasetActionresults": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "results"
- }
+ "top": 227
},
+ "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",
@@ -354,8 +380,14 @@
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"tool_version": "3.2.1.0",
"type": "tool",
- "uuid": "8ce8c990-39ce-4725-892b-4216a75f487d",
- "workflow_outputs": []
+ "uuid": "d6072bb6-036d-4fbf-893c-d25f139a05ac",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "results",
+ "uuid": "ff817e04-d0ce-461f-a97a-843e36a25aca"
+ }
+ ]
},
"9": {
"annotation": "",
@@ -384,15 +416,9 @@
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- "post_job_actions": {
- "HideDatasetActionresults": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "results"
- }
+ "top": 227
},
+ "post_job_actions": {},
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"tool_shed_repository": {
"changeset_revision": "64e36c3f0dd6",
@@ -400,14 +426,20 @@
"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\": \"popylpeptide\"}], \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "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": "3.2.1.0",
"type": "tool",
- "uuid": "04600903-dd16-4db1-b562-552aeb003e6c",
- "workflow_outputs": []
+ "uuid": "9d39d394-7375-4187-86f3-6dc676c9ca30",
+ "workflow_outputs": [
+ {
+ "label": null,
+ "output_name": "results",
+ "uuid": "5047a899-60e2-4acc-a95f-4f60f83c32ae"
+ }
+ ]
}
},
"tags": [],
- "uuid": "4c66363e-ff14-4c79-8edf-9ab05cafa33d",
- "version": 2
+ "uuid": "00c4d6e1-f470-4b31-9cc1-402aa9b598e2",
+ "version": 1
}
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diff --git a/workflows/Chado_load_Tripal_synchronize.ga.bak b/workflows/Chado_load_Tripal_synchronize.ga.bak
new file mode 100644
index 0000000..a194b03
--- /dev/null
+++ b/workflows/Chado_load_Tripal_synchronize.ga.bak
@@ -0,0 +1,413 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "Chado load Tripal synchronize",
+ "steps": {
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+ "annotation": "",
+ "content_id": null,
+ "errors": null,
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+ "input_connections": {},
+ "inputs": [],
+ "label": null,
+ "name": "Input dataset",
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+ "position": {
+ "left": 200,
+ "top": 200
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "89e7487e-004d-4db1-b5eb-1676b98aebde",
+ "workflow_outputs": []
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+ "content_id": null,
+ "errors": null,
+ "id": 1,
+ "input_connections": {},
+ "inputs": [],
+ "label": null,
+ "name": "Input dataset",
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+ "position": {
+ "left": 200,
+ "top": 290
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
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+ "content_id": null,
+ "errors": null,
+ "id": 2,
+ "input_connections": {},
+ "inputs": [],
+ "label": null,
+ "name": "Input dataset",
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+ "position": {
+ "left": 200,
+ "top": 380
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "6c1a20fa-828a-404c-b107-76fb8ddf3954",
+ "workflow_outputs": []
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+ "content_id": null,
+ "errors": null,
+ "id": 3,
+ "input_connections": {},
+ "inputs": [],
+ "label": null,
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 200,
+ "top": 470
+ },
+ "tool_id": null,
+ "tool_state": "{\"optional\": false}",
+ "tool_version": null,
+ "type": "data_input",
+ "uuid": "74f22d9b-e764-45e4-b0eb-579c9b647ea0",
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+ "4": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_fasta/feature_load_fasta/2.3.4+galaxy0",
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+ "id": 4,
+ "input_connections": {
+ "fasta": {
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+ "output_name": "output"
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+ "wait_for": {
+ "id": 3,
+ "output_name": "output"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool Chado load fasta",
+ "name": "fasta"
+ },
+ {
+ "description": "runtime parameter for tool Chado load fasta",
+ "name": "wait_for"
+ }
+ ],
+ "label": null,
+ "name": "Chado load fasta",
+ "outputs": [
+ {
+ "name": "results",
+ "type": "json"
+ }
+ ],
+ "position": {
+ "left": 486,
+ "top": 200
+ },
+ "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\": \"1\", \"do_update\": \"false\", \"ext_db\": {\"db\": \"\", \"re_db_accession\": \"\"}, \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"match_on_name\": \"false\", \"organism\": \"2\", \"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}",
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+ "workflow_outputs": [
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+ "output_name": "results",
+ "uuid": "c617e0d3-a44c-4fb1-b831-22a487a6be6a"
+ }
+ ]
+ },
+ "5": {
+ "annotation": "",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/chado_feature_load_gff/feature_load_gff/2.3.4+galaxy0",
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+ "id": 5,
+ "input_connections": {
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+ "output_name": "output"
+ },
+ "gff": {
+ "id": 1,
+ "output_name": "output"
+ },
+ "wait_for": {
+ "id": 4,
+ "output_name": "results"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool Chado load gff",
+ "name": "fasta"
+ },
+ {
+ "description": "runtime parameter for tool Chado load gff",
+ "name": "gff"
+ },
+ {
+ "description": "runtime parameter for tool Chado load gff",
+ "name": "wait_for"
+ }
+ ],
+ "label": null,
+ "name": "Chado load gff",
+ "outputs": [
+ {
+ "name": "results",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 772,
+ "top": 200
+ },
+ "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\": \"1\", \"fasta\": {\"__class__\": \"RuntimeValue\"}, \"gff\": {\"__class__\": \"RuntimeValue\"}, \"landmark_type\": \"\", \"no_seq_compute\": \"false\", \"organism\": \"2\", \"prot_naming\": {\"method\": \"auto\", \"__current_case__\": 0}, \"psql_target\": {\"method\": \"remote\", \"__current_case__\": 0}, \"wait_for\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "2.3.4+galaxy0",
+ "type": "tool",
+ "uuid": "0b5746d7-952d-4aff-b688-4666c13cab8a",
+ "workflow_outputs": [
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+ "label": null,
+ "output_name": "results",
+ "uuid": "5da80c86-c510-425a-b8e1-475ab26436f3"
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+ "id": 6,
+ "input_connections": {
+ "wait_for": {
+ "id": 5,
+ "output_name": "results"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool Synchronize an organism",
+ "name": "organism_id"
+ }
+ ],
+ "label": null,
+ "name": "Synchronize an organism",
+ "outputs": [
+ {
+ "name": "results",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 1058,
+ "top": 200
+ },
+ "post_job_actions": {
+ "HideDatasetActionresults": {
+ "action_arguments": {},
+ "action_type": "HideDatasetAction",
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+ }
+ },
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_organism_sync/organism_sync/3.2.1.0",
+ "tool_shed_repository": {
+ "changeset_revision": "afd5d92745fb",
+ "name": "tripal_organism_sync",
+ "owner": "gga",
+ "tool_shed": "toolshed.g2.bx.psu.edu"
+ },
+ "tool_state": "{\"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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+ "output_name": "results"
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+ },
+ "inputs": [
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+ "description": "runtime parameter for tool Synchronize an analysis",
+ "name": "analysis_id"
+ }
+ ],
+ "label": null,
+ "name": "Synchronize an analysis",
+ "outputs": [
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+ "type": "json"
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+ "position": {
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+ "top": 200
+ },
+ "post_job_actions": {
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+ "changeset_revision": "f487ff676088",
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+ "owner": "gga",
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+ "type": "tool",
+ "uuid": "44c7cc7c-0848-47a7-872c-351f057803c1",
+ "workflow_outputs": []
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+ "8": {
+ "annotation": "",
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+ "id": 8,
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+ "inputs": [
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+ "name": "analysis_id"
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+ ],
+ "label": null,
+ "name": "Synchronize an analysis",
+ "outputs": [
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+ "position": {
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+ "top": 200
+ },
+ "post_job_actions": {
+ "HideDatasetActionresults": {
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+ "action_type": "HideDatasetAction",
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+ }
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+ "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"
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+ "tool_state": "{\"analysis_id\": {\"__class__\": \"RuntimeValue\"}, \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_version": "3.2.1.0",
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+ "9": {
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+ "content_id": "toolshed.g2.bx.psu.edu/repos/gga/tripal_feature_sync/feature_sync/3.2.1.0",
+ "errors": null,
+ "id": 9,
+ "input_connections": {
+ "wait_for": {
+ "id": 8,
+ "output_name": "results"
+ }
+ },
+ "inputs": [
+ {
+ "description": "runtime parameter for tool Synchronize features",
+ "name": "organism_id"
+ }
+ ],
+ "label": null,
+ "name": "Synchronize features",
+ "outputs": [
+ {
+ "name": "results",
+ "type": "txt"
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+ "position": {
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+ "top": 200
+ },
+ "post_job_actions": {
+ "HideDatasetActionresults": {
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+ "changeset_revision": "64e36c3f0dd6",
+ "name": "tripal_feature_sync",
+ "owner": "gga",
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+ "tool_state": "{\"organism_id\": {\"__class__\": \"RuntimeValue\"}, \"repeat_ids\": [], \"repeat_types\": [{\"__index__\": 0, \"types\": \"mRNA\"}, {\"__index__\": 1, \"types\": \"popylpeptide\"}], \"wait_for\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
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+}
\ No newline at end of file
diff --git a/workflows/Demo.ga b/workflows/Demo.ga
deleted file mode 100644
index c59f6ee..0000000
--- a/workflows/Demo.ga
+++ /dev/null
@@ -1,91 +0,0 @@
-{
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- "inputs": [
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- {
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- {
- "description": "runtime parameter for tool Chado load fasta",
- "name": "organism"
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- {
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- "name": "wait_for"
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- ],
- "label": null,
- "name": "Chado load fasta",
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index 5291ff0..5c4ac95 100644
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--
GitLab