1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ba56d4746f7a/ changeset: ba56d4746f7a user: carlfeberhard date: 2012-08-03 19:31:48 summary: minor docstring adds in /scripts affected #: 7 files diff -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 scripts/check_eggs.py --- a/scripts/check_eggs.py +++ b/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python """ -usage: check_eggs.py +Compares local dependency eggs to those in eggs.ini, displaying a warning if +any are out of date.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 diff -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 scripts/check_python.py --- a/scripts/check_python.py +++ b/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 diff -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 scripts/create_db.py --- a/scripts/create_db.py +++ b/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" ) ] diff -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 scripts/dist-scramble.py --- a/scripts/dist-scramble.py +++ b/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 diff -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 scripts/drmaa_external_killer.py --- a/scripts/drmaa_external_killer.py +++ b/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 diff -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 scripts/drmaa_external_runner.py --- a/scripts/drmaa_external_runner.py +++ b/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 diff -r 53aacf94c5fc2e837975d15cc1bcc22d146db659 -r ba56d4746f7ade81c3cd7caf8d0d66a437ae7087 scripts/fetch_eggs.py --- a/scripts/fetch_eggs.py +++ b/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 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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