Add config files for dev

src/dgenies/.gitignore

+application-dev.properties.local
+tools-dev.yaml.local

src/dgenies/application-dev.properties

+[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 = 

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()

src/dgenies/tools-dev.yaml

+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

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)