From 476f437d4e8640c55fff1d507fae16245dfa3a7c Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Sun, 30 May 2021 22:44:15 +0200
Subject: [PATCH] fix config
---
gga_run_workflow_phaeo_jbrowse.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/gga_run_workflow_phaeo_jbrowse.py b/gga_run_workflow_phaeo_jbrowse.py
index b7a9a24..f73976f 100644
--- a/gga_run_workflow_phaeo_jbrowse.py
+++ b/gga_run_workflow_phaeo_jbrowse.py
@@ -171,7 +171,7 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
return org_id
- def import_datasets_into_history(self):
+ def import_datasets_into_history(self, config):
"""
Find datasets in a library, get their ID and import them into the current history if they are not already
"""
@@ -187,8 +187,8 @@ class RunWorkflowJbrowse(runWorkflowPhaeo.RunWorkflow):
proteins_hda_id = None
gio = GalaxyInstance(url=self.instance_url,
- email=self.config[constants.CONF_GALAXY_DEFAULT_ADMIN_EMAIL],
- password=self.config[constants.CONF_GALAXY_DEFAULT_ADMIN_PASSWORD]
+ email=config[constants.CONF_GALAXY_DEFAULT_ADMIN_EMAIL],
+ password=config[constants.CONF_GALAXY_DEFAULT_ADMIN_PASSWORD]
)
prj_lib = gio.libraries.get_previews(constants.GALAXY_LIBRARY_NAME)
if len(prj_lib) == 1:
@@ -284,7 +284,7 @@ def prepare_history_and_get_wf_param(sp_dict_list, main_dir, config):
run_workflow_for_current_organism.set_galaxy_instance(config)
run_workflow_for_current_organism.set_history()
run_workflow_for_current_organism.install_individual_tools()
- run_workflow_for_current_organism.import_datasets_into_history()
+ run_workflow_for_current_organism.import_datasets_into_history(config)
analyses_dict_list = run_workflow_for_current_organism.get_analyses()
--
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