natefoo

<?xml version="1.0"?>
<!DOCTYPE service_bundle SYSTEM "/usr/share/lib/xml/dtd/service_bundle.dtd.1">
<service_bundle type='manifest' name='SUNWcsr:ndd'>

<service
    name='network/linkprop'
    type='service'
    version='1'>

        <create_default_instance enabled='true' />

natefoo

diff -r 2b456e221582 lib/galaxy/datatypes/metadata.py
--- a/lib/galaxy/datatypes/metadata.py  Mon May 20 16:51:05 2013 -0400
+++ b/lib/galaxy/datatypes/metadata.py	Tue May 21 15:31:59 2013 -0400
@@ -85,8 +85,8 @@
     def __getattr__( self, name ):
         if name in self.spec:
             if name in self.parent._metadata:
-                return self.spec[name].wrap( self.parent._metadata[name] )
-            return self.spec[name].wrap( self.spec[name].default )
+                return self.spec[name].wrap( self.parent._metadata[name], object_session( self.parent ) )

natefoo

--- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py  Wed Jun 12 11:48:09 2013 -0400
+++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py	Wed Jun 12 16:09:07 2013 -0400
@@ -284,7 +284,7 @@
                             setup_command = "python %s/virtualenv.py --no-site-packages '%s'" % (venv_src_directory, venv_directory)
                             # POSIXLY_CORRECT forces shell commands . and source to have the same
                             # and well defined behavior in bash/zsh.
-                            activate_command = "POSIXLY_CORRECT=1; . %s" % os.path.join( venv_directory, "bin", "activate" )
+                            activate_command = "POSIXLY_CORRECT=1 PYTHONUSERSITE=1; . %s" % os.path.join( venv_directory, "bin", "activate" )
                             install_command = "pip install -r '%s'" % requirements_path
                             full_setup_command = "%s; %s; %s" % ( setup_command, activate_command, install_command )

natefoo

root@7e86f459-a39d-4966-a74e-c8843cbcb2df:~/heimdal-1.6~git20130731.galaxy.1/lib/hdb# make -n
make  all-am
make[1]: Entering directory `/root/heimdal-1.6~git20130731.galaxy.1/lib/hdb'
rm -f test_dbinfo
echo "  CCLD  " test_dbinfo;/bin/bash ../../libtool --silent --tag=CC   --mode=link gcc  -Wall -Wextra -Wno-sign-compare -Wno-unused-parameter -Wmissing-prototypes -Wpointer-arith -Wbad-function-cast -Wmissing-declarations -Wnested-externs -Wshadow  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wformat-security  -Wl,--as-needed -o test_dbinfo test_dbinfo.o libhdb.la -L/usr/lib -lldap -llber   ../krb5/libkrb5.la ../asn1/libasn1.la ../../lib/hcrypto/libhcrypto.la ../../lib/vers/libvers.la ../../lib/roken/libroken.la -lcrypt   -lresolv -pthread -lpthread
echo "  CC    " test_hdbkeys.o;gcc  -DHAVE_CONFIG_H -I. -I. -I../../include -I../../include  -I../../lib/roken -I../../lib/roken -I../asn1 -I./../asn1  -I/usr/include -DHDB_DB_DIR=\"/var/lib/heimdal-kdc\" -I./../krb5 -I/usr/include   -I/usr/include/

natefoo

128.118.200.95 - - [23/Sep/2013:09:13:11 -0500] "GET /datasets/427635/display_at/ucsc_main?redirect_url=http%3A%2F%2Fgenome.ucsc.edu%2Fcgi-bin%2FhgTracks%3Fdb%3Dhg18%26position%3Dchr1%3A147962192-148185276%26hgt.customText%3D%25s&display_url=https%3A%2F%2Fgalaxy01.tacc.utexas.edu%2Froot%2Fdisplay_as%3Fid%3D427635%26display_app%3Ducsc%26authz_method%3Ddisplay_at HTTP/1.1" 302 - "-
" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/30.0.1599.47 Safari/537.36"

headers <type 'list'>: [('content-type', 'text/html'), ('location', u'http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:147962192-148185276&hgt.customText=https%3A%2F%2Fgalaxy01.tacc.utexas.edu%2Froot%2Fdisplay_as%3Fid%3D427635%26display_app%3Ducsc%26authz_method%3Ddisplay_at')]

Traceback (most recent call last):
  File "lib/galaxy/web/framework/middleware/request_id.py", line 12, in __call__
    return self.app( environ, start_response )
  File "lib/galaxy/web/framework/middleware/xforwardedhost.p

natefoo

diff -r a973453e1e68 lib/galaxy/jobs/runners/pbs.py
--- a/lib/galaxy/jobs/runners/pbs.py	Fri Nov 15 10:50:49 2013 -0500
+++ b/lib/galaxy/jobs/runners/pbs.py	Fri Nov 15 13:58:42 2013 -0500
@@ -49,7 +49,7 @@
 """

 PBS_ARGMAP = {
-    'destination'           : '-d',
+    'destination'           : '-q',
     'Execution_Time'        : '-a',

natefoo

<destinations default="cluster">
    <destination id="local" runner="local"/>
    <destination id="cluster" runner="pbs">
        <param ... />
    </destination>
</destinations>
<tools>
    <tool id="upload1" destination="local"/>
    <tool id="ucsc_table_direct1" destination="local"/>
</tools>

natefoo

---
# file: group_vars/dbservers

postgresql_data_dir: /var/lib/pgsql/9.2/data

---
# file: group_vars/dbservers-main

postgresql_role: dbservers-main

natefoo

---
# file: test.yml
- hosts: localhost
  vars:
    foodata: null
  roles:
    - { role: foo, when: foodata }
---
# file: roles/foo/tasks/main.yml

natefoo

Fetched 1,586 MB in 1min 40s (15.8 MB/s)
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