diff --git a/gga_init.py b/gga_init.py
index be5f3c3967accd1c5df1931145fcc4af4b14aaaf..6691f306eb0b562fc5e2cb0961f0d866ac8f6b20 100755
--- a/gga_init.py
+++ b/gga_init.py
@@ -127,12 +127,13 @@ class DeploySpeciesStack(speciesData.SpeciesData):
gspecies_compose_file.write(gspecies_compose_output)
- galaxy_nginx_conf_template = env.get_template("galaxy_nginx.conf.j2")
- galaxy_nginx_conf_output = galaxy_nginx_conf_template.render(render_vars)
- with open(os.path.join(self.main_dir, "galaxy_nginx.conf"), "w") as galaxy_nginx_conf_file:
- logging.debug("Writing the galaxy_nginx.conf file for %s" % self.genus_species)
- galaxy_nginx_conf_file.truncate(0)
- galaxy_nginx_conf_file.write(galaxy_nginx_conf_output)
+ if not os.path.isfile(os.path.join(self.main_dir, "galaxy_nginx.conf")):
+ galaxy_nginx_conf_template = env.get_template("galaxy_nginx.conf.j2")
+ galaxy_nginx_conf_output = galaxy_nginx_conf_template.render(render_vars)
+ with open(os.path.join(self.main_dir, "galaxy_nginx.conf"), "w") as galaxy_nginx_conf_file:
+ logging.debug("Writing the galaxy_nginx.conf file for %s" % self.genus_species)
+ galaxy_nginx_conf_file.truncate(0)
+ galaxy_nginx_conf_file.write(galaxy_nginx_conf_output)
# Create the volumes (directory) of the species docker-compose file
create_mounts(working_dir=".", main_dir=self.main_dir)
diff --git a/gga_load_data.py b/gga_load_data.py
index e349e78cd685a66b34f20a3073afc7f50dd27859..cf506c107dc01c46e63064e4f0d8fc80317df6f3 100755
--- a/gga_load_data.py
+++ b/gga_load_data.py
@@ -81,43 +81,46 @@ class LoadData(speciesData.SpeciesData):
"""
- get_organism_tool = self.instance.tools.show_tool("toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/2.3.3")
+ get_organism_tool = self.instance.tools.show_tool("toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/2.3.4+galaxy0")
delete_organism_tool = self.instance.tools.show_tool("toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.4+galaxy0")
- if delete_organism_tool["version"] != "2.3.4+galaxy0":
- toolshed_dict = delete_organism_tool["tool_shed_repository"]
- logging.warning("Changeset for %s is not installed" % toolshed_dict["name"])
- changeset_revision = "b1aa4f9d82fe"
- name = toolshed_dict["name"]
- owner = toolshed_dict["owner"]
- toolshed = "https://" + toolshed_dict["tool_shed"]
- logging.warning("Installing changeset for %s" % toolshed_dict["name"])
-
- self.instance.toolshed.install_repository_revision(tool_shed_url=toolshed, name=name, owner=owner,
- changeset_revision=changeset_revision,
- install_tool_dependencies=True,
- install_repository_dependencies=False,
- install_resolver_dependencies=True)
-
-
- if get_organism_tool["version"] != "2.3.3":
- toolshed_dict = get_organism_tool["tool_shed_repository"]
- logging.warning("Changeset for %s is not installed" % toolshed_dict["name"])
- changeset_revision = "b07279b5f3bf"
- name = toolshed_dict["name"]
- owner = toolshed_dict["owner"]
- toolshed = "https://" + toolshed_dict["tool_shed"]
- logging.warning("Installing changeset for %s" % toolshed_dict["name"])
-
- self.instance.toolshed.install_repository_revision(tool_shed_url=toolshed, name=name, owner=owner,
- changeset_revision=changeset_revision,
- install_tool_dependencies=True,
- install_repository_dependencies=False,
- install_resolver_dependencies=True)
+ get_organism_tool_version = get_organism_tool["version"]
+ delete_organism_tool_version = delete_organism_tool["version"]
+
+ # if delete_organism_tool["version"] != "2.3.4+galaxy0":
+ # toolshed_dict = delete_organism_tool["tool_shed_repository"]
+ # logging.warning("Changeset for %s is not installed" % toolshed_dict["name"])
+ # changeset_revision = "b1aa4f9d82fe"
+ # name = toolshed_dict["name"]
+ # owner = toolshed_dict["owner"]
+ # toolshed = "https://" + toolshed_dict["tool_shed"]
+ # logging.warning("Installing changeset for %s" % toolshed_dict["name"])
+
+ # self.instance.toolshed.install_repository_revision(tool_shed_url=toolshed, name=name, owner=owner,
+ # changeset_revision=changeset_revision,
+ # install_tool_dependencies=True,
+ # install_repository_dependencies=False,
+ # install_resolver_dependencies=True)
+
+
+ # if get_organism_tool["version"] != "2.3.4+galaxy0":
+ # toolshed_dict = get_organism_tool["tool_shed_repository"]
+ # logging.warning("Changeset for %s is not installed" % toolshed_dict["name"])
+ # changeset_revision = "831229e6cda2"
+ # name = toolshed_dict["name"]
+ # owner = toolshed_dict["owner"]
+ # toolshed = "https://" + toolshed_dict["tool_shed"]
+ # logging.warning("Installing changeset for %s" % toolshed_dict["name"])
+
+ # self.instance.toolshed.install_repository_revision(tool_shed_url=toolshed, name=name, owner=owner,
+ # changeset_revision=changeset_revision,
+ # install_tool_dependencies=True,
+ # install_repository_dependencies=False,
+ # install_resolver_dependencies=True)
logging.debug("Getting 'Homo sapiens' ID in instance's chado database")
get_sapiens_id_job = self.instance.tools.run_tool(
- tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/2.3.4+galaxy0",
+ tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_get_organisms/organism_get_organisms/%s" % get_organism_tool_version,
history_id=self.history_id,
tool_inputs={"genus": "Homo", "species": "sapiens"})
get_sapiens_id_job_output = get_sapiens_id_job["outputs"][0]["id"]
@@ -128,7 +131,7 @@ class LoadData(speciesData.SpeciesData):
sapiens_id = str(
get_sapiens_id_final_output["organism_id"]) # needs to be str to be recognized by the chado tool
self.instance.tools.run_tool(
- tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/2.3.4+galaxy0",
+ tool_id="toolshed.g2.bx.psu.edu/repos/gga/chado_organism_delete_organisms/organism_delete_organisms/%s" % delete_organism_tool_version,
history_id=self.history_id,
tool_inputs={"organism": str(sapiens_id)})
except bioblend.ConnectionError:
diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py
index 36c4de91504112d083c97a7a88545fc4b79f5ebc..62389d44aa488831b906229ea84880c20749d083 100755
--- a/run_workflow_phaeoexplorer.py
+++ b/run_workflow_phaeoexplorer.py
@@ -640,25 +640,26 @@ class RunWorkflow(speciesData.SpeciesData):
if dataset_dict["history_id"] == self.history_id:
if dataset_dict["name"] == self.datasets_name["genome_file"] and dataset_dict["id"] not in imported_datasets_ids:
genome_dataset_hda_id = dataset_dict["id"]
- logging.debug("Genome dataset hda id: %s" % genome_dataset_hda_id)
elif dataset_dict["name"] == self.datasets_name["proteins_file"] and dataset_dict["id"] not in imported_datasets_ids:
proteins_datasets_hda_id = dataset_dict["id"]
- logging.debug("Proteins dataset hda ID: %s" % proteins_datasets_hda_id)
elif dataset_dict["name"] == self.datasets_name["transcripts_file"] and dataset_dict["id"] not in imported_datasets_ids:
transcripts_dataset_hda_id = dataset_dict["id"]
- logging.debug("Transcripts dataset hda ID: %s" % transcripts_dataset_hda_id)
elif dataset_dict["name"] == self.datasets_name["gff_file"] and dataset_dict["id"] not in imported_datasets_ids:
gff_dataset_hda_id = dataset_dict["id"]
- logging.debug("GFF dataset hda ID: %s" % gff_dataset_hda_id)
-
if "interproscan_file" in self.datasets_name.keys():
if dataset_dict["name"] == self.datasets_name["interproscan_file"] and dataset_dict["id"] not in imported_datasets_ids:
interproscan_dataset_hda_id = dataset_dict["id"]
- logging.debug("InterproScan dataset hda ID: %s" % gff_dataset_hda_id)
+
if "blast_diamond_file" in self.datasets_name.keys():
if dataset_dict["name"] == self.datasets_name["blast_diamond_file"] and dataset_dict["id"] not in imported_datasets_ids:
blast_diamond_dataset_hda_id = dataset_dict["id"]
- logging.debug("Blast Diamond dataset hda ID: %s" % gff_dataset_hda_id)
+
+ logging.debug("Genome dataset hda id: %s" % genome_dataset_hda_id)
+ logging.debug("Proteins dataset hda ID: %s" % proteins_datasets_hda_id)
+ logging.debug("Transcripts dataset hda ID: %s" % transcripts_dataset_hda_id)
+ logging.debug("GFF dataset hda ID: %s" % gff_dataset_hda_id)
+ logging.debug("InterproScan dataset hda ID: %s" % gff_dataset_hda_id)
+ logging.debug("Blast Diamond dataset hda ID: %s" % gff_dataset_hda_id)
# Add datasets IDs to already imported IDs (so we don't assign all the wrong IDs to the next organism if there is one)
imported_datasets_ids.append(genome_dataset_hda_id)
@@ -1200,6 +1201,8 @@ if __name__ == "__main__":
workflow_dict["steps"]["10"]["tool_state"] = workflow_dict["steps"]["10"]["tool_state"].replace("__FULL_NAME_ORG1__", org1_full_name).replace("__UNIQUE_ID_ORG1__", org1_species_folder_name)
workflow_dict["steps"]["10"]["tool_state"] = workflow_dict["steps"]["10"]["tool_state"].replace("__FULL_NAME_ORG2__", org2_full_name).replace("__UNIQUE_ID_ORG2__", org2_species_folder_name)
+ print(workflow_dict)
+
# Import the workflow in galaxy as a dict
instance.workflows.import_workflow_dict(workflow_dict=workflow_dict)
diff --git a/speciesData.py b/speciesData.py
index 2dbd9527a0120195c0f774cd302482cb52b34569..77f6752544ba96fc901b13b0f6c762a55de2fbd6 100755
--- a/speciesData.py
+++ b/speciesData.py
@@ -87,7 +87,9 @@ class SpeciesData:
self.datasets = dict()
self.config = None # Custom config used to set environment variables inside containers
self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items([self.genus_lowercase.lower(), self.species.lower(), self.strain.lower(), self.sex.lower()])["not_empty"])
- self.species_folder_name = self.species_folder_name .replace("-", "_").replace('__', '_')
+ self.species_folder_name = self.species_folder_name .replace("-", "_").replace('__', '_').replace("(", "_").replace(")", "_")
+ if self.species_folder_name.endswith("_"):
+ self.species_folder_name = self.species_folder_name[0:-2]
self.existing_folders_cache = {}
self.bam_metadata_cache = {}