minor docstring adds in /scripts

scripts/check_eggs.py

@@ -1,7 +1,11 @@
 #!/usr/bin/env python
 """
-usage: check_eggs.py
+Compares local dependency eggs to those in eggs.ini, displaying a warning if
+any are out of date.
+
+usage: check_eggs.py [options]
 """
+
 import os, sys, logging
 from optparse import OptionParser
 

scripts/check_python.py

@@ -1,3 +1,8 @@
+"""
+If the current installed python version is not 2.5 to 2.7, prints an error
+message to stderr and returns 1
+"""
+
 import os, sys
 
 msg = """ERROR: Your Python version is: %s

scripts/create_db.py

@@ -1,3 +1,21 @@
+"""
+Creates the initial galaxy database schema using the settings defined in
+universe_wsgi.ini.
+
+This script is also wrapped by create_db.sh.
+
+.. note: pass '-c /location/to/your_config.ini' for non-standard ini file
+locations.
+
+.. note: if no database_connection is set in universe_wsgi.ini, the default,
+sqlite database will be constructed.
+    Using the database_file setting in universe_wsgi.ini will create the file
+    at the settings location (??)
+
+.. seealso: universe_wsgi.ini, specifically the settings: database_connection
+and database file
+"""
+
 import sys, os.path, logging
 
 new_path = [ os.path.join( os.getcwd(), "lib" ) ]

scripts/dist-scramble.py

@@ -1,3 +1,36 @@
+"""
+Scrambles eggs for distribution on multiple platforms.
+
+(from http://wiki.g2.bx.psu.edu/Admin/Config/Eggs)
+This is mostly designed for use by Galaxy Developers at Penn State who are
+building eggs for distribution via the Galaxy Eggs distribution site.
+dist-scramble.py uses the dist-eggs.ini config file to determine what platforms
+to build for, and which hosts to build on.
+
+dist-scramble.py works the same way as scramble.py: ::
+
+% python scripts/dist-scramble.py galaxy_egg
+
+Called with only the egg argument, dist-scramble.py will build for all the
+platforms under the all group in its config file (for platform-specific eggs)
+or the noplatform group (for platform-inspecific eggs). The [[hosts]|section
+contains information about which hosts will be used for building on each desired
+platform. If you don't want to build for all the platforms listed under the all
+group, you can add a platform argument (any lvalue in the [hosts]] or [groups]
+section is valid): ::
+
+% python scripts/dist-scramble.py galaxy_egg linux
+
+The platform argument is ignored for platform-inspecific eggs. An assumption is
+made that your Galaxy distribution is located at the same place on all of the
+hosts on which you're building (i.e. via a network filesystem).
+
+Once dist-scramble.py finishes, it will output a list of platforms on which it
+failed to scramble the egg. Successful eggs will be put in a new dist-eggs
+subdirectory of your Galaxy distribution. These eggs can then be copied to your
+distribution site.
+"""
+
 import os, sys, logging
 from optparse import OptionParser
 

scripts/drmaa_external_killer.py

@@ -1,4 +1,9 @@
 #!/usr/bin/env python
+
+"""
+Terminates a DRMAA job if given a job id and (appropriate) user id.
+"""
+
 import os
 import sys
 import errno

scripts/drmaa_external_runner.py

@@ -1,4 +1,11 @@
 #!/usr/bin/env python
+
+"""
+Submit a DRMAA job given a user id and a job template file (in JSON format)
+defining any or all of the following: args, remoteCommand, outputPath,
+errorPath, nativeSpecification, name, email, project
+"""
+
 import os
 import sys
 import errno

scripts/fetch_eggs.py

@@ -1,3 +1,10 @@
+"""
+Connects to the Galaxy Eggs distribution site and downloads any eggs needed.
+
+If eggs for your platform are unavailable, fetch_eggs.py will direct you to run
+scramble.py.
+"""
+
 import os, sys, logging
 from optparse import OptionParser