diff --git a/src/dgenies/.gitignore b/src/dgenies/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..df27293f58d5af6582d104ff4d92fbbba408f6bf
--- /dev/null
+++ b/src/dgenies/.gitignore
@@ -0,0 +1,2 @@
+application-dev.properties.local
+tools-dev.yaml.local
diff --git a/src/dgenies/application-dev.properties b/src/dgenies/application-dev.properties
new file mode 100644
index 0000000000000000000000000000000000000000..85088576ca056538c34b10616c7b3e3ef5bfba53
--- /dev/null
+++ b/src/dgenies/application-dev.properties
@@ -0,0 +1,97 @@
+[global]
+config_dir = ###USER###/.dgenies
+upload_folder = /tmp/dgenies
+data_folder = ###CONFIG###/data
+
+# batch system type: local, sge, slurm
+batch_system_type = local
+
+web_url = http://localhost:5000
+
+# Max size of uploaded files (also for files from URL, size uncompressed):
+# Please set the unit: M for Megabyte or G for Gigabyte (-1 without unit to don't set a limit)
+max_upload_size = 3G
+# Max upload file size for all-vs-all (only target):
+# Please set the unit: M for Megabyte or G for Gigabyte (-1 without unit to don't set a limit)
+max_upload_size_ava = 1G
+# Max upload file size (compressed or not, only for uploaded files, not from URL):
+# Please set the unit: M for Megabyte or G for Gigabyte (-1 without unit to don't set a limit)
+max_upload_file_size = 1G
+
+
+[softwares]
+minimap2 = ###DEFAULT###
+minimap2_cluster = ###DEFAULT###
+
+
+[debug]
+# Debug (enable only for tests)
+enable = False
+log_dir = ###CONFIG###/logs
+# List of allowed IPs for tests, comma separated:
+allowed_ip_tests =
+
+
+[cluster]
+drmaa_lib_path = ###SET_IT###
+#Native specs: options passed to the scheduler
+### Slurm: --mem-per-cpu={0} --ntasks={1} --time={2}
+### SGE: -l mem={0},h_vmem={0} -pe parallel_smp {1}
+### Note: copy&paste specifications for your scheduler. You can customize it.
+### Always use {0} for memory, {1} for number of CPUs ({2} for duration time if slurm). All are required.
+### If you don't want to change anything, don't edit anything.
+native_specs = ###DEFAULT###
+
+# If batch_system_type is not local, small jobs can be still run locally.
+# Set to 0 to run all jobs on the cluster
+max_run_local = 10
+max_wait_local = 5
+
+# To run only big jobs on the cluster, set the min query and target size (if max_run_local is reached, these parameters are ignores):
+# Default parameters is for jobs that runs in approx. more than 3-4 minutes and consume approx. more than 9 GO of RAM
+# Please set the unit: M for Megabyte or G for Gigabyte
+min_query_size = 500M
+min_target_size = 700M
+
+prepare_script = ###PROGRAM###/bin/all_prepare.py
+python3_exec = python3
+# Max memory:
+memory = 32
+# Max memory for all-vs-all mode:
+memory_ava = 32
+
+
+[database]
+type = sqlite
+url = ###USER###/.dgenies/database.sqlite
+# Not used for sqlite:
+port = 3306
+db =
+user =
+password =
+
+
+[mail]
+status = mail@dgenies
+reply = mail@dgenies
+org = "Dgenies team"
+send_mail_status = True
+
+
+[cron]
+### Menage
+# Time to launch the cron:
+clean_time = 1h00
+# Frequency (days):
+clean_freq = 1
+
+
+[jobs]
+# Number of parallel runs for local jobs:
+run_local = 1
+data_prepare = 2
+max_concurrent_dl = 5
+
+[example]
+query =
+target =
diff --git a/src/dgenies/config_reader.py b/src/dgenies/config_reader.py
index f76c0fb19b58d9175cff1359fcdea16d0fff43bd..308ce6f5273ca26018c108ead24dd10c483cd0b6 100644
--- a/src/dgenies/config_reader.py
+++ b/src/dgenies/config_reader.py
@@ -32,6 +32,10 @@ class AppConfigReader:
for my_config_file in config_file_search:
if os.path.exists(my_config_file):
config_file.append(my_config_file)
+
+ config_file.append(os.path.join(self.app_dir, "application-dev.properties"))
+ config_file.append(os.path.join(self.app_dir, "application-dev.properties.local"))
+
if len(config_file) == 0:
raise FileNotFoundError("ERROR: application.properties not found.")
self.reader = RawConfigParser()
diff --git a/src/dgenies/tools-dev.yaml b/src/dgenies/tools-dev.yaml
new file mode 100644
index 0000000000000000000000000000000000000000..4999012d00159fc08fa44a9d743b5fdbeb627d6a
--- /dev/null
+++ b/src/dgenies/tools-dev.yaml
@@ -0,0 +1,21 @@
+minimap2:
+ exec: default
+ command_line: "{exe} -t {threads} {target} {query} > {out}"
+ all_vs_all: "{exe} -t {threads} -X {target} {target} > {out}"
+ max_memory: 40
+ threads: 8
+ parser: !!null
+ split_before: True
+ help: "Better for low similar fasta files"
+ order: 0
+
+mashmap:
+ exec: default
+ command_line: "{exe} -t {threads} -r {target} -q {query} -o {out}"
+ all_vs_all: !!null
+ max_memory: 20
+ threads: 8
+ parser: mashmap2paf
+ split_before: False
+ help: "Faster for high similar fasta files"
+ order: 1
diff --git a/src/dgenies/tools.py b/src/dgenies/tools.py
index 10b632a695f57156f69d41f803f2668f793e5fdb..824782177741a483f9168da6788198c8e2304160 100644
--- a/src/dgenies/tools.py
+++ b/src/dgenies/tools.py
@@ -102,27 +102,31 @@ class Tools:
self.load_yaml()
def load_yaml(self):
- config_file = []
+ yaml_file = None
config_file_search = [os.path.join(os.path.abspath(os.sep), "dgenies", "tools.yaml"),
"/etc/dgenies/tools.yaml",
"/etc/dgenies/tools.yaml.local",
os.path.join(str(Path.home()), ".dgenies", "tools.yaml.local")]
if os.name == "nt":
- config_file.insert(1, os.path.join(sys.executable, '..', "tools.yaml"))
- config_file.insert(1, os.path.join(sys.executable, '..', "tools.yaml.local"))
+ config_file_search.insert(1, os.path.join(sys.executable, '..', "tools.yaml"))
+ config_file_search.insert(1, os.path.join(sys.executable, '..', "tools.yaml.local"))
- for my_config_file in config_file_search:
+ app_dir = os.path.dirname(inspect.getfile(self.__class__))
+ config_file_search.append(os.path.join(app_dir, "tools-dev.yaml"))
+ config_file_search.append(os.path.join(app_dir, "tools-dev.yaml.local"))
+
+ for my_config_file in reversed(config_file_search):
if os.path.exists(my_config_file):
- config_file.append(my_config_file)
- if len(config_file) == 0:
+ yaml_file = my_config_file
+ break
+ if yaml_file is None:
raise FileNotFoundError("ERROR: tools.yaml not found.")
- for yaml_file in config_file:
- with open(yaml_file, "r") as yml_f:
- tools_dict = yaml.load(yml_f)
- tools = {}
- for name, props in tools_dict.items():
- tools[name] = Tool(name=name, **props)
- print(tools)
- self.tools.update(tools)
+ with open(yaml_file, "r") as yml_f:
+ tools_dict = yaml.load(yml_f)
+ tools = {}
+ for name, props in tools_dict.items():
+ tools[name] = Tool(name=name, **props)
+ print(tools)
+ self.tools.update(tools)