Remove docopt requirements + update requirements in doc + minor fixes

requirements.txt

@@ -2,7 +2,6 @@ flask==0.12.*
 Flask-Mail==0.9.*
 Jinja2==2.9.*
 peewee==2.10.2
-docopt==0.6.*
 numpy
 wget==3.2
 requests==2.18.*

src/bin/dgenies

@@ -81,6 +81,10 @@ def parse_args():
         return "clear", args
     if args.subparser_name == "gallery":
         return "gallery_" + args.which, args
+    else:
+        parser.print_help()
+        print("\nYou must specify the command to launch")
+        return None, None
 
 
 def start_browser(host, port):

src/dgenies/INSTALL.md

@@ -43,23 +43,29 @@ install your own from [their repository](https://github.com/lh3/minimap2).
 Some python modules are required (will be automatically installed by the commands above):
 
     flask==0.12.*
-    Flask-Mail==0.9.*
     Jinja2==2.9.*
-    peewee==2.10.2
-    docopt==0.6.*
     numpy
     wget==3.2
     requests==2.18.*
     biopython==1.70
-    python-crontab==2.2.*
     psutil==5.4.*
     tendo==0.2.*
     matplotlib==2.1.*
-    drmaa==0.7.*
     intervaltree==2.1.*
     argparse==1.4
     Markdown==2.6.*
     
+Additional modules for webserver mode:
+
+    Flask-Mail==0.9.*
+    peewee==2.10.2
+    python-crontab==2.2.*
+    
+And if you use a cluster (webserver mode):
+
+    drmaa==0.7.*
+    
+In webserver mode, you must install `mysqlclient` python module (will not be installed automatically) if you use mysql as RDBM.
     
     
 How to start
@@ -82,6 +88,8 @@ Optional arguments:
 
 ### Webserver mode
 
+*Note: this mode is only available for Unix systems and will NOT work on MS Windows.*
+
 #### Recommended method
 
 Flask webserver (which is used in standalone mode) is not recommended in production servers.  
@@ -285,6 +293,8 @@ The `dgenies` command can be used to do some maintenance staff.
 Gallery
 -------
 
+Note: gallery is only available in webserver mode.
+
 To add a job to the gallery, copy illustrating picture file into the *gallery* folder inside the data folder (*~/.dgenies/data/gallery* as default, create it if not exists). Then use the *dgenies* command:
 
     dgenies gallery add -i <id_job> -n <name> -q <query_name> -t <target_name> -p <pict_filename>

src/dgenies/bin/clean_jobs.py

@@ -61,7 +61,7 @@ def parse_database(app_data, max_age, fake=False):
 
 def parse_data_folders(app_data, now, max_age, gallery_jobs, fake=False):
     for file in os.listdir(app_data):
-        if file not in gallery_jobs:
+        if file not in gallery_jobs and file not in ["gallery"]:
             file = os.path.join(app_data, file)
             create_date = os.path.getctime(file)
             age = (now - create_date) / 86400  # Age in days

src/dgenies/bin/sort_paf.py

 #!/usr/bin/env python3
 
-"""Sort PAF file
-
-Short desc: Sort PAF file with size of matches (DESC)
-Details: Sort PAF file with size of matches (DESC)
-
-Usage:
-    sort_paf.py -i PAF -o OUT
-    sort_paf.py -v | --version
-
-Options:
-    -i --input=PAF  Input PAF file
-    -o --output=OUT Output sorted PAF file
-    -h --help   Show this screen
-    -v --version    Show version
-"""
-
 import os
 from math import sqrt
 
@@ -125,13 +109,17 @@ class Sorter:
 
 
 if __name__ == '__main__':
-    from docopt import docopt
+    import argparse
+
+    parser = argparse.ArgumentParser(description="Sort PAF file with size of matches (DESC)")
+    parser.add_argument('-i', '--input', type=str, required=True, help="Input PAF file")
+    parser.add_argument('-o', '--output', type=str, required=True, help="Output PAF file")
 
-    args = docopt(__doc__)
+    args = parser.parse_args()
     if args["--version"]:
         print(__NAME__, __VERSION__)
     else:
-        if not os.path.exists(args["--input"]):
-            raise Exception("Input PAF file %s does not exists" % args["--input"])
-        sorter = Sorter(args["--input"], args["--output"])
+        if not os.path.exists(args.input):
+            raise Exception("Input PAF file %s does not exists" % args.input)
+        sorter = Sorter(args.input, args.output)
         sorter.sort()