From d68ab85c5fc0669a2d13224ec9f6f94a039a8ca1 Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Mon, 31 May 2021 11:12:32 +0200
Subject: [PATCH] Minor fix
---
gga_run_workflow_phaeo_jbrowse.py | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/gga_run_workflow_phaeo_jbrowse.py b/gga_run_workflow_phaeo_jbrowse.py
index 893c418..e0f42fb 100644
--- a/gga_run_workflow_phaeo_jbrowse.py
+++ b/gga_run_workflow_phaeo_jbrowse.py
@@ -450,12 +450,13 @@ if __name__ == "__main__":
root_url = "https://{0}".format(config[constants.CONF_ALL_HOSTNAME])
else:
root_url = config[constants.CONF_JBROWSE_MENU_URL]
+ # Set "Genus" and "species" as they are given in the add_organism tool (with spaces replaced by "_")
species_strain_sex = org_wf_param.chado_species_name.replace(" ", "-")
- jbrowse_menu_url = "{root_url}/sp/{genus_sp}/feature/{Genus}/{species_strain_sex}/mRNA/{id}".format(
+ jbrowse_menu_url = "{root_url}/sp/{genus_sp}/feature/{Genus}/{species}/mRNA/{id}".format(
root_url=root_url,
genus_sp=genus_species,
Genus=org_wf_param.genus_uppercase,
- species_strain_sex=species_strain_sex,
+ species=species_strain_sex,
id="{id}")
# Replace values in the workflow dictionary
workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_1_ORG_STEP_JBROWSE]["tool_state"] = \
@@ -568,19 +569,20 @@ if __name__ == "__main__":
root_url = "https://{0}".format(config[constants.CONF_ALL_HOSTNAME])
else:
root_url = config[constants.CONF_JBROWSE_MENU_URL]
+ # Set "Genus" and "species" as they are given in the add_organism tool (with spaces replaced by "_")
species_strain_sex_org1 = sp_wf_param_org1.chado_species_name.replace(" ", "-")
species_strain_sex_org2 = sp_wf_param_org2.chado_species_name.replace(" ", "-")
- jbrowse_menu_url_org1 = "{root_url}/sp/{genus_sp}/feature/{Genus}/{species_strain_sex}/mRNA/{id}".format(
+ jbrowse_menu_url_org1 = "{root_url}/sp/{genus_sp}/feature/{Genus}/{species}/mRNA/{id}".format(
root_url=root_url,
genus_sp=genus_species,
Genus=sp_wf_param_org1.genus_uppercase,
- species_strain_sex=species_strain_sex_org1,
+ species=species_strain_sex_org1,
id="{id}")
- jbrowse_menu_url_org2 = "{root_url}/sp/{genus_sp}/feature/{Genus}/{species_strain_sex}/mRNA/{id}".format(
+ jbrowse_menu_url_org2 = "{root_url}/sp/{genus_sp}/feature/{Genus}/{species}/mRNA/{id}".format(
root_url=root_url,
genus_sp=genus_species,
Genus=sp_wf_param_org2.genus_uppercase,
- species_strain_sex=species_strain_sex_org2,
+ species=species_strain_sex_org2,
id="{id}")
# Replace values in the workflow dictionary
workflow_dict["steps"][constants_phaeo.WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1]["tool_state"] = \
--
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