From 58b951d24fd75b7c753d49cc948c17bab7b7a509 Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Mon, 18 Jan 2021 15:22:34 +0100
Subject: [PATCH] Restored a previous workflow version
(Galaxy-Workflow-preset_workflow.ga)
---
deprecated/xlsx_example_input.xlsx | Bin 5651 -> 5650 bytes
gga_load_data.py | 3 ++-
speciesData.py | 2 +-
templates/compose_template.yml | 2 +-
4 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/deprecated/xlsx_example_input.xlsx b/deprecated/xlsx_example_input.xlsx
index 8530103dd049d58ff2f90dd1fe7799e427ba8218..4d75e1ae55b74c096ce229daf452e911b426a165 100644
GIT binary patch
delta 126
zcmbQNGf8KID>Eb4W;f<rj9grcW>h6aZZwGDnykfY&&V}7i!~KUUSQn~RMEqBhY?6+
za-0HElTEmafSl!A?I4amPay}_x8rAiBs}BVyn?5Wak4t!N1(JM|4t@OF24B1)$<Kb
VaBaRV_?ro+`nrfGkW>`?1OU=iDGdMs
delta 128
zcmbQFGg)VYD>EbSW;f<rj9k2nW>h6aZZwGDovg)b&&WGDi!~KUUSQn~RMEqBhY?6+
za-0HElTEmafSl!A?I4amPay~Ix8rAiBs}BYyn?3=B&Npq5vV|de<u?sFJJuP>iGsI
VcsJh?{LKWEyC&iZBo#zI0RS0LDM<hT
diff --git a/gga_load_data.py b/gga_load_data.py
index f3eb17e..c499ca1 100644
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -91,7 +91,7 @@ class LoadData(speciesData.SpeciesData):
subprocess.run(["mv", annotation_dir + "/outfile_proteins.fa", proteins_file],
stdout=subprocess.PIPE,
cwd=annotation_dir)
- subprocess.run(["rm", annotation_dir + "/outfile_proteins.fa"], stdout=subprocess.PIPE, cwd=annotation_dir)
+ # subprocess.run(["rm", annotation_dir + "/outfile_proteins.fa"], stdout=subprocess.PIPE, cwd=annotation_dir)
else:
logging.warning("Skipping proteins fasta headers formatting (FileNotFound)")
@@ -663,6 +663,7 @@ if __name__ == "__main__":
# Set the instance url attribute
for env_variable, value in load_data_for_current_species.config.items():
if env_variable == "custom_host":
+ # TODO:
load_data_for_current_species.instance_url = "http://{0}:8888/sp/{1}_{2}/galaxy/".format(
value, load_data_for_current_species.genus_lowercase, load_data_for_current_species.species)
break
diff --git a/speciesData.py b/speciesData.py
index 530fc67..1e9305b 100644
--- a/speciesData.py
+++ b/speciesData.py
@@ -40,7 +40,7 @@ class SpeciesData:
self.full_name_lowercase = self.full_name.lower()
self.abbreviation = "_".join(utilities.filter_empty_not_empty_items([self.genus_lowercase[0], self.species, self.strain, self.sex])["not_empty"])
self.genus_species = self.genus_lowercase + "_" + self.species
- self.instance_url = "http://scratchgmodv1:8888/sp/" + self.genus_lowercase + "_" + self.species + "/galaxy/" # Testing with scratchgmodv1 (replace by what?)
+ self.instance_url = "http://scratchgmodv1:8888/sp/" + self.genus_lowercase + "_" + self.species + "/galaxy/" # Testing with scratchgmodv1, is overwritten in the script by the provided hostname anyway
self.instance = None
self.history_id = None
self.library = None
diff --git a/templates/compose_template.yml b/templates/compose_template.yml
index f56eac8..1fe698f 100644
--- a/templates/compose_template.yml
+++ b/templates/compose_template.yml
@@ -48,7 +48,7 @@ services:
TRIPAL_ENABLE_MODULES: "tripal_analysis_blast tripal_analysis_interpro tripal_analysis_go tripal_rest_api tripal_elasticsearch"
SITE_NAME: "Genus species"
ELASTICSEARCH_HOST: elasticsearch.genus_species
- ENABLE_JBROWSE: /jbrowse/?data=data/genus_species_strain_sex
+ ENABLE_JBROWSE: /jbrowse/?data=data/genus_species_sex
ENABLE_APOLLO: 0
ENABLE_BLAST: 1
ENABLE_DOWNLOAD: 1
--
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