From 02a416e96ea48d76884631aa6163d3bfee20255b Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Mon, 22 Feb 2021 17:01:47 +0100
Subject: [PATCH] cleanup repo
---
deprecated/__init__.py | 0
deprecated/create_mounts.py | 64 ----
deprecated/galaxy_data_libs_SI.py | 197 ----------
deprecated/json_example_input.json | 28 --
deprecated/table_parser.py | 79 ----
deprecated/templates/compose-template.yml | 230 ------------
.../templates/nginx_organism_template.conf | 124 ------
deprecated/templates/proxy_template.yml | 9 -
deprecated/xlsx_example_input.xlsx | Bin 5650 -> 0 bytes
examples/authelia_config_example.yml | 355 ------------------
examples/config | 21 --
examples/config_demo.yaml | 21 --
examples/example.yml | 68 ----
examples/input_demo.yaml | 41 --
utils/__init__.py | 0
utils/blastdb.py | 298 ---------------
utils/common-stringSubsitute.py | 37 --
utils/docker_compose_generator.py | 73 ----
utils/metadata_generator.py | 36 --
.../phaeoexplorer-change_pep_fasta_header.sh | 17 -
...explorer-change_transcript_fasta_header.sh | 4 -
...orer-change_transcript_fasta_header.sh.bak | 7 -
.../phaeoexplorer_ec32_orthologs_transfer.py | 96 -----
utils/phaeoexplorer_hectar_transfer.py | 95 -----
workflows/Jbrowse.ga.bak | 162 --------
25 files changed, 2062 deletions(-)
delete mode 100644 deprecated/__init__.py
delete mode 100644 deprecated/create_mounts.py
delete mode 100644 deprecated/galaxy_data_libs_SI.py
delete mode 100644 deprecated/json_example_input.json
delete mode 100644 deprecated/table_parser.py
delete mode 100644 deprecated/templates/compose-template.yml
delete mode 100644 deprecated/templates/nginx_organism_template.conf
delete mode 100644 deprecated/templates/proxy_template.yml
delete mode 100644 deprecated/xlsx_example_input.xlsx
delete mode 100644 examples/authelia_config_example.yml
delete mode 100644 examples/config
delete mode 100644 examples/config_demo.yaml
delete mode 100644 examples/example.yml
delete mode 100644 examples/input_demo.yaml
delete mode 100755 utils/__init__.py
delete mode 100755 utils/blastdb.py
delete mode 100755 utils/common-stringSubsitute.py
delete mode 100755 utils/docker_compose_generator.py
delete mode 100755 utils/metadata_generator.py
delete mode 100755 utils/phaeoexplorer-change_pep_fasta_header.sh
delete mode 100755 utils/phaeoexplorer-change_transcript_fasta_header.sh
delete mode 100755 utils/phaeoexplorer-change_transcript_fasta_header.sh.bak
delete mode 100644 utils/phaeoexplorer_ec32_orthologs_transfer.py
delete mode 100644 utils/phaeoexplorer_hectar_transfer.py
delete mode 100644 workflows/Jbrowse.ga.bak
diff --git a/deprecated/__init__.py b/deprecated/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/deprecated/create_mounts.py b/deprecated/create_mounts.py
deleted file mode 100644
index 91e2f81..0000000
--- a/deprecated/create_mounts.py
+++ /dev/null
@@ -1,64 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-import logging as log
-import os
-import re
-import yaml
-
-from pathlib import Path
-
-
-def main(args):
-
- compose_yml = os.path.abspath('./docker-compose.yml')
- if not os.path.isfile(compose_yml):
- raise Exception("Could not find docker-compose.yml at %s" % compose_yml)
-
- with open(compose_yml) as f:
- compose = yaml.safe_load(f)
-
- if 'services' not in compose:
- raise Exception("Could not find services tag in docker-compose.yml")
-
- for service in compose['services']:
- log.info("Service '%s'" % service)
- if 'volumes' in compose['services'][service]:
- for volume in compose['services'][service]['volumes']:
- log.info(" Volume '%s'" % (volume))
- reg = re.match(r"^(\./[^:]+/):[^:]+(:\w+)?$", volume)
- if reg:
- vol_dir = os.path.abspath('./' + reg.group(1))
- log.info(" mkdir '%s' (from %s)" % (vol_dir, volume))
- if not args.dry_run and not os.path.exists(vol_dir):
- os.makedirs(vol_dir, exist_ok=True)
- else:
- reg = re.match(r"^(\./[^:]+):[^:]+(:\w+)?$", volume)
- if reg:
- vol_file = os.path.abspath('./' + reg.group(1))
- vol_dir = os.path.dirname(vol_file)
- log.info(" mkdir '%s' (from %s)" % (vol_dir, volume))
- if not args.dry_run and not os.path.exists(vol_dir):
- os.makedirs(vol_dir, exist_ok=True)
- log.info(" touch '%s' (from %s)" % (vol_file, volume))
- if not args.dry_run and not os.path.exists(vol_file):
- Path(vol_file).touch()
- else:
- log.info(" skip")
-
-
-if __name__ == '__main__':
- parser = argparse.ArgumentParser(
- description='Create local volume directories.'
- )
- parser.add_argument("-v", "--verbose", help="Increase output verbosity.",
- action="store_true")
- parser.add_argument("-d", "--dry-run", help="Dry run: no modification will be done, for testing purpose.",
- action="store_true")
-
- args = parser.parse_args()
- log.basicConfig(level=log.INFO)
- if args.verbose:
- log.basicConfig(level=log.DEBUG)
-
- main(args)
diff --git a/deprecated/galaxy_data_libs_SI.py b/deprecated/galaxy_data_libs_SI.py
deleted file mode 100644
index 1fa378e..0000000
--- a/deprecated/galaxy_data_libs_SI.py
+++ /dev/null
@@ -1,197 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-import logging as log
-import os
-import subprocess
-import time
-from subprocess import CalledProcessError
-
-from bioblend.galaxy.objects import GalaxyInstance
-
-import yaml
-
-
-class DataLibLoader:
-
- def __init__(self):
- self.existing_folders_cache = {}
- self.bam_metadata_cache = {}
-
- def create_deep_folder(self, prj_lib, path, parent_folder=None, deep_name=""):
-
- segments = path.split(os.sep)
-
- deeper_name = os.sep.join([deep_name, segments[0]])
- if deeper_name in self.existing_folders_cache:
- new_folder = self.existing_folders_cache[deeper_name]
- else:
- new_folder = prj_lib.create_folder(segments[0], base_folder=parent_folder)
- self.existing_folders_cache[deeper_name] = new_folder
-
- if len(segments) > 1:
- new_folder = self.create_deep_folder(prj_lib, os.sep.join(segments[1:]), new_folder, deeper_name)
-
- return new_folder
-
- def get_bam_label(self, dirname, bam_file):
-
- bam_id = bam_file
- if bam_id.endswith('.bam'):
- bam_id = bam_id[:-4]
-
- if dirname in self.bam_metadata_cache:
- if bam_id in self.bam_metadata_cache[dirname] and 'label' in self.bam_metadata_cache[dirname][bam_id] and self.bam_metadata_cache[dirname][bam_id]['label']:
- return self.bam_metadata_cache[dirname][bam_id]['label']
- else:
- return None
- else:
- meta_file = os.path.join(dirname, 'metadata.yml')
- if os.path.exists(meta_file):
- with open(meta_file) as f:
- self.bam_metadata_cache[dirname] = yaml.safe_load(f)
- log.info("Found metadata in %s " % meta_file)
- else:
- self.bam_metadata_cache[dirname] = {}
- log.info("Did not find metadata in %s " % meta_file)
- return self.get_bam_label(dirname, bam_file)
-
- def main(self, args, data_dir_root='/project_data'):
- """
- Load files into a Galaxy data library.
- """
-
- log.info("Importing data libraries.")
-
- url = "http://localhost"
- # The environment variables are set by the parent container
- admin_email = os.environ.get('GALAXY_DEFAULT_ADMIN_USER', 'admin@galaxy.org')
- admin_pass = os.environ.get('GALAXY_DEFAULT_ADMIN_PASSWORD', 'password')
-
- # Establish connection to galaxy instance
- gio = GalaxyInstance(url=url, email=admin_email, password=admin_pass)
-
- log.info("Looking for project data in %s" % data_dir_root)
- folders = dict()
- for root, dirs, files in os.walk(data_dir_root, followlinks=True):
- file_list = [os.path.join(root, filename) for filename in files]
- folders[root] = file_list
-
- post_renaming = {}
- if folders:
- # Delete pre-existing lib (probably created by a previous call)
- existing = gio.libraries.get_previews(name='Project Data')
- for lib in existing:
- if not lib.deleted:
- log.info('Pre-existing "Project Data" library %s found, removing it.' % lib.id)
- gio.libraries.delete(lib.id)
-
- log.info("Creating new 'Project Data' library.")
- prj_lib = gio.libraries.create('Project Data', 'Data for current genome annotation project')
-
- for fname, files in folders.items():
- if fname and files:
- folder_name = fname[len(data_dir_root) + 1:]
- log.info("Creating folder: %s" % folder_name)
- folder = None
- if not args.dry_run:
- folder = self.create_deep_folder(prj_lib, folder_name)
-
- for single_file in files:
- ftype = 'auto'
-
- clean_name = os.path.basename(single_file)
- clean_name = clean_name.replace('_', ' ')
-
- if single_file.endswith('.bam'):
- ftype = 'bam'
- bam_label = self.get_bam_label(fname, os.path.basename(single_file))
- if bam_label:
- clean_name = bam_label
- else:
- clean_name = os.path.splitext(clean_name)[0]
- if clean_name.endswith("Aligned.sortedByCoord.out"): # Stupid thing for many local bam files
- clean_name = clean_name[:-25]
- elif single_file.endswith('.fasta') or single_file.endswith('.fa') or single_file.endswith('.faa') or single_file.endswith('.fna'):
- ftype = 'fasta'
- elif single_file.endswith('.gff') or single_file.endswith('.gff3'):
- ftype = 'gff3'
- clean_name = os.path.splitext(clean_name)[0]
- elif single_file.endswith('.xml'):
- ftype = 'xml'
- elif single_file.endswith('.bw'):
- ftype = 'bigwig'
- elif single_file.endswith('.gaf'):
- ftype = 'tabular'
- elif single_file.endswith('_tree.txt'):
- # We don't want to pollute the logs with 20000 useless lines
- log.debug("Skipping useless file '%s'." % single_file)
- continue
- elif single_file.endswith('.tar.gz') and 'newick' in fname:
- ftype = 'tar'
- elif single_file.endswith('.bai') or single_file.endswith('.tar.gz') or single_file.endswith('.tar.bz2') or single_file.endswith('.raw') or single_file.endswith('.pdf'):
- log.info("Skipping useless file '%s'." % single_file)
- continue
-
- log.info("Adding file '%s' with type '%s' and name '%s'." % (single_file, ftype, clean_name))
- if not args.dry_run:
- datasets = prj_lib.upload_from_galaxy_fs(
- single_file,
- folder=folder,
- link_data_only='link_to_files',
- file_type=ftype,
- tag_using_filenames=False
- )
-
- # Rename dataset
- # Need to do it AFTER the datasets import is finished, otherwise the new names are not kept by galaxy
- # (erased by metadata generation I guess)
- post_renaming[datasets[0]] = clean_name
-
- time.sleep(1)
-
- if args.dry_run:
- log.info("Finished in DRY RUN mode")
- return
-
- # Wait for uploads to complete
- log.info("Waiting for import jobs to finish... please wait")
- while True:
- try:
- # "C" state means the job is completed, no need to wait for it
- ret = subprocess.check_output("squeue | grep -v \"C debug\" | grep -v \"JOBID\" || true", shell=True)
- if not len(ret):
- break
- time.sleep(3)
- except CalledProcessError as inst:
- if inst.returncode == 153: # queue is empty
- break
- else:
- raise
-
- time.sleep(10)
-
- log.info("Import finished, now renaming datasets with pretty names")
- for dataset in post_renaming:
- dataset.update(name=post_renaming[dataset])
-
- log.info("Finished importing data.")
-
-
-if __name__ == '__main__':
- parser = argparse.ArgumentParser(
- description='Populate the Galaxy data library with files.'
- )
- parser.add_argument("-v", "--verbose", help="Increase output verbosity.",
- action="store_true")
- parser.add_argument("-d", "--dry-run", help="Don't update the data library, just show what it would do.",
- action="store_true")
-
- args = parser.parse_args()
- if args.verbose:
- log.basicConfig(level=log.DEBUG)
- else:
- log.basicConfig(level=log.INFO)
-
- dll = DataLibLoader()
- dll.main(args)
diff --git a/deprecated/json_example_input.json b/deprecated/json_example_input.json
deleted file mode 100644
index 669bc88..0000000
--- a/deprecated/json_example_input.json
+++ /dev/null
@@ -1,28 +0,0 @@
-[
- {
- "genus" : "genus1",
- "species" : "Species1",
- "common" : "Common1",
- "strain" : "strain1",
- "sex" : "male",
- "origin" : "Unknown",
- "version" : "1.0",
- "performed by" : "Institute John Doe",
- "genome version" : "1.0",
- "ogs version" : "1.0",
- "date" : "2020-01-01"
- },
- {
- "genus" : "genus2",
- "species" : "Species2",
- "common" : "Common2",
- "strain" : "strain2",
- "sex" : "female",
- "origin" : "Unknown",
- "version" : "1.0",
- "performed by" : "Institute Jane Doe",
- "genome version" : "1.0",
- "ogs version" : "1.0",
- "date" : "2020-01-01"
- }
-]
diff --git a/deprecated/table_parser.py b/deprecated/table_parser.py
deleted file mode 100644
index 9314b91..0000000
--- a/deprecated/table_parser.py
+++ /dev/null
@@ -1,79 +0,0 @@
-import os
-import sys
-import pandas # xlrd required for excel files reading
-import numpy
-import json
-import argparse
-import logging
-from datetime import datetime
-
-"""
-!! OBSOLETE !!
-
-Input parser script.
-Does not work for ods spreadsheets (save as xls or xlsx instead) --> need to handle with pandas_ods_reader (requires ezodf, lxml)
-Does not support multiple sheets (TODO: "integration" and "update" sheets (1 and 2))
-See example toy table (toy_table.xls)
-
-standalone usage: python3 table_parser.py <tabulated_file> -d <directory_to_write_json_to (default: cwd)>
-
-"""
-
-
-class TableParser:
-
- def __init__(self, table_file, dir):
- self.dir = os.path.abspath(args.dir)
- self.table_file = table_file
- self.method = None # TODO: instant launch or just parse (standalone)
- self.extension = None
- self.meta = dict()
- self.json_file = None
-
- def parse_table(self, extension):
- if extension == "xls":
- pandas_table = pandas.DataFrame(pandas.read_excel(self.table_file))
- elif extension == "csv":
- pandas_table = pandas.DataFrame(pandas.read_csv(self.table_file))
- else:
- logging.info("wrong format: input tabulated file cannot be read (supported formats: xls, xlsx, csv)")
- sys.exit()
- pandas_table = pandas_table.replace(numpy.nan, "", regex=True)
-
- for char in " ,.()-/":
- pandas_table = pandas_table.replace("\\" + char, "_", regex=True)
- pandas_table = pandas_table.replace("\\__", "_", regex=True)
- pandas_table.loc[pandas_table["genome version"] == "", "genome version"] = "1.0"
- pandas_table.loc[pandas_table["ogs version"] == "", "ogs version"] = "1.0"
- pandas_table.loc[pandas_table["version"] == "", "version"] = "1.0"
- pandas_table.loc[pandas_table["date"] == "", "date"] = datetime.today().strftime("%Y-%m-%d")
- with open(os.path.join(self.dir, self.json_file), 'w') as json_file:
- json_file.truncate(0)
- json_content = list()
- for organism in range(0, len(pandas_table.index)):
- organism_dict = pandas_table.iloc[organism].to_dict()
- for k, v in organism_dict.items():
- v = str(v).split(" ")
- v = "_".join(v)
- v = v.replace("__", "_")
- if v.endswith("_"):
- v = v[:-1]
- json_content.append(organism_dict)
- json.dump(json_content, json_file, indent=4)
-
- def write_json(self, data, filename):
- with open(filename, 'w') as f:
- json.dump(data, f, indent=4)
-
-
-if __name__ == "__main__":
- parser = argparse.ArgumentParser(description="Table parser for phaeoexplorer data")
- parser.add_argument("input", type=str, help="input table")
- parser.add_argument("-d", "--dir", type=str, help="Where to write the output json file that is be used for integration", default = os.getcwd())
- args = parser.parse_args()
-
- if args.input.endswith("xlsx") or args.input.endswith("xls"):
- tp = TableParser(table_file=args.input, dir=args.dir)
- tp.extension = args.input.split(".")[1]
- tp.json_file = tp.dir + "/dataloader_" + datetime.today().strftime("%Y%m%d") + ".json"
- tp.parse_table(extension="xls")
diff --git a/deprecated/templates/compose-template.yml b/deprecated/templates/compose-template.yml
deleted file mode 100644
index f15a9f7..0000000
--- a/deprecated/templates/compose-template.yml
+++ /dev/null
@@ -1,230 +0,0 @@
-# ./docker_data is created and filled with persistent data that should be backuped
-
-version: '2'
-services:
- proxy:
- image: quay.io/abretaud/nginx-ldap:latest # Not using the default nginx image as we need the ldap module
- ports:
- - "9170:80"
- links:
- - galaxy
- - jbrowse
- - tripal
- - apollo
- - apollo-report
- - blast
- - wiki
- volumes:
- - ./src_data/:/project_data/
- #- /groups/XXX/:/groups/XXX/:ro # We do this when we have symlinks in src_data pointing to /groups/XXX/...
- - ./nginx/conf:/etc/nginx/conf.d
-
- tripal:
- image: quay.io/galaxy-genome-annotation/tripal@sha256:4451cc3a601d109c07c7aedcc76bd41a5da7c438c8fa0862488680bd462f125b
- links:
- - tripaldb:postgres
- - elasticsearch:elasticsearch
- volumes_from:
- - "galaxy"
- volumes:
- - ./src_data:/data:ro
- environment:
- BASE_URL_PATH: /sp/genus_species
- UPLOAD_LIMIT: 20M
- MEMORY_LIMIT: 512M
- TRIPAL_GIT_CLONE_MODULES: "https://github.com/abretaud/tripal_rest_api.git[@c6f9021ea5d4c6d7c67c5bd363a7dd9359228bbc] https://github.com/tripal/tripal_elasticsearch.git[@dc7f276046e394a80a7dfc9404cf1a149006eb2a] https://github.com/tripal/tripal_analysis_interpro.git https://github.com/tripal/tripal_analysis_go.git https://github.com/tripal/tripal_analysis_blast.git https://github.com/tripal/tripal_analysis_expression.git[@7240039fdeb4579afd06bbcb989cb7795bd4c342]"
- TRIPAL_DOWNLOAD_MODULES: ""
- TRIPAL_ENABLE_MODULES: "tripal_analysis_blast tripal_analysis_interpro tripal_analysis_go tripal_rest_api tripal_elasticsearch"
- SITE_NAME: "Genus species"
- ENABLE_JBROWSE: /jbrowse/?data=data/gspecies
- ENABLE_APOLLO: 1
- ENABLE_BLAST: 1
- ENABLE_DOWNLOAD: 1
- ENABLE_WIKI: 1
- ENABLE_GO: /organism/Genus/species?pane=GO
- ENABLE_ORTHOLOGY: 0
- ENABLE_ORTHOLOGY_LINKS: http://localhost/sp/orthology/
- #THEME: "bipaa" # Use this to use another theme
- #THEME_GIT_CLONE: "https://gitlab.inria.fr/abretaud/tripal_bipaa.git" # Use this to install another theme
- ADMIN_PASSWORD: XXXXXX # You need to define it and update it in galaxy config below
-
- tripaldb:
- image: quay.io/galaxy-genome-annotation/chado:1.31-jenkins110.1-pg9.5
- environment:
- - POSTGRES_PASSWORD=postgres
- # The default chado image would try to install the schema on first run,
- # we just want the tools to be available.
- - INSTALL_CHADO_SCHEMA=0
- volumes:
- - ./docker_data/tripal_db/:/var/lib/postgresql/data/
-
- elasticsearch:
- image: docker.elastic.co/elasticsearch/elasticsearch:6.6.1
- #mem_limit: 500m # This is to limit usage, but can make the docker crash when ram is exhausted, not recommended while indexing all data, ok once indexing is done
- ulimits:
- memlock:
- soft: -1
- hard: -1
- volumes:
- - ./docker_data/elastic_search_index/:/usr/share/elasticsearch/data
- environment:
- bootstrap.memory_lock: "true"
- xpack.security.enabled: "false"
- xpack.monitoring.enabled: "false"
- xpack.ml.enabled: "false"
- xpack.graph.enabled: "false"
- xpack.watcher.enabled: "false"
- cluster.routing.allocation.disk.threshold_enabled: "false"
- ES_JAVA_OPTS: "-Xms200m -Xmx200m"
- TAKE_FILE_OWNERSHIP: "true"
-
- galaxy:
- image: quay.io/galaxy-genome-annotation/docker-galaxy-annotation:gmod
- volumes:
- - ../galaxy_data_libs_SI.py:/opt/galaxy_data_libs_SI.py
- - ./docker_data/galaxy:/export
- - ./src_data/:/project_data:ro
- #- /groups/XXX/:/groups/XXX/:ro # We do this when we have symlinks in src_data pointing to /groups/XXX/...
- - ./docker_data/jbrowse/:/jbrowse/data/
- - ./docker_data/apollo/:/apollo-data/
- links:
- - "tripaldb:chado"
- environment:
- NONUSE: nodejs,proftp,reports
- GALAXY_LOGGING: full
- GALAXY_CONFIG_BRAND: "Genus species"
- GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE: "True"
- GALAXY_CONFIG_USE_REMOTE_USER: "True"
- GALAXY_CONFIG_REMOTE_USER_MAILDOMAIN: "bipaa"
- GALAXY_CONFIG_ADMIN_USERS: "admin@galaxy.org,gogepp@bipaa" # admin@galaxy.org is the default (leave it), gogepp@bipaa is a shared ldap user we use to connect
- ENABLE_FIX_PERMS: 0
- PROXY_PREFIX: /sp/genus_species/galaxy
- GALAXY_CONFIG_COOKIE_PATH: /galaxy
- GALAXY_TRIPAL_PASSWORD: XXXXXX # See tripal config above
- GALAXY_WEBAPOLLO_URL: http://apollo:8080
- GALAXY_WEBAPOLLO_USER: "admin_apollo@bipaa"
- GALAXY_WEBAPOLLO_PASSWORD: "XXXXXX" # See tripal config below
- GALAXY_WEBAPOLLO_EXT_URL: /sp/genus_species/apollo
- GALAXY_CHADO_DBHOST: chado
- GALAXY_CHADO_DBSCHEMA: chado
- GALAXY_AUTO_UPDATE_DB: 1
- GALAXY_AUTO_UPDATE_CONDA: 1
- GALAXY_AUTO_UPDATE_TOOLS: "/galaxy-central/tools_1.yaml"
- MASTER_API_KEY: dev
- BLAT_ENABLED: 1
-
- jbrowse:
- image: quay.io/galaxy-genome-annotation/jbrowse:v1.16.5
- volumes:
- - /data
- volumes_from:
- - "galaxy:ro"
- ports:
- - "80"
-
- apollo:
- image: quay.io/abretaud/apollo:bipaa
- links:
- - "apollo_db:db"
- environment:
- APOLLO_ADMIN_EMAIL: "admin_apollo@bipaa" # internal admin user, used by some scripts/api
- APOLLO_ADMIN_PASSWORD: "XXXXXX" # define it and adapt galaxy config above
- APOLLO_BASE_HOST: "http://localhost"
- APOLLO_PATH_PREFIX: "/sp/genus_species/apollo/"
- APOLLO_REMOTE_ADMINS: "gogepp@bipaa,abretaud@bipaa,srobin@bipaa,flegeai@bipaa" # all ldap users that we use to connect as admin
- WEBAPOLLO_DB_USERNAME: postgres
- WEBAPOLLO_DB_PASSWORD: password
- WEBAPOLLO_DB_DRIVER: "org.postgresql.Driver"
- WEBAPOLLO_DB_DIALECT: "org.hibernate.dialect.PostgresPlusDialect"
- WEBAPOLLO_DB_URI: "jdbc:postgresql://db/postgres"
- WEBAPOLLO_FEATURE_HAS_DBXREFS: "true"
- WEBAPOLLO_FEATURE_HAS_ATTRS: "true"
- WEBAPOLLO_FEATURE_HAS_PUBMED: "true"
- WEBAPOLLO_FEATURE_HAS_GO: "true"
- WEBAPOLLO_FEATURE_HAS_COMMENTS: "true"
- WEBAPOLLO_FEATURE_HAS_STATUS: "true"
- CATALINA_OPTS: "-Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC"
- volumes_from:
- - "galaxy:ro"
- volumes:
- - ./apollo/annotation_groups.tsv:/bootstrap/canned_values.txt:ro # Other canned things are preloaded in the docker image https://github.com/abretaud/docker-apollo/blob/bipaa/bootstrap.sh
- #- ../blat/:/opt/blat/:ro # Mount the blat binary if you want to use it (could not include it in the docker image due to license issue)
-
- apollo_db:
- image: postgres:9.5
- environment:
- POSTGRES_PASSWORD: password
- volumes:
- - ./docker_data/apollo_db/:/var/lib/postgresql/data/
-
- apollo-report: # A report app following guidelines from https://bipaa.genouest.org/is/how-to-annotate-a-genome/
- links:
- - apollo:apollo
- image: quay.io/abretaud/apollo-report:latest
- environment:
- APOLLO_EXT_URL: http://localhost/sp/genus_species/apollo/
- APOLLO_USER: admin_apollo@bipaa
- APOLLO_PASS: XXXXX # See apollo conf above
- ADMIN_USERS: login1,login2 # ldap users that should see an extended report
- APOLLO_MOUNTPOINT: /apollo-data/
- volumes:
- - ./docker_data/apollo/:/apollo-data/:ro
- - ./apollo/annotation_groups.tsv:/data/annotation_groups.tsv:ro
- - ./docker_data/apollo_report/:/data/report/
-
- blast:
- image: quay.io/abretaud/sf-blast:latest
- links:
- - blast_db:postgres
- #hostname: gogepp-blast.genouest.org # Hostname declare as submit node in sge conf (for drmaa mode only)
- environment:
- UPLOAD_LIMIT: 20M
- MEMORY_LIMIT: 128M
- DB_NAME: 'postgres'
- ADMIN_EMAIL: 'xxx@example.org' # email sender
- ADMIN_NAME: 'xxxxx' # email sender name
- JOBS_METHOD: 'local' # Can be local (= no sge jobs, but run inside the container) or drmaa (= to submit to a cluster)
- JOBS_WORK_DIR: '/xxxx/blast_jobs/' # disk accessible both from compute nodes and mounted in this docker (at the same path)
- CDD_DELTA_PATH: '/db/cdd_delta/current/flat/cdd_delta'
- BLAST_TITLE: 'Genus species blast server'
- JOBS_SCHED_NAME: 'blast_gspecies' # job names
- PRE_CMD: '. /local/env/envblast-2.6.0.sh; . /local/env/envpython-2.7.sh;' # executed at the beginning of each job
- APACHE_RUN_USER: 'bipaaweb' # username known by sge
- APACHE_RUN_GROUP: 'bipaa' # group known by sge
- BASE_URL_PATH: '/sp/genus_species/blast/'
- UID: 55914 # username known by sge (for drmaa mode only)
- GID: 40259 # group known by sge (for drmaa mode only)
- volumes:
- #- ../blast-themes/xxx/:/var/www/blast/app/Resources/:ro # You can theme the app
- - /data1/sge/:/usr/local/sge/:ro # the sge install
- #- /xxxx/blast_jobs/:/xxxx/blast_jobs/ # (for drmaa mode only)
- - ./blast/banks.yml:/var/www/blast/app/config/banks.yml:ro
- - ./blast/links.yml:/etc/blast_links/links.yml:ro
-
- blast_db:
- image: postgres:9.5
- environment:
- - POSTGRES_PASSWORD=postgres
- - PGDATA=/var/lib/postgresql/data/
- volumes:
- - ./docker_data/blast_db/:/var/lib/postgresql/data/
-
- wiki:
- image: quay.io/abretaud/mediawiki
- environment:
- MEDIAWIKI_SERVER: http://localhost
- MEDIAWIKI_PROXY_PREFIX: /sp/genus_species/wiki
- MEDIAWIKI_SITENAME: Genus species
- MEDIAWIKI_SECRET_KEY: XXXXXXXXXX
- MEDIAWIKI_DB_PASSWORD: password
- MEDIAWIKI_ADMIN_USER: abretaud # ldap user
- links:
- - wiki_db:db
- volumes:
- - ./docker_data/wiki_uploads:/images
- #- ../bipaa_wiki.png:/var/www/mediawiki/resources/assets/wiki.png:ro # To cange the logo at the top left
-
- wiki_db:
- image: postgres:9.5
- volumes:
- - ./docker_data/wiki_db/:/var/lib/postgresql/data/
diff --git a/deprecated/templates/nginx_organism_template.conf b/deprecated/templates/nginx_organism_template.conf
deleted file mode 100644
index c2ae6c2..0000000
--- a/deprecated/templates/nginx_organism_template.conf
+++ /dev/null
@@ -1,124 +0,0 @@
-# This is to restrict access to galaxy server to users in an admin ldap group
-#ldap_server adminldap {
-# url ldap://ldap.sb-roscoff.fr/o=sb-roscoff,c=fr?uid?sub?(&(objectClass=person)(uid=gga));
-# require valid_user;
-# satisfy all;
-#}
-
-# This is to authenticate users allowed to access the genome (required by apollo, even if the rest is public)
-#ldap_server gspeciesldap {
-# url ldap://ldap.sb-roscoff.fr/o=sb-roscoff,c=fr?uid?sub?(&(objectClass=person)(businessCategory=phaeoexplorer));
-# require valid_user;
-# satisfy all;
-#}
-
-# WebSocket stuff for Apollo
-map $http_upgrade $connection_upgrade {
- default upgrade;
- '' close;
-}
-
-server {
- listen 80;
- server_name ~.;
-
- # When ldap is configured
- # auth_ldap "Restricted access";
- # auth_ldap_servers gspeciesldap;
- # auth_basic "Restricted Content";
- # auth_basic_user_file /etc/nginx/conf.d/htpasswd_all_users;
- proxy_set_header REMOTE_USER $remote_user;
-
- location / {
- proxy_redirect http://tripal/tripal/ http://$http_host/tripal/;
- proxy_pass http://tripal/tripal/;
- }
-
- location /download/ {
- alias /project_data/;
- autoindex on;
- }
-
- location /galaxy {
- # When ldap is configured
- # auth_ldap "Restricted access";
- # auth_ldap_servers adminldap;
- # auth_basic "Restricted Content";
- # auth_basic_user_file /etc/nginx/conf.d/htpasswd_admin_only;
- proxy_set_header REMOTE_USER $remote_user;
-
- client_max_body_size 50g;
- proxy_redirect http://galaxy http://$host;
- proxy_pass http://galaxy/;
- proxy_cookie_path ~*^/([^/]*) /galaxy/$1;
- }
-
- location /api/ {
- proxy_pass http://galaxy/;
- satisfy any;
- allow all;
- }
-
- rewrite ^/jbrowse$ http://localhost/sp/undaria_pinnatifida/jbrowse/ permanent;
- rewrite ^/blast$ http://localhost/sp/undaria_pinnatifida/blast/ permanent;
- rewrite ^/download$ http://localhost/sp/undaria_pinnatifida/download/ permanent;
- rewrite ^/apollo$ http://localhost/sp/undaria_pinnatifida/apollo/ permanent;
- rewrite ^/blast$ http://localhost/sp/undaria_pinnatifida/blast/ permanent;
- rewrite ^/apollo_report$ localhost/sp/undaria_pinnatifida/apollo_report/ permanent;
- rewrite ^/wiki$ http://localhost/sp/undaria_pinnatifida/wiki/ permanent;
-
- location /jbrowse {
- proxy_redirect http://jbrowse http://$host;
- proxy_pass http://jbrowse/;
-
- add_header Last-Modified $date_gmt;
- }
-
-# location /apollo/ {
-# proxy_set_header REMOTE_USER $remote_user@sb-roscoff.fr;
-#
-# # WebSocket stuff
-# proxy_http_version 1.1;
-# proxy_set_header Upgrade $http_upgrade;
-# proxy_set_header Connection $connection_upgrade;
-#
-# if ($args ~* (.*)addStores=(.*)) {
-# set_unescape_uri $addStores $2;
-# set_escape_uri $addStores_fixed $addStores;
-# set $args $1addStores=$addStores_fixed;
-# }
-#
-# if ($args ~* (.*)addTracks=(.*)) {
-# set_unescape_uri $addTracks $2;
-# set_escape_uri $addTracks_fixed $addTracks;
-# set $args $1addTracks=$addTracks_fixed;
-# }
-#
-# proxy_redirect / http://$http_host/apollo/;
-# proxy_redirect http://apollo:8080/ http://$http_host/apollo/;
-# proxy_pass http://apollo:8080/;
-# proxy_cookie_path ~*^/([^/]*) /apollo/$1;
-# subs_filter (href|action)=('|")/(?!sp/) $1=$2/sp/ectocarpus_siliculosus_1a/apollo/ gir;
-# }
-
- #location /blast/ {
- # client_max_body_size 20m;
-#
-# proxy_pass http://blast/;
-# proxy_redirect / http://$http_host/blast/;
-# }
-
-# location /apollo_report/ {
-# proxy_pass http://apollo-report/;
-# proxy_redirect / http://$http_host/apollo_report/;
-# }
-
-# location /wiki/ {
-# proxy_set_header X-Forwarded-Host $host;
-# proxy_set_header X-Forwarded-Server $host;
-# proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
-
-# proxy_redirect http://wiki/ http://$host/wiki/;
-# proxy_pass http://wiki/;
-# }
-}
diff --git a/deprecated/templates/proxy_template.yml b/deprecated/templates/proxy_template.yml
deleted file mode 100644
index c9909be..0000000
--- a/deprecated/templates/proxy_template.yml
+++ /dev/null
@@ -1,9 +0,0 @@
-version: '2'
-services:
- proxy:
- image: quay.io/abretaud/nginx-ldap:latest # Not using the default nginx image as we need the ldap module
- # ports:
- # - "9178:80" # This is not used when using network_mode=host
- volumes:
- - ./nginx/conf:/etc/nginx/conf.d
- network_mode: "host" # This is to be able to use localhost in nginx conf, you can prefer to remove it here and replace localhost by the docker host address in nginx config
diff --git a/deprecated/xlsx_example_input.xlsx b/deprecated/xlsx_example_input.xlsx
deleted file mode 100644
index 4d75e1ae55b74c096ce229daf452e911b426a165..0000000000000000000000000000000000000000
GIT binary patch
literal 0
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diff --git a/examples/authelia_config_example.yml b/examples/authelia_config_example.yml
deleted file mode 100644
index c0bd77a..0000000
--- a/examples/authelia_config_example.yml
+++ /dev/null
@@ -1,355 +0,0 @@
-###############################################################
-# Authelia configuration #
-###############################################################
-
-# The host and port to listen on
-host: 0.0.0.0
-port: 9091
-# tls_key: /var/lib/authelia/ssl/key.pem
-# tls_cert: /var/lib/authelia/ssl/cert.pem
-
-# Level of verbosity for logs: info, debug, trace
-log_level: info
-## File path where the logs will be written. If not set logs are written to stdout.
-# log_file_path: /var/log/authelia
-
-# The secret used to generate JWT tokens when validating user identity by
-# email confirmation.
-# This secret can also be set using the env variables AUTHELIA_JWT_SECRET
-jwt_secret: XXXXXXXXXXXXXXXXX
-
-# Default redirection URL
-#
-# If user tries to authenticate without any referer, Authelia
-# does not know where to redirect the user to at the end of the
-# authentication process.
-# This parameter allows you to specify the default redirection
-# URL Authelia will use in such a case.
-#
-# Note: this parameter is optional. If not provided, user won't
-# be redirected upon successful authentication.
-default_redirection_url: https://localhost/
-
-# Google Analytics Tracking ID to track the usage of the portal
-# using a Google Analytics dashboard.
-#
-## google_analytics: UA-00000-01
-
-# TOTP Settings
-#
-# Parameters used for TOTP generation
-#totp:
- # The issuer name displayed in the Authenticator application of your choice
- # See: https://github.com/google/google-authenticator/wiki/Key-Uri-Format for more info on issuer names
- #issuer: authelia.com
- # The period in seconds a one-time password is current for. Changing this will require all users to register
- # their TOTP applications again.
- # Warning: before changing period read the docs link below.
- #period: 30
- # The skew controls number of one-time passwords either side of the current one that are valid.
- # Warning: before changing skew read the docs link below.
- #skew: 1
- # See: https://docs.authelia.com/configuration/one-time-password.html#period-and-skew to read the documentation.
-
-# Duo Push API
-#
-# Parameters used to contact the Duo API. Those are generated when you protect an application
-# of type "Partner Auth API" in the management panel.
-#duo_api:
- #hostname: api-123456789.example.com
- #integration_key: ABCDEF
- # This secret can also be set using the env variables AUTHELIA_DUO_API_SECRET_KEY
- #secret_key: 1234567890abcdefghifjkl
-
-# The authentication backend to use for verifying user passwords
-# and retrieve information such as email address and groups
-# users belong to.
-#
-# There are two supported backends: 'ldap' and 'file'.
-authentication_backend:
- # Disable both the HTML element and the API for reset password functionality
- disable_reset_password: true
-
- # LDAP backend configuration.
- #
- # This backend allows Authelia to be scaled to more
- # than one instance and therefore is recommended for
- # production.
-# ldap:
- # The url to the ldap server. Scheme can be ldap:// or ldaps://
-# url: ldap://ldap-host-name
- # Skip verifying the server certificate (to allow self-signed certificate).
-# skip_verify: false
-
- # The base dn for every entries
-# base_dn: dc=genouest,dc=org
-
- # The attribute holding the username of the user. This attribute is used to populate
- # the username in the session information. It was introduced due to #561 to handle case
- # insensitive search queries.
- # For you information, Microsoft Active Directory usually uses 'sAMAccountName' and OpenLDAP
- # usually uses 'uid'
- username_attribute: uid
-
- # An additional dn to define the scope to all users
-# additional_users_dn: ou=users
-
- # The users filter used in search queries to find the user profile based on input filled in login form.
- # Various placeholders are available to represent the user input and back reference other options of the configuration:
- # - {input} is a placeholder replaced by what the user inputs in the login form.
- # - {username_attribute} is a placeholder replaced by what is configured in `username_attribute`.
- # - {mail_attribute} is a placeholder replaced by what is configured in `mail_attribute`.
- # - DON'T USE - {0} is an alias for {input} supported for backward compatibility but it will be deprecated in later versions, so please don't use it.
- #
- # Recommended settings are as follows:
- # - Microsoft Active Directory: (&({username_attribute}={input})(objectCategory=person)(objectClass=user))
- # - OpenLDAP: (&({username_attribute}={input})(objectClass=person))' or '(&({username_attribute}={input})(objectClass=inetOrgPerson))
- #
- # To allow sign in both with username and email, one can use a filter like
- # (&(|({username_attribute}={input})({mail_attribute}={input}))(objectClass=person))
- users_filter: (&({username_attribute}={input})(objectClass=bipaaPerson)(isActive=TRUE))
-
- # An additional dn to define the scope of groups
-# additional_groups_dn: ou=groups
-
- # The groups filter used in search queries to find the groups of the user.
- # - {input} is a placeholder replaced by what the user inputs in the login form.
- # - {username} is a placeholder replace by the username stored in LDAP (based on `username_attribute`).
- # - {dn} is a matcher replaced by the user distinguished name, aka, user DN.
- # - {username_attribute} is a placeholder replaced by what is configured in `username_attribute`.
- # - {mail_attribute} is a placeholder replaced by what is configured in `mail_attribute`.
- # - DON'T USE - {0} is an alias for {input} supported for backward compatibility but it will be deprecated in later versions, so please don't use it.
- # - DON'T USE - {1} is an alias for {username} supported for backward compatibility but it will be deprecated in later version, so please don't use it.
-# groups_filter: (&(member={dn})(objectclass=bipaaGroup))
-
- # The attribute holding the name of the group
-# group_name_attribute: cn
-
- # The attribute holding the mail address of the user
-# mail_attribute: mail
-
- # The username and password of the admin user.
-# user: cn=admin,dc=genouest,dc=org
- # This secret can also be set using the env variables AUTHELIA_AUTHENTICATION_BACKEND_LDAP_PASSWORD
-# password: XXXXXXXXXXXXXX
-
- # File backend configuration.
- #
- # With this backend, the users database is stored in a file
- # which is updated when users reset their passwords.
- # Therefore, this backend is meant to be used in a dev environment
- # and not in production since it prevents Authelia to be scaled to
- # more than one instance. The options under password_options have sane
- # defaults, and as it has security implications it is highly recommended
- # you leave the default values. Before considering changing these settings
- # please read the docs page below:
- # https://docs.authelia.com/configuration/authentication/file.html#password-hash-algorithm-tuning
- #
- ## file:
- ## path: ./users_database.yml
- file:
- path: /etc/authelia/users.yml
- password_options:
- algorithm: argon2id
- iterations: 1
- key_length: 32
- salt_length: 16
- memory: 1024
- parallelism: 8
-
-
-# Access Control
-#
-# Access control is a list of rules defining the authorizations applied for one
-# resource to users or group of users.
-#
-# If 'access_control' is not defined, ACL rules are disabled and the 'bypass'
-# rule is applied, i.e., access is allowed to anyone. Otherwise restrictions follow
-# the rules defined.
-#
-# Note: One can use the wildcard * to match any subdomain.
-# It must stand at the beginning of the pattern. (example: *.mydomain.com)
-#
-# Note: You must put patterns containing wildcards between simple quotes for the YAML
-# to be syntactically correct.
-#
-# Definition: A 'rule' is an object with the following keys: 'domain', 'subject',
-# 'policy' and 'resources'.
-#
-# - 'domain' defines which domain or set of domains the rule applies to.
-#
-# - 'subject' defines the subject to apply authorizations to. This parameter is
-# optional and matching any user if not provided. If provided, the parameter
-# represents either a user or a group. It should be of the form 'user:<username>'
-# or 'group:<groupname>'.
-#
-# - 'policy' is the policy to apply to resources. It must be either 'bypass',
-# 'one_factor', 'two_factor' or 'deny'.
-#
-# - 'resources' is a list of regular expressions that matches a set of resources to
-# apply the policy to. This parameter is optional and matches any resource if not
-# provided.
-#
-# Note: the order of the rules is important. The first policy matching
-# (domain, resource, subject) applies.
-access_control:
- # Default policy can either be 'bypass', 'one_factor', 'two_factor' or 'deny'.
- # It is the policy applied to any resource if there is no policy to be applied
- # to the user.
- default_policy: bypass
-
- rules:
- # The login portal is freely accessible (redirectino loop otherwise)
- - domain: auth.example.org
- policy: bypass
-
- # Apollo needs to be authenticated
- - domain: localhost
- resources:
- - "^/apollo/.*$"
- policy: one_factor
-
- # traefik dashboard is restricted to a group from ldap
- - domain: localhost
- resources:
- - "^/traefik/.*$"
- policy: one_factor
- subject: "group:ldap_admin"
- - domain: localhost
- resources:
- - "^/traefik/.*$"
- policy: deny
-
- # All galaxies are restricted to a group from ldap
- - domain: localhost
- resources:
- - "^/sp/.+/galaxy/.*$"
- policy: one_factor
- subject: "group:ldap_admin"
- - domain: localhost
- resources:
- - "^/sp/.+/galaxy$"
- policy: deny
-
- # A genome restricted to an ldap group
- - domain: localhost
- resources:
- - "^/sp/genus_species/.*$"
- policy: one_factor
- subject: "group:gspecies"
- - domain: localhost
- resources:
- - "^/sp/genus_species/.*$"
- policy: deny
-
-
-# Configuration of session cookies
-#
-# The session cookies identify the user once logged in.
-session:
- # The name of the session cookie. (default: authelia_session).
- name: authelia_bipaa_session
-
- # The secret to encrypt the session data. This is only used with Redis.
- # This secret can also be set using the env variables AUTHELIA_SESSION_SECRET
- secret: WXXXXXXXXXXXXXXXXXXXcXXXXXXXXXXXXXX
-
- # The time in seconds before the cookie expires and session is reset.
- expiration: 3600000 # 1000 hour
-
- # The inactivity time in seconds before the session is reset.
- # abretaud: We get an Unauthorized message when reaching this threshold => disabling by making > cookie lifetime
- inactivity: 3700000 # 5 minutes
-
- # The remember me duration.
- # Value of 0 disables remember me.
- # Value is in seconds, or duration notation. See: https://docs.authelia.com/configuration/index.html#duration-notation-format
- # Longer periods are considered less secure because a stolen cookie will last longer giving attackers more time to spy
- # or attack. Currently the default is 1M or 1 month.
- remember_me_duration: 1M
-
- # The domain to protect.
- # Note: the authenticator must also be in that domain. If empty, the cookie
- # is restricted to the subdomain of the issuer.
- domain: genouest.org
-
- # The redis connection details
- redis:
- host: authelia-redis
- port: 6379
- # This secret can also be set using the env variables AUTHELIA_SESSION_REDIS_PASSWORD
- #password: authelia
- # This is the Redis DB Index https://redis.io/commands/select (sometimes referred to as database number, DB, etc).
- #database_index: 0
-
-# Configuration of the authentication regulation mechanism.
-#
-# This mechanism prevents attackers from brute forcing the first factor.
-# It bans the user if too many attempts are done in a short period of
-# time.
-regulation:
- # The number of failed login attempts before user is banned.
- # Set it to 0 to disable regulation.
- max_retries: 3
-
- # The time range during which the user can attempt login before being banned.
- # The user is banned if the authentication failed 'max_retries' times in a 'find_time' seconds window.
- # Find Time accepts duration notation. See: https://docs.authelia.com/configuration/index.html#duration-notation-format
- find_time: 2m
-
- # The length of time before a banned user can login again.
- # Ban Time accepts duration notation. See: https://docs.authelia.com/configuration/index.html#duration-notation-format
- ban_time: 5m
-
-# Configuration of the storage backend used to store data and secrets.
-#
-# You must use only an available configuration: local, mysql, postgres
-storage:
- postgres:
- host: authelia-db
- port: 5432
- database: postgres
- username: postgres
- # # This secret can also be set using the env variables AUTHELIA_STORAGE_POSTGRES_PASSWORD
- password: XXXXXXXX
-
-# Configuration of the notification system.
-#
-# Notifications are sent to users when they require a password reset, a u2f
-# registration or a TOTP registration.
-# Use only an available configuration: filesystem, gmail
-notifier:
- # For testing purpose, notifications can be sent in a file
- ## filesystem:
- ## filename: /tmp/authelia/notification.txt
-
- # Use a SMTP server for sending notifications. Authelia uses PLAIN or LOGIN method to authenticate.
- # [Security] By default Authelia will:
- # - force all SMTP connections over TLS including unauthenticated connections
- # - use the disable_require_tls boolean value to disable this requirement (only works for unauthenticated connections)
- # - validate the SMTP server x509 certificate during the TLS handshake against the hosts trusted certificates
- # - trusted_cert option:
- # - this is a string value, that may specify the path of a PEM format cert, it is completely optional
- # - if it is not set, a blank string, or an invalid path; will still trust the host machine/containers cert store
- # - defaults to the host machine (or docker container's) trusted certificate chain for validation
- # - use the trusted_cert string value to specify the path of a PEM format public cert to trust in addition to the hosts trusted certificates
- # - use the disable_verify_cert boolean value to disable the validation (prefer the trusted_cert option as it's more secure)
- smtp:
- #username: test
- # This secret can also be set using the env variables AUTHELIA_NOTIFIER_SMTP_PASSWORD
- #password: password
- #secure: false
- host: smtp-server-hostname
- port: 25
- disable_require_tls: true
- sender: bipaa@inrae.fr
-
- # Sending an email using a Gmail account is as simple as the next section.
- # You need to create an app password by following: https://support.google.com/accounts/answer/185833?hl=en
- ## smtp:
- ## username: myaccount@gmail.com
- ## # This secret can also be set using the env variables AUTHELIA_NOTIFIER_SMTP_PASSWORD
- ## password: yourapppassword
- ## sender: admin@example.com
- ## host: smtp.gmail.com
- ## port: 587
diff --git a/examples/config b/examples/config
deleted file mode 100644
index 527f310..0000000
--- a/examples/config
+++ /dev/null
@@ -1,21 +0,0 @@
-# This is the configuration file used by the gga_init.py, gga_load_data.py and run_workflow.py scripts
-# It contains (sensible) variables to set up different docker services
-
-# "all" section contains variables used by several services at once or the paths to import sensible files that cannot be procedurally generated/formatted using the scripts
-all:
- custom_host: localhost # The hosting machine name
- custom_authelia_config_path: /path/to/your/authelia/config # The path to the authelia config yml to use, an example is available in the "examples" folder at the repo root
-# "galaxy" section contains variables used to set up the galaxy service
-galaxy:
- custom_galaxy_default_admin_email: admin@galaxy.org # The default admin email (used to connect to the instance)
- custom_galaxy_defaut_admin_user: admin # The default admin user
- custom_galaxy_default_admin_password: password # The default admin password (used to connect to the instance)
- custom_galaxy_config_master_api_key: master # The master API key (not in use at the moment so you can skip this)
- custom_galaxy_tripal_password: galaxy_tripal_password # Same as custom_tripal_admin_password (connection to db relies on this)
- custom_galaxy_web_apollo_user: admin_apollo@galaxy.org # Apollo user
- custom_galaxy_web_apollo_password: galaxy_apollo_password # Apollo password tied to the user above
-tripal:
- custom_tripal_admin_password: galaxy_tripal_password # Same as custom_galay_tripal_password (connection to db relies on this)
- custom_banner: /path/to/banner # Custom banner, TODO: defaults to a generic banner
- custom_theme: "abims_gga" # Use this to use another theme
- custom_theme_git_clone: "http://gitlab.sb-roscoff.fr/abims/e-infra/tripal_gga.git" # Use this to install another theme than the default one
\ No newline at end of file
diff --git a/examples/config_demo.yaml b/examples/config_demo.yaml
deleted file mode 100644
index 3023e86..0000000
--- a/examples/config_demo.yaml
+++ /dev/null
@@ -1,21 +0,0 @@
-# This is the configuration file used by the gga_init.py, gga_load_data.py and run_workflow.py scripts
-# It contains (sensible) variables to set up different docker services
-
-# "all" section contains variables used by several services at once or the paths to import sensible files that cannot be procedurally generated/formatted using the scripts
-all:
- custom_host: localhost # The hosting machine name
- custom_authelia_config_path: /path/to/your/authelia/config # The path to the authelia config yml to use, an example is available in the "examples" folder at the repo root
-# "galaxy" section contains variables used to set up the galaxy service
-galaxy:
- custom_galaxy_default_admin_email: admin@galaxy.org # The default admin email (used to connect to the instance)
- custom_galaxy_defaut_admin_user: admin # The default admin user
- custom_galaxy_default_admin_password: password # The default admin password (used to connect to the instance)
- custom_galaxy_config_master_api_key: master # The master API key (not in use at the moment so you can skip this)
- custom_galaxy_tripal_password: galaxy_tripal_password # Same as custom_tripal_admin_password (connection to db relies on this)
- custom_galaxy_web_apollo_user: admin_apollo@galaxy.org # OPTIONAL - Apollo user
- custom_galaxy_web_apollo_password: galaxy_apollo_password # MANDATORY - Apollo password tied to the user above
-tripal:
- custom_tripal_admin_password: galaxy_tripal_password # MANDATORY - Same as custom_galay_tripal_password (connection to db relies on this)
- custom_banner: /path/to/banner # OPTIONAL - Custom banner
- custom_theme: "abims_gga" # OPTIONAL - Use this to use another theme
- custom_theme_git_clone: "http://gitlab.sb-roscoff.fr/abims/e-infra/tripal_gga.git" # OPTIONAL - Use this to install another theme than the default one
\ No newline at end of file
diff --git a/examples/example.yml b/examples/example.yml
deleted file mode 100644
index e718673..0000000
--- a/examples/example.yml
+++ /dev/null
@@ -1,68 +0,0 @@
-# Input file for the automated creation GGA docker stacks
-# The file consists in a "list" of species for which the script will have to create these stacks/load data into galaxy/run workflows
-# This file is internally turned into a list of dictionaries by the scripts
-
-ectocarpus_sp2_male: # Dummy value the user gives to designate the species (isn't used by the script)
- description:
- # Species description, leave blank if unknown or you don't want it to be used
- # These parameters are used to set up the various urls and adresses in different containers
- # The script requires at least the genus to be specified
- genus: "ectocarpus" # Mandatory!
- species: "sp2" # # Mandatory!
- sex: "male"
- strain: ""
- common_name: ""
- origin: ""
- # the sex and strain, the script will look for files containing the genus, species, sex and strain of the species)
- # If no file corresponding to the description is found, this path will be considered empty and the script will
- # proceed to the next step (create the directory tree for the GGA docker stack)
- data:
- # Sequence of paths to the different datasets to copy and import into galaxy
- # Paths must be absolute paths
- genome_path: "/path/to/fasta" # Mandatory!
- transcripts_path: "/path/to/fasta" # Mandatory!
- proteins_path: "/path/to/fasta" # Mandatory!
- gff_path: "/path/to/gff" # Mandatory!
- interpro_path: "/path/to/interpro"
- orthofinder_path: "/path/to/orthofinder"
- blastp_path: "/path/to/blastx"
- blastx_path: "/path/to/blastp"
- # If the user has several datasets of the same 'nature' (gff, genomes, ...) to upload to galaxy, the next scalar is used by the script to differentiate
- # between these different versions and name directories according to it and not overwrite the existing data
- # If left empty, the genome will be considered version "1.0"
- genome_version: "1.0"
- # Same as genome version, but for the OGS analysis
- ogs_version: ""
- performed_by: ""
- services:
- # Describe what optional services to deploy for the stack
- # By default, only tripal, tripaldb and galaxy services will be deployed
- blast: "False"
- wiki: "False"
- apollo: "False"
-
-# Second example without the explanation
-ectocarpus_sp2_female:
- description:
- genus: "ectocarpus"
- species: "sp2"
- sex: "female"
- strain: ""
- common_name: ""
- origin: ""
- data:
- genome_path: "/path/to/fasta"
- transcripts_path: "/path/to/fasta"
- proteins_path: "/path/to/fasta"
- gff_path: "/path/to/gff"
- interpro_path: "/path/to/interpro"
- orthofinder_path: "/path/to/orthofinder"
- blastp_path: "/path/to/blastx"
- blastx_path: "/path/to/blastp"
- genome_version: "1.0"
- ogs_version: "1.0"
- performed_by: ""
- services:
- blast: "False"
- wiki: "False"
- apollo: "False"
\ No newline at end of file
diff --git a/examples/input_demo.yaml b/examples/input_demo.yaml
deleted file mode 100644
index 79aaaa4..0000000
--- a/examples/input_demo.yaml
+++ /dev/null
@@ -1,41 +0,0 @@
-# Input file for the automated creation GGA docker stacks
-# The file consists in a "list" of species for which the script will have to create these stacks/load data into galaxy/run workflows
-
-ectocarpus_sp2_male: # Dummy value the user gives to designate the species (isn't used by the script)
- # Species description, leave blank if unknown or you don't want it to be used
- # These parameters are used to set up the various urls and adresses in different containers
- # The script requires at least the genus to be specified
- description:
- genus: "ectocarpus" # Mandatory!
- species: "sp4"
- sex: "male"
- strain: ""
- common_name: ""
- origin: ""
- # Data files scalars contain paths to the source files that have to be loaded into galaxy
- # WARNING: The paths must be absolute paths!
- # If any path is left blank and the "parent_directory" scalar is specified, this directory and ALL its subdirectories will be
- # scanned for files corresponding to the description provided for the species (i.e if the user specified
- # the sex and strain, the script will look for files containing the genus, species, sex and strain of the species)
- # If no file corresponding to the description is found, this path will be considered empty and the script will
- # proceed to the next step (create the directory tree for the GGA docker stack)
- # If a path is left blank and the "parent_directory" scalar is also blank, no file will be loaded for this "path" scalar
- # If the files are not named using this nomenclature, please provide all the paths in the corresponding scalars below
- data:
- # "parent_directory": (optional) directory from where to search files if a "***_path" scalar is empty
- # NOTE: Try to set a parent directory "close" to the data files so as not to increase runtime
- # If empty (""), the script will not search for files and no dataset will be loaded for the corresponding scalar
- parent_directory: "/path/to/closest/parent/dir"
- # "***_path": path to the file (optional if parent_directory is set and species "description" scalars are precised)
- # TODO Not implemented yet
- genome_path: "/path/to/fasta"
- transcripts_path: "/path/to/fasta"
- proteins_path: "/path/to/fasta"
- gff_path: "/path/to/gff"
- # If the user has several genomes to upload to galaxy, the next scalar is used by the script to differentiate
- # between these different versions and name directories according to it.
- # If left empty, the genome will be considered version "1.0"
- genome_version: "1.0"
- # Same as genome version, but for the analysis
- ogs_version: ""
- performed_by: ""
\ No newline at end of file
diff --git a/utils/__init__.py b/utils/__init__.py
deleted file mode 100755
index e69de29..0000000
diff --git a/utils/blastdb.py b/utils/blastdb.py
deleted file mode 100755
index 2794ccb..0000000
--- a/utils/blastdb.py
+++ /dev/null
@@ -1,298 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
-
-import argparse
-import collections
-import json
-import logging as log
-import os
-import sys
-
-from shutil import copyfile
-from subprocess import call
-
-
-class BlastBank:
-
- def __init__(self, raw_org, data_dir_root, rel_path, fasta_file_name, db_dir_root, seq_type, path, is_multi):
- self.raw_org = raw_org
- self.org = prettify(raw_org)
- self.data_dir_root = data_dir_root
- self.rel_path = rel_path
- self.fasta_file_name = fasta_file_name
- self.db_dir_root = db_dir_root
- self.seq_type = seq_type
- self.path = path # http://bipaa.genouest.org/sp/xxx/ Can be the same as raw_org, or something else when having multiple genomes.
- self.is_multi = is_multi
-
- self.fasta = os.path.join(data_dir_root, rel_path, fasta_file_name)
- self.dest_path = os.path.splitext(os.path.join(db_dir_root, self.path, rel_path, fasta_file_name))[0]
- self.title = sanitize(rel_path + '_' + os.path.splitext(self.fasta_file_name)[0])
- if self.is_multi:
- fake_path = rel_path.split('/')
- if len(fake_path) > 2:
- fake_path = [fake_path[1]] + [fake_path[0]] + fake_path[2:]
- fake_path = '/'.join(fake_path)
- self.pretty_name = prettify(fake_path, True)
- else:
- self.pretty_name = self.org + ' ' + prettify(rel_path, False)
-
- with open(self.fasta, 'r') as f:
- self.first_id = f.readline()[1:].rstrip()
-
- if self.seq_type == 'nucl':
- if 'transcript' in self.fasta_file_name.lower() or 'cdna' in self.fasta_file_name.lower():
- self.pretty_name += " transcripts"
- elif 'cds' in self.fasta_file_name.lower():
- self.pretty_name += " CDS"
- else:
- if 'protein' in self.fasta_file_name.lower() or 'pep' in self.fasta_file_name.lower() or 'proteome' in self.fasta_file_name.lower() or self.fasta_file_name.endswith('.faa'):
- self.pretty_name += " proteins"
-
- # Just a stupid/hacky string used for sorting bank list
- self.sort_key = 'a_' if 'genome' in self.title else 'b_'
- self.sort_key += self.pretty_name
-
- def __str__(self):
- return str({
- 'raw_org': self.raw_org,
- 'org': self.org,
- 'data_dir_root': self.data_dir_root,
- 'rel_path': self.rel_path,
- 'fasta_file_name': self.fasta_file_name,
- 'db_dir_root': self.db_dir_root,
- 'seq_type': self.seq_type,
- 'path': self.path,
- 'fasta': self.fasta,
- 'dest_path': self.dest_path,
- 'title': self.title,
- 'pretty_name': self.pretty_name,
- })
-
-
-def main(args):
-
- genome_path = os.path.basename(os.getcwd())
- if not args.multi_org:
- genome_name = genome_path
- data_dir_root = os.path.abspath(os.path.join('src_data'))
- if not os.path.isdir(data_dir_root):
- raise Exception("Could not find data dir: %s" % data_dir_root)
-
- db_dir_root = os.path.abspath(args.dest)
-
- ignore_list = ['func_annot', "apollo_source"]
- if args.ignore:
- ignore_list += args.ignore
-
- # Looking for files
- log.info("Looking for fasta files in %s:" % data_dir_root)
- banks = []
- for root, dirs, files in os.walk(data_dir_root, followlinks=True):
- file_list = [os.path.realpath(os.path.join(root, filename)) for filename in files]
- rel_path = root[len(data_dir_root) + 1:]
-
- skip_current = False
- for ign in ignore_list:
- if ign in rel_path:
- skip_current = True
-
- if not skip_current: # skip useless data
- for f in file_list:
- f = os.path.basename(f)
- if f.endswith('.fasta') or f.endswith('.fa') or f.endswith('.fna') or f.endswith('.faa'):
- if args.multi_org:
- genome_name = rel_path.split('/')[1]
-
- if 'protein' in f or 'pep.' in f or 'proteome' in f or f.endswith('.faa'):
- seq_type = 'prot'
- else:
- seq_type = 'nucl'
- new_bank = BlastBank(genome_name, data_dir_root, rel_path, f, db_dir_root, seq_type, genome_path, args.multi_org)
- log.info("Found '%s' of type: %s" % (new_bank.fasta, new_bank.seq_type))
- banks.append(new_bank)
-
- if not banks:
- log.info("No fasta file found.")
- else:
- for b in banks:
- makeblastdb(b, args.dry_run, args.no_parse_seqids)
-
- nuc_list = collections.OrderedDict()
- prot_list = collections.OrderedDict()
- banks.sort(key=lambda x: x.sort_key)
- for b in banks:
- if b.seq_type == 'nucl':
- if b.pretty_name not in nuc_list:
- nuc_list[b.dest_path] = b.pretty_name
- else:
- nuc_list[b.dest_path] = "%s (%s)" % (b.pretty_name, b.fasta_file_name)
- else:
- if b.pretty_name not in prot_list:
- prot_list[b.dest_path] = b.pretty_name
- else:
- prot_list[b.dest_path] = "%s (%s)" % (b.pretty_name, b.fasta_file_name)
-
- yml_dir = os.path.abspath('blast')
- yml_file_path = os.path.abspath(os.path.join(yml_dir, 'banks.yml'))
- links_file_path = os.path.abspath(os.path.join(yml_dir, 'links.yml'))
- if not args.dry_run:
-
- log.info("List of bank names (to use in links.yml):")
- write_titles(banks)
-
- log.info("Writing bank list in '%s'" % yml_file_path)
- if not os.path.exists(yml_dir):
- os.makedirs(yml_dir, mode=0o755)
- yml_file = open(yml_file_path, 'w')
- write_yml(yml_file, nuc_list, prot_list)
-
- log.info("Writing automatic links to links.yml in '%s'" % links_file_path)
- if os.path.exists(links_file_path):
- log.info("Making backup of previous links.yml to '%s'" % (links_file_path + '.back'))
- copyfile(links_file_path, links_file_path + '.back')
- links_yml_file = open(links_file_path, 'w')
- write_links_yml(links_yml_file, banks, args.apollo)
-
- else:
- log.info("List of bank names (to use in links.yml):")
- write_titles(banks)
- log.info("Would write bank list in '%s'" % yml_file_path)
- write_yml(sys.stdout, nuc_list, prot_list)
- log.info("Would write links.yml in '%s'" % links_file_path)
- write_links_yml(sys.stdout, banks, args.apollo)
-
-
-def write_yml(yml_file, nuc_list, prot_list):
-
- nuc = "~"
- prot = "~"
-
- if nuc_list:
- nuc = "\n ".join(['%s: %s' % (json.dumps(k), json.dumps(v)) for k, v in nuc_list.items()])
- if prot_list:
- prot = "\n ".join(['%s: %s' % (json.dumps(k), json.dumps(v)) for k, v in prot_list.items()])
-
- print("genouest_blast:", file=yml_file)
- print(" db_provider:", file=yml_file)
- print(" list:", file=yml_file)
- print(" nucleic:", file=yml_file)
- print(" %s" % nuc, file=yml_file)
- print(" proteic:", file=yml_file)
- print(" %s" % prot, file=yml_file)
-
-
-def write_links_yml(yml_file, banks, apollo):
-
- for bank in banks:
- print("", file=yml_file)
- print("# %s" % (bank.pretty_name), file=yml_file)
-
- link = ''
- if bank.seq_type == 'prot':
- spl = bank.org.split()
- if len(spl) > 2:
- sp_str = '/'.join(spl[:2])
- sp_str += '-' + '-'.join(spl[2:])
- else:
- sp_str = '/'.join(spl)
- link = 'http://abims-gga.sb-roscoff.fr/sp/%s/feature/%s/polypeptide/{id}' % (bank.path, sp_str)
- elif 'genome' in bank.title:
- dataset_id = bank.org.lower()
- spl = dataset_id.split()
- if len(spl) == 2: # Genus species => gspecies
- dataset_id = spl[0][:1] + spl[1]
- elif len(spl) == 3: # Genus species strain1 => gsstrain1
- dataset_id = spl[0][:1] + spl[1][:1] + spl[2]
- else: # Genus species some garbage => genus_species_some_garbage
- dataset_id = dataset_id.replace(' ', '_')
- if apollo:
- link = '<a href="http://abims-gga.sb-roscoff.fr/sp/' + bank.path + '/jbrowse/?data=data%2F' + dataset_id + '&loc={id}{jbrowse_track}">{id}</a> <a href="http://abims-gga.sb-roscoff.fr/sp/' + bank.path + '/apollo/annotator/loadLink?loc={id}:1{apollo_track}">Apollo</a>'
- else:
- link = '<a href="http://abims-gga.sb-roscoff.fr/sp/' + bank.path + '/jbrowse/?data=data%2F' + dataset_id + '&loc={id}{jbrowse_track}">{id}</a>'
- else:
- spl = bank.org.split()
- if len(spl) > 2:
- sp_str = '/'.join(spl[:2])
- sp_str += '-' + '-'.join(spl[2:])
- else:
- sp_str = '/'.join(spl)
- link = 'http://abims-gga.sb-roscoff.fr/sp/%s/feature/%s/mRNA/{id}' % (bank.path, sp_str)
-
- if link:
- print("%s:" % (bank.title), file=yml_file)
- print(" db: '%s'" % (bank.title), file=yml_file)
- print(" '*': '%s'" % (link), file=yml_file)
- else:
- print("# Skipped", file=yml_file)
-
-
-def write_titles(banks):
-
- for bank in banks:
- print("'%s' -> '%s' [%s]" % (bank.pretty_name, bank.title, bank.first_id))
-
-
-def makeblastdb(bank, dry_run, no_parse_seqids):
- log.info("Formatting bank: %s ---> %s" % (bank.fasta, bank.dest_path))
- dest_dir = os.path.realpath(os.path.join(bank.dest_path, '..'))
- if not os.path.exists(dest_dir):
- log.info("Creating folder: %s" % dest_dir)
- if not dry_run:
- os.makedirs(dest_dir, mode=0o755)
- parse = "-parse_seqids"
- if no_parse_seqids:
- parse = ""
- cmd = "makeblastdb -in '%s' -dbtype '%s' %s -out '%s' -title '%s'" % (bank.fasta, bank.seq_type, parse, bank.dest_path, bank.title)
- log.info("Running: %s" % cmd)
- if not dry_run:
- try:
- retcode = call(cmd, shell=True)
- if retcode != 0:
- raise RuntimeError("Child was terminated by signal " + str(retcode))
- except OSError as e:
- print("Execution failed:" + e, file=sys.stderr)
- sys.exit(1)
-
-
-def prettify(name, capital=True):
- name = name.replace('_', ' ')
- name = name.replace('/', ' ')
- if capital:
- name = name[0].upper() + name[1:]
-
- return name
-
-
-def sanitize(name):
- name = name.lower()
- name = name.replace(' ', '_')
- name = name.replace('/', '_')
-
- return name
-
-
-if __name__ == '__main__':
- parser = argparse.ArgumentParser(
- description='Generate blast databanks and update blast forms.'
- )
- parser.add_argument("-v", "--verbose", help="Increase output verbosity.",
- action="store_true")
- parser.add_argument("-d", "--dry-run", help="Dry run: no modification will be done, for testing purpose.",
- action="store_true")
- parser.add_argument("-m", "--multi-org", help="Add this flag if there are multiple organisms in src_data.",
- action="store_true")
- parser.add_argument("-a", "--apollo", help="Add this flag to generate links to apollo.",
- action="store_true")
- parser.add_argument("-p", "--no-parse-seqids", help="Don't use the makeblastdb -parse_seqids option (use this in case you have strange looking sequence ids that make html files unreadable)",
- action="store_true")
- parser.add_argument("--ignore", help='Files or directories to ignore', nargs='*')
- parser.add_argument("dest", help="Destination directory (not including the genome name, should be mounted on compute nodes)")
-
- args = parser.parse_args()
- log.basicConfig(level=log.INFO)
- if args.verbose:
- log.basicConfig(level=log.DEBUG)
-
- main(args)
diff --git a/utils/common-stringSubsitute.py b/utils/common-stringSubsitute.py
deleted file mode 100755
index c4d22a9..0000000
--- a/utils/common-stringSubsitute.py
+++ /dev/null
@@ -1,37 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-import argparse
-import os
-import re
-import sys
-
-# Return the file obtained by replacing the occurrences of pattern by the replacement string.
-#Â Use of python method re.sub()
-# python common-stringSubsitute.py -f file -p pattern -r replacement_string
-# ex : python common-stringSubsitute.py -f file -p '(tRNA)(\w{3})(\w{3})' -r '\g<1>-\g<2>(\g<3>)'
-
-if __name__ == '__main__':
-
- #Get arguments
- parser = argparse.ArgumentParser(description="Return the file obtained by replacing the occurrences of pattern by the replacement string. Use of python method re.sub(). Example: python common-stringSubsitute.py -f file -p '(tRNA)(\w{3})(\w{3})' -r '\g<1>-\g<2>(\g<3>)'")
- parser.add_argument('-i','--infile', help='Input file', required=True)
- parser.add_argument('-o','--outfile', help='Output file', default='outfile')
- parser.add_argument('-p','--pattern', help='Pattern string to be replaced', required=True)
- parser.add_argument('-r','--repl', help='Replacement string', required=True)
- args = parser.parse_args()
-
- infilename=args.infile
- outfilename=args.outfile
- pattern=args.pattern
- repl=args.repl
-
- infile=open(infilename,'r')
- outfile=open(outfilename,'w')
-
- lines=infile.readlines()
-
- for line in lines :
- line_out=re.sub(pattern,repl,line)
- outfile.write(line_out)
-
- outfile.close()
\ No newline at end of file
diff --git a/utils/docker_compose_generator.py b/utils/docker_compose_generator.py
deleted file mode 100755
index 30747b1..0000000
--- a/utils/docker_compose_generator.py
+++ /dev/null
@@ -1,73 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-import os
-import argparse
-import logging
-# import yaml
-# import ruamel.yaml
-# import json
-
-"""
-docker-compose_generator.py
-
-This method will write a formatted docker-compose.yml for the specified organism (only requires genus and species)
-"""
-
-
-class DockerComposeGenerator:
-
- def __init__(self):
- self.mode = None
- self.genus = None
- self.species = None
- self.organism_template = None
- self.traefik_template = None
- self.outdir = None
-
- def generate(self):
- if self.organism_template is None:
- self.organism_template = str(os.getcwd() + "/templates/gspecies_compose_template.yml")
- else:
- with open(self.organism_template, 'r') as infile:
- organism_content = list()
- for line in infile:
- # Replace placeholders by the genus and species
- organism_content.append(line.replace("genus_species", str(self.genus.lower() + "_" + self.species)).replace("Genus species", str(self.genus + " " + self.species)).replace("Genus/species", str(self.genus + "/" + self.species)).replace("gspecies", str(self.genus.lower()[0] + self.species)))
- self.write_yml(content=organism_content)
-
- if self.traefik_template is None:
- self.traefik_template = str(os.getcwd() + "/templates/gspecies_compose_template.yml")
- else:
- with open(self.traefik_template, 'r') as infile:
- traefik_content = list()
- for line in infile:
- # Replace placeholders by the genus and species
- traefik_content.append(line.replace("genus_species", str(self.genus.lower() + "_" + self.species)).replace("Genus species", str(self.genus + " " + self.species)).replace("Genus/species", str(self.genus + "/" + self.species)).replace("gspecies", str(self.genus.lower()[0] + self.species)))
- self.write_yml(content=traefik_content)
-
- def write_yml(self, content):
- with open(self.outdir + "/docker-compose.yml", 'w') as outfile:
- for line in content:
- outfile.write(line)
-
-
-if __name__ == "__main__":
- parser = argparse.ArgumentParser(description="Generator of docker-compose.yml for GGA automated integration "
- "following the templates available @ "
- "https://gitlab.inria.fr/abretaud/genodock_demo/")
- parser.add_argument("-g", "--genus", type=str, help="input genus")
- parser.add_argument("-s", "--species", type=str, help="input species")
- parser.add_argument("-o", "--organism-template", type=str, help="input organism template docker-compose.yml (compose or stack), optional")
- parser.add_argument("-t", "--traefik-template", type=str, help="input organism template docker-compose.yml (compose or stack), optional")
- parser.add_argument("-m", "--main-dir", type=str, help="where to write the output traefik docker-compose.yml (defaults to cd, autoload places it in main directory)")
- parser.add_argument("-d", "--organism-dir", type=str, help="where to write the output organism docker-compose.yml (defaults to cd, autoload places it in organism directory)")
- args = parser.parse_args()
-
- dc_generator = DockerComposeGenerator()
- dc_generator.genus = args.genus
- dc_generator.species = args.species
- if args.template:
- dc_generator.template = args.template
- dc_generator.outdir = args.outdir
- dc_generator.generate()
diff --git a/utils/metadata_generator.py b/utils/metadata_generator.py
deleted file mode 100755
index c03ff0c..0000000
--- a/utils/metadata_generator.py
+++ /dev/null
@@ -1,36 +0,0 @@
-import os
-import logging
-import yaml
-
-"""
-Metadata generator for gga_auto_load
-
-Creates a file that summarizes actions taken by the autoload script (e.g what was done in the dedicated galaxy instance)
-This organism metadata file is located in the metadata directory of the organism directory (i.e /genus_species/metadata)
-By default, will also create/update a general metadata file (located in the parent directory i.e where all the organisms
-directories are located)
-
-TODO: move inside autoload
-
-Metadata format: .yml
-"""
-
-
-class MetadataGenerator:
-
- def __init__(self, maindir):
- self.maindir = maindir
- self.genus = None
- self.species = None
- self.metadata = None
- self.do_update = False
- self.date = "01/01/2020"
-
-
- # def read_metadata(self):
- # for label, content in metadata.items():
- # print("FOO")
-
- def write_metadata(self):
- with open(self.maindir + "/main_metadata.yml", "a") as metadata:
- metadata.write("\n\nAdded " + self.genus + " " + self.species + "")
\ No newline at end of file
diff --git a/utils/phaeoexplorer-change_pep_fasta_header.sh b/utils/phaeoexplorer-change_pep_fasta_header.sh
deleted file mode 100755
index 3cf614f..0000000
--- a/utils/phaeoexplorer-change_pep_fasta_header.sh
+++ /dev/null
@@ -1,17 +0,0 @@
-#!/usr/bin/env bash
-
-INFILE=$1
-OUTFILE=tmpfile
-
-FILE_HEADER_START=$(grep ">" $INFILE | cut -c 1-6 | sort | uniq)
-HEADER_START_STRING=">mRNA."
-
-if [[ "$FILE_HEADER_START" == "$HEADER_START_STRING" ]]
-then
- /usr/local/genome2/mmo/scripts/common/common-stringSubstitute.py -i $INFILE -o $OUTFILE -p '^>mRNA' -r '>protein'
- mv $OUTFILE $INFILE
- echo "'>mRNA' replaced by '>protein'"
-else
- echo "Abort. Not all headers start with '>mRNA.':"
- echo "$FILE_HEADER_START"
-fi
\ No newline at end of file
diff --git a/utils/phaeoexplorer-change_transcript_fasta_header.sh b/utils/phaeoexplorer-change_transcript_fasta_header.sh
deleted file mode 100755
index 99bd3ff..0000000
--- a/utils/phaeoexplorer-change_transcript_fasta_header.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/usr/bin/env bash
-INFILE=$1
-OUTFILE=tmpfile
-./common-stringSubsitute.py -i $INFILE -o $OUTFILE -p '^>\d+ mRNA' -r '>mRNA' || mv $OUTFILE $INFILE || echo "'>[0-9]+ mRNA' replaced by '>mRNA' in $1"
\ No newline at end of file
diff --git a/utils/phaeoexplorer-change_transcript_fasta_header.sh.bak b/utils/phaeoexplorer-change_transcript_fasta_header.sh.bak
deleted file mode 100755
index 12ce4e5..0000000
--- a/utils/phaeoexplorer-change_transcript_fasta_header.sh.bak
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/usr/bin/env bash
-
-INFILE=$1
-OUTFILE=tmpfile
-/home/fr2424/sib/alebars/gga_load_data/ext_scripts/common-stringSubsitute.py -i $INFILE -o $OUTFILE -p '^>\d+ mRNA' -r '>mRNA'
-mv $OUTFILE $INFILE
-echo "'>[0-9]+ mRNA' replaced by '>mRNA' in $1"
diff --git a/utils/phaeoexplorer_ec32_orthologs_transfer.py b/utils/phaeoexplorer_ec32_orthologs_transfer.py
deleted file mode 100644
index 20e6750..0000000
--- a/utils/phaeoexplorer_ec32_orthologs_transfer.py
+++ /dev/null
@@ -1,96 +0,0 @@
-#!/usr/bin/python
-# -*- coding: utf-8 -*-
-
-import sys
-import os
-import argparse
-import pickle
-import logging
-
-def orthologs_transfer(manual_annotation_file, orthofinder_file, gff_file, outdir):
- """
- Transfer of description between a manual annotation file and a gff file, using an orthofinder output file
- to find the corresponding IDs between the two files
-
- :param manual_annotation_file:
- :param orthofinder_file:
- :param gff_file:
- :param outdir:
- :return:
- """
-
- manual_annotations_dict, orthofinder_dict, gff_dict = {}, {}, {}
- species_filename = ""
-
- with open(orthofinder_file, 'r') as orthofinder:
- next(orthofinder) # Skip header
- # Mapping orthofinder's IDs to manual annotation's description
- logging.info("Mapping Orthofinder's IDs to manual annotation's IDs...")
- for orthofiner_line in orthofinder:
- orthofiner_line_split = orthofiner_line.rstrip().split("\t")
- orthofinder_dict[orthofiner_line_split[1].split(" ")[0]] = orthofiner_line_split[2].split(" ")[0]
-
-
- with open(manual_annotation_file, 'r') as manual_annotation:
- # Mapping orthofinder's IDs to manual annotation's description
- logging.info("Mapping Orthofinder's IDs to descriptions...")
- next(manual_annotation) # Skip header
- for manual_annotation_line in manual_annotation:
- manual_annotation_line_split = manual_annotation_line.rstrip().split("\t")
- manual_annotations_dict[manual_annotation_line_split[0]] = ";".join([manual_annotation_line_split[0], manual_annotation_line_split[6]])
-
- # Opening GFF, appending manual annotation's description to matching IDs
- logging.info("Transferring manual descriptions to the GFF file...")
- output_filename = str(os.path.join(os.path.abspath(outdir), os.path.basename(gff_file).split(".")[0]) + "_TRANSFERED.gff")
-
- with open(output_filename, 'a') as output_file:
- output_file.truncate(0) # Erase previous file content
- with open(gff_file, 'r') as gff:
- for gff_line in gff:
- if "ID=mRNA" in gff_line: # Look for mRNA items
- gff_line_id = gff_line.split("\t")[8].split("=")[1].split(";")[0] # GFF file ID (matches manual annotation IDs)
- if gff_line_id in orthofinder_dict.keys(): # The gff ID is supposed to match a unique ID (key) in the orthofinder file
- try:
- manual_annotation_value = orthofinder_dict[gff_line_id] # Find the corresponding manual annotation to transfer
- gff_line = "{0};ec32_ortholog={1};ec32_ortholog_description={2}\n".format(gff_line.strip(), orthofinder_dict[gff_line_id], manual_annotation_value)
- except KeyError: # Just in case some values are missing in the manual annotation file (optional, can be removed, it will then exit instead)
- continue
- output_file.write(gff_line)
- logging.info("Finished transferring descriptions for %s" % str(os.path.basename(gff_file)))
-
-
-if __name__ == "__main__":
-
- parser = argparse.ArgumentParser(description="Orthologs_transfer between a reference manual annotation and Orthofinder outputs. \
- \n\nRun example: python3 ec32_orthologs_transfer.py -d /path/to/desired/dir/ -o orthofinder_file.tsv \
- -g gff_file.gff -m manual_annotation_file.txt")
- parser.add_argument("-o", "--orthofinder",
- help="Orthofinder output (tabulated)")
- parser.add_argument("-m", "--manual-annotation",
- help="Manual annotation file (tabulated) or pickle file containing the dicionary (automatically generated when you input a new manual annotation file)")
- parser.add_argument("-g", "--gff",
- help="GFF input file (tabulated)")
- parser.add_argument("-d", "--out-dir",
- help="Output directory")
- args = parser.parse_args()
-
- # WARNING for shell use case:
- # The script doesn't check if the inout files are valid.
- # Files must be put in this order: $1=orthofinder file, $2=manual annotation file, $3=GFF file, $4=optional output directory)
-
- if not args.manual_annotation:
- logging.info("Please input a manual annotation file or a pickled manual annotation dictionary")
- sys.exit()
- if not args.orthofinder:
- logging.info("Please input an orthofinder output file")
- sys.exit()
- if not args.gff:
- logging.info("Please input a gff file")
- sys.exit()
- if not args.out_dir:
- args.out = "."
-
- orthologs_transfer(manual_annotation_file=args.manual_annotation,
- orthofinder_file=args.orthofinder,
- gff_file=args.gff,
- outdir=args.out_dir)
diff --git a/utils/phaeoexplorer_hectar_transfer.py b/utils/phaeoexplorer_hectar_transfer.py
deleted file mode 100644
index ec9a62d..0000000
--- a/utils/phaeoexplorer_hectar_transfer.py
+++ /dev/null
@@ -1,95 +0,0 @@
-#!/usr/bin/python
-# -*- coding: utf-8 -*-
-
-import sys
-import os
-import argparse
-import logging
-
-def hectar_transfer(hectar_file, orthofinder_file, gff_file, outdir):
- """
- Transfer of description between a manual annotation file and a gff file, using an orthofinder output file
- to find the corresponding IDs between the two files
-
- :param hectar_file:
- :param orthofinder_file:
- :param gff_file:
- :param outdir:
- :return:
- """
-
- manual_annotations_dict, orthofinder_dict, gff_dict = {}, {}, {}
- species_filename = ""
-
- with open(orthofinder_file, 'r') as orthofinder:
- next(orthofinder) # Skip header
- # Mapping orthofinder's IDs to hectar IDs
- logging.info("Mapping Orthofinder's IDs to hectar IDs...")
- for orthofiner_line in orthofinder:
- orthofiner_line_split = orthofiner_line.rstrip().split("\t")
- orthofinder_dict[orthofiner_line_split[1].split(" ")[0]] = orthofiner_line_split[2].split(" ")[0]
-
- hectar_dict = {}
- with open(hectar_file, 'r') as hectar:
- # Mapping orthofinder's IDs to hectar description
- logging.info("Mapping Orthofinder's IDs to descriptions...")
- next(hectar) # Skip header
- for hectar_line in hectar:
- hectar_line_split = hectar_line.rstrip().split("\t")
- hectar_dict[hectar_line_split[0].split(" ")[0]] = hectar_line_split[1]
-
- # Opening GFF, appending hectar description to matching IDs
- logging.info("Transferring manual descriptions to the GFF file...")
- output_filename = str(os.path.join(os.path.abspath(outdir), os.path.basename(gff_file).split(".")[0]) + "_TRANSFERED_HECTAR.gff")
-
- with open(output_filename, 'a') as output_file:
- output_file.truncate(0) # Erase previous file content
- with open(gff_file, 'r') as gff:
- for gff_line in gff:
- if "ID=mRNA" in gff_line: # Look for mRNA items
- gff_line_id = gff_line.split("\t")[8].split("=")[1].split(";")[0] # GFF file ID (matches hectar IDs)
- if gff_line_id in hectar_dict.keys(): # The gff ID is supposed to match a unique ID (key) in the orthofinder file
- try:
- hectar_value = hectar_dict[gff_line_id] # Find the corresponding manual annotation to transfer
- gff_line = "{0};HECTAR_predicted_targeting_category={1}\n".format(gff_line.strip(), hectar_value)
- except KeyError: # Just in case some values are missing in the hectar file (If removed it will then exit instead)
- continue
- output_file.write(gff_line)
- logging.info("Finished transferring descriptions for %s" % str(os.path.basename(gff_file)))
-
-
-if __name__ == "__main__":
-
- parser = argparse.ArgumentParser(description="Orthologs_transfer between a reference manual annotation and Orthofinder outputs. \
- \n\nRun example: python3 ec32_orthologs_transfer.py -d /path/to/desired/dir/ -h hectar_file.tsv \
- -g gff_file.gff -m manual_annotation_file.txt")
- parser.add_argument("-i", "--hectar",
- help="Hectar output (tabulated)")
- parser.add_argument("-o", "--orthofinder",
- help="Manual annotation file (tabulated) or pickle file containing the dicionary (automatically generated when you input a new manual annotation file)")
- parser.add_argument("-g", "--gff",
- help="GFF input file (tabulated)")
- parser.add_argument("-d", "--out-dir",
- help="Output directory")
- args = parser.parse_args()
-
- # WARNING for shell use case:
- # The script doesn't check if the inout files are valid.
- # Files must be put in this order: $1=orthofinder file, $2=manual annotation file, $3=GFF file, $4=optional output directory)
-
- if not args.hectar:
- logging.info("Please input a hectar file")
- sys.exit()
- if not args.orthofinder:
- logging.info("Please input a hectar output file")
- sys.exit()
- if not args.gff:
- logging.info("Please input a gff file")
- sys.exit()
- if not args.out_dir:
- args.out = "."
-
- hectar_transfer(hectar_file=args.hectar,
- orthofinder_file=args.orthofinder,
- gff_file=args.gff,
- outdir=args.out_dir)
diff --git a/workflows/Jbrowse.ga.bak b/workflows/Jbrowse.ga.bak
deleted file mode 100644
index 091a955..0000000
--- a/workflows/Jbrowse.ga.bak
+++ /dev/null
@@ -1,162 +0,0 @@
-{
- "a_galaxy_workflow": "true",
- "annotation": "",
- "format-version": "0.1",
- "name": "Jbrowse",
- "steps": {
- "0": {
- "annotation": "",
- "content_id": null,
- "errors": null,
- "id": 0,
- "input_connections": {},
- "inputs": [],
- "label": null,
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "left": 200,
- "top": 200
- },
- "tool_id": null,
- "tool_state": "{\"optional\": false}",
- "tool_version": null,
- "type": "data_input",
- "uuid": "751caac1-d015-4d77-8a68-2c3debae0caf",
- "workflow_outputs": [
- {
- "label": null,
- "output_name": "output",
- "uuid": "ac834ebd-236e-4539-86da-916da1ac8c5a"
- }
- ]
- },
- "1": {
- "annotation": "",
- "content_id": null,
- "errors": null,
- "id": 1,
- "input_connections": {},
- "inputs": [],
- "label": null,
- "name": "Input dataset",
- "outputs": [],
- "position": {
- "left": 200,
- "top": 290
- },
- "tool_id": null,
- "tool_state": "{\"optional\": false}",
- "tool_version": null,
- "type": "data_input",
- "uuid": "5cb81c38-64fe-4bdc-9043-bd862bdefc6d",
- "workflow_outputs": [
- {
- "label": null,
- "output_name": "output",
- "uuid": "a9c468b7-935b-49b3-83d0-6eabafae8daf"
- }
- ]
- },
- "2": {
- "annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
- "errors": null,
- "id": 2,
- "input_connections": {
- "reference_genome|genome": {
- "id": 0,
- "output_name": "output"
- },
- "track_groups_0|data_tracks_0|data_format|annotation": {
- "id": 1,
- "output_name": "output"
- }
- },
- "inputs": [
- {
- "description": "runtime parameter for tool JBrowse",
- "name": "reference_genome"
- }
- ],
- "label": null,
- "name": "JBrowse",
- "outputs": [
- {
- "name": "output",
- "type": "html"
- }
- ],
- "position": {
- "left": 486,
- "top": 200
- },
- "post_job_actions": {},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.10+galaxy0",
- "tool_shed_repository": {
- "changeset_revision": "8774b28235bb",
- "name": "jbrowse",
- "owner": "iuc",
- "tool_shed": "toolshed.g2.bx.psu.edu"
- },
- "tool_state": "{\"action\": {\"action_select\": \"create\", \"__current_case__\": 0}, \"gencode\": \"1\", \"jbgen\": {\"defaultLocation\": \"test\", \"trackPadding\": \"20\", \"shareLink\": \"true\", \"aboutDescription\": \"test\", \"show_tracklist\": \"true\", \"show_nav\": \"true\", \"show_overview\": \"true\", \"show_menu\": \"true\", \"hideGenomeOptions\": \"false\"}, \"plugins\": {\"BlastView\": \"true\", \"ComboTrackSelector\": \"false\", \"GCContent\": \"false\"}, \"reference_genome\": {\"genome_type_select\": \"history\", \"__current_case__\": 1, \"genome\": {\"__class__\": \"RuntimeValue\"}}, \"standalone\": \"minimal\", \"track_groups\": [{\"__index__\": 0, \"category\": \"Annotation\", \"data_tracks\": [{\"__index__\": 0, \"data_format\": {\"data_format_select\": \"gene_calls\", \"__current_case__\": 2, \"annotation\": {\"__class__\": \"RuntimeValue\"}, \"match_part\": {\"match_part_select\": \"false\", \"__current_case__\": 1}, \"index\": \"false\", \"track_config\": {\"track_class\": \"NeatHTMLFeatures/View/Track/NeatFeatures\", \"__current_case__\": 3, \"html_options\": {\"topLevelFeatures\": \"mRNA\"}}, \"jbstyle\": {\"style_classname\": \"transcript\", \"style_label\": \"product,name,id\", \"style_description\": \"note,description\", \"style_height\": \"10px\", \"max_height\": \"600\"}, \"jbcolor_scale\": {\"color_score\": {\"color_score_select\": \"none\", \"__current_case__\": 0, \"color\": {\"color_select\": \"automatic\", \"__current_case__\": 0}}}, \"jb_custom_config\": {\"option\": []}, \"jbmenu\": {\"track_menu\": [{\"__index__\": 0, \"menu_action\": \"iframeDialog\", \"menu_label\": \"View transcript report\", \"menu_title\": \"Transcript {id}\", \"menu_url\": \"{{ MENU_URL }}\", \"menu_icon\": \"dijitIconBookmark\"}]}, \"track_visibility\": \"default_off\", \"override_apollo_plugins\": \"False\", \"override_apollo_drag\": \"False\"}}]}], \"uglyTestingHack\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "1.16.10+galaxy0",
- "type": "tool",
- "uuid": "ba7d15fd-8ffd-407d-9a45-47cd4be68bd2",
- "workflow_outputs": [
- {
- "label": null,
- "output_name": "output",
- "uuid": "519355d7-82cc-47f0-a96c-3ee0e39aa7df"
- }
- ]
- },
- "3": {
- "annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/gga/jbrowse_to_container/jbrowse_to_container/0.5.1",
- "errors": null,
- "id": 3,
- "input_connections": {
- "organisms_0|jbrowse": {
- "id": 2,
- "output_name": "output"
- }
- },
- "inputs": [],
- "label": null,
- "name": "Add organisms to JBrowse container",
- "outputs": [
- {
- "name": "output",
- "type": "html"
- }
- ],
- "position": {
- "left": 772,
- "top": 200
- },
- "post_job_actions": {},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/gga/jbrowse_to_container/jbrowse_to_container/0.5.1",
- "tool_shed_repository": {
- "changeset_revision": "11033bdad2ca",
- "name": "jbrowse_to_container",
- "owner": "gga",
- "tool_shed": "toolshed.g2.bx.psu.edu"
- },
- "tool_state": "{\"organisms\": [{\"__index__\": 0, \"jbrowse\": {\"__class__\": \"ConnectedValue\"}, \"name\": {\"__class__\": \"RuntimeValue\"}, \"advanced\": {\"unique_id\": {\"__class__\": \"RuntimeValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "0.5.1",
- "type": "tool",
- "uuid": "1cf25ca3-2287-4b82-9e93-b8828eed70a2",
- "workflow_outputs": [
- {
- "label": null,
- "output_name": "output",
- "uuid": "f78c7496-18a9-4c47-ad7f-a3ac31456749"
- }
- ]
- }
- },
- "tags": [],
- "uuid": "77f04b69-2dec-430b-891f-f4ddbf04d1db",
- "version": 1
-}
\ No newline at end of file
--
GitLab