[galaxy-dev] extract_genomic_dna.py

2014-03-28 Thread Adhemar 
Hi,
In order to have the transcript_id for each sequence extracted from the
cuffmerge .gtf file I had to change the extract_genomic_dna.py by adding
the following lines after line 153:

attributes = gff_util.parse_gff_attributes( feature[8] )
if ( transcript_id in attributes ):
 name = attributes.get( transcript_id, None )


This way the variable name gets the transcript_id if it exists.

If it's correct, I would appreciate this modification in future galaxy
distributions.

Thanks!
Adhemar
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[galaxy-dev] mpileup - ImportError: cannot import name stylesheet_link_tag

2014-02-07 Thread Adhemar 
Hi!
I was running mpileup and it's showing the error bellow.
The strange thing is that 'galaxy/web/framework/helpers/__init__.py' is
trying to import 'stylesheet_link_tag' and it's not available in the
webhelpers I've installed for both python versions 2.6.6 or 2.7.3
Could you help me with this?
Thanx,
Adhemar


Traceback (most recent call last):
  File ./scripts/set_metadata.py, line 29, in module
import galaxy.model.mapping #need to load this before we unpickle,
in order to setup properties assigned by the mappers
  File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/model/__init__.py,
line 23, in module
import galaxy.datatypes.registry
  File 
/opt/bioinformatics/share/galaxy20130410/lib/galaxy/datatypes/registry.py,
line 5, in module
import data, tabular, interval, images, sequence, qualityscore,
genetics, xml, coverage, tracks, chrominfo, binary, assembly,
ngsindex, graph
  File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/datatypes/data.py,
line 2, in module
import metadata
  File 
/opt/bioinformatics/share/galaxy20130410/lib/galaxy/datatypes/metadata.py,
line 24, in module
from galaxy.web import form_builder
  File /opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/__init__.py,
line 4, in module
from framework import expose
  File 
/opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/__init__.py,
line 28, in module
import helpers
  File 
/opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/helpers/__init__.py,
line 4, in module
from webhelpers import date, stylesheet_link_tag,
javascript_include_tag, url_for
ImportError: cannot import name stylesheet_link_tag
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Re: [galaxy-dev] AttributeError: type object 'InvalidJobException' has no attribute 'name'

2013-10-08 Thread Adhemar 
In order to test that, I've just downloaded a new galaxy-central and
configured it to submit jobs in our SGE cluster. Same problem. The job
starts and finishes, but galaxy keeps informing it's still running.
I've also attached the job_conf.xml file.
Need help, please!
-Adhemar


galaxy.jobs.runners ERROR 2013-10-08 15:29:16,721 Unhandled exception
checking active jobs
Traceback (most recent call last):
  File
/opt/bioinformatics/share/galaxy20131008/lib/galaxy/jobs/runners/__init__.py,
line 362, in monitor
self.check_watched_items()
  File
/opt/bioinformatics/share/galaxy20131008/lib/galaxy/jobs/runners/drmaa.py,
line 217, in check_watched_items
log.warning( (%s/%s) job check resulted in %s: %s, galaxy_id_tag,
external_job_id, e.__class__.name, e )
AttributeError: type object 'InvalidJobException' has no attribute 'name'



?xml version=1.0?
job_conf
plugins workers=10
!-- plugin id=local type=runner
load=galaxy.jobs.runners.local:LocalJobRunner workers=10/ --
plugin id=sge type=runner
load=galaxy.jobs.runners.drmaa:DRMAAJobRunner workers=10/
/plugins
handlers default=handlers
handler id=main/
handler id=handler0 tags=handlers/
handler id=handler1 tags=handlers/
handler id=handler2 tags=handlers/
handler id=handler3 tags=handlers/
handler id=handler4 tags=handlers/
handler id=handler5 tags=handlers/
handler id=handler6 tags=handlers/
handler id=handler7 tags=handlers/
handler id=handler8 tags=handlers/
handler id=handler9 tags=handlers/
/handlers
destinations default=sge_cluster
!--
destination id=local runner=local/
--
destination id=sge_cluster runner=sge tags=longjobs
param id=nativeSpecification-V -q galaxy.q/param
/destination
/destinations
/job_conf







2013/10/8 Adhemar azn...@gmail.com

 Hi,
 After the last update I'm getting the following error.
 The job is submitted to SGE e executed, but galaxy doesn't get the result
 and keeps showing the job is executing (yellow box).
 Any clues?
 Thanks,
 Adhemar



 galaxy.jobs.runners ERROR 2013-10-08 13:01:18,488 Unhandled exception
 checking active jobs
 Traceback (most recent call last):
   File
 /opt/bioinformatics/share/galaxy20130410/lib/galaxy/jobs/runners/__init__.py,
 line 362, in monitor
 self.check_watched_items()
   File
 /opt/bioinformatics/share/galaxy20130410/lib/galaxy/jobs/runners/drmaa.py,
 line 217, in check_watched_items
 log.warning( (%s/%s) job check resulted in %s: %s, galaxy_id_tag,
 external_job_id, e.__class__.name, e )
 AttributeError: type object 'InvalidJobException' has no attribute 'name'


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[galaxy-dev] tool shed can't install via admin user

2013-09-10 Thread Adhemar 
Hi,
I've just updated my galaxy-central version and I can't use the tool shed
installer via admin user any more. When I click 'Install to Galaxy' it
throws and 500 error.
Could you please verify that? I tried the URL from tool_shed_url in the
browser and it also doesn't open.
Thanks,
Adhemar





10.129.9.38, 10.129.0.1 - - [10/Sep/2013:16:05:59 -0200] GET
/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=
http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282HTTP/1.0;
500 - 
http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=c45d6c51a4fcfc6cchangeset_revision=bf1c3f9f8282;
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/28.0.1500.95 Safari/537.36
Error - class 'urllib2.HTTPError': HTTP Error 500: Internal Server Error
URL:
https://www.lmb.cnptia.embrapa.br/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282
File
'/opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File '/usr/lib/python2.6/site-packages/paste/recursive.py', line 80 in
__call__
  return self.application(environ, start_response)
File
'/opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/middleware/remoteuser.py',
line 91 in __call__
  return self.app( environ, start_response )
File '/usr/lib/python2.6/site-packages/paste/httpexceptions.py', line 633
in __call__
  return self.application(environ, start_response)
File
'/opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/base.py',
line 132 in __call__
  return self.handle_request( environ, start_response )
File
'/opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/base.py',
line 190 in handle_request
  body = method( trans, **kwargs )
File
'/opt/bioinformatics/share/galaxy20130410/lib/galaxy/web/framework/__init__.py',
line 221 in decorator
  return func( self, trans, *args, **kwargs )
File
'/opt/bioinformatics/share/galaxy20130410/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
line 908 in prepare_for_install
  includes_tool_dependencies )
File
'/opt/bioinformatics/share/galaxy20130410/lib/tool_shed/util/common_install_util.py',
line 130 in get_dependencies_for_repository
  all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url,
util.listify( repo_info_dict ) )
File
'/opt/bioinformatics/share/galaxy20130410/lib/tool_shed/util/common_install_util.py',
line 360 in get_required_repo_info_dicts
  response = urllib2.urlopen( request ).read()
File '/usr/lib64/python2.6/urllib2.py', line 126 in urlopen
  return _opener.open(url, data, timeout)
File '/usr/lib64/python2.6/urllib2.py', line 397 in open
  response = meth(req, response)
File '/usr/lib64/python2.6/urllib2.py', line 510 in http_response
  'http', request, response, code, msg, hdrs)
File '/usr/lib64/python2.6/urllib2.py', line 435 in error
  return self._call_chain(*args)
File '/usr/lib64/python2.6/urllib2.py', line 369 in _call_chain
  result = func(*args)
File '/usr/lib64/python2.6/urllib2.py', line 518 in http_error_default
  raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error


CGI Variables
-
  CONTENT_LENGTH: '0'
  HTTP_ACCEPT:
'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
  HTTP_ACCEPT_ENCODING: 'gzip,deflate,sdch'
  HTTP_ACCEPT_LANGUAGE: 'pt-BR,pt;q=0.8,en-US;q=0.6,en;q=0.4'
  HTTP_AUTHORIZATION: 'Basic YWRoZW1hcjpDYWxsIG1lIHRoZSBicmVlemUh'
  HTTP_COOKIE:
'galaxysession=c6ca0ddb55be603a7b1853fca2041c148b00044fe9cfda0f39abd5fcb4fe71a0bc3b556f2ab9d86b;
GUEST_LANGUAGE_ID=pt_BR; COOKIE_SUPPORT=true;
JSESSIONID=EC393E44F6CC64AB7CECE0B38408E133'
  HTTP_HOST: 'www.lmb.cnptia.embrapa.br'
  HTTP_REFERER: '
http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=c45d6c51a4fcfc6cchangeset_revision=bf1c3f9f8282
'
  HTTP_REMOTE_USER: 'adhemar@'
  HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36
(KHTML, like Gecko) Chrome/28.0.1500.95 Safari/537.36'
  HTTP_X_URL_SCHEME: 'https'
  PATH_INFO: '/admin_toolshed/prepare_for_install'
  QUERY_STRING: 'tool_shed_url=
http://toolshed.g2.bx.psu.edu/repository_ids=c45d6c51a4fcfc6cchangeset_revisions=bf1c3f9f8282
'
  REMOTE_ADDR: '10.129.9.38, 10.129.0.1'
  REQUEST_METHOD: 'GET'
  SCRIPT_NAME: '/galaxy'
  SERVER_NAME: 'www.lmb.cnptia.embrapa.br'
  SERVER_PORT: '8080'
  SERVER_PROTOCOL: 'HTTP/1.0'


WSGI Variables
--
  application: paste.recursive.RecursiveMiddleware object at 0x8c58d90
  is_api_request: False
  original_wsgi.url_scheme: 'http'
  paste.cookies: (SimpleCookie: COOKIE_SUPPORT='true'
GUEST_LANGUAGE_ID='pt_BR' JSESSIONID='EC393E44F6CC64AB7CECE0B38408E133'
galaxysession='c6ca0ddb55be603a7b1853fca2041c148b00044fe9cfda0f39abd5fcb4fe71a0bc3b556f2ab9d86b',
'galaxysession

Re: [galaxy-dev] galaxy-dev Digest, Vol 74, Issue 21

2012-08-22 Thread Adhemar 
Here is a copy of the whole VirtualHost section.
Thanks,
Adhemar



VirtualHost lbas046.cnptia.embrapa.br:443

ServerName lbas046.cnptia.embrapa.br
ErrorLog logs/galaxy_ssl_error_log
TransferLog logs/galaxy_ssl_access_log
LogLevel warn

SSLEngine on

SSLCertificateFile /etc/pki/tls/certs/lbas046.cnptia.embrapa.br.crt
SSLCertificateKeyFile
/etc/pki/tls/private/lbas046.cnptia.embrapa.br.key.insecure
SSLCACertificateFile /etc/pki/tls/certs/cacert.pem



   RewriteEngine on
   RewriteRule ^/galaxy$ /galaxy/ [R]
   RewriteRule ^/galaxy/static/style/(.*)
/opt/bioinformatics/share/galaxy-central/static/june_2007_style/blue/$1 [L]
   RewriteRule ^/galaxy/static/scripts/(.*)
/opt/bioinformatics/share/galaxy-central/static/scripts/packed/$1 [L]
   RewriteRule ^/galaxy/static/(.*)
/opt/bioinformatics/share/galaxy-central/static/$1 [L]
   RewriteRule ^/galaxy/favicon.ico
/opt/bioinformatics/share/galaxy-central/static/favicon.ico [L]
   RewriteRule ^/galaxy/robots.txt
/opt/bioinformatics/share/galaxy-central/static/robots.txt [L]
   RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]


 Location /galaxy
   AuthType Basic
   AuthName Galaxy_pam
   AuthPAM_Enabled on
   Require valid-user

RewriteEngine On
RewriteCond %{LA-U:REMOTE_USER} (.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER %{RU}e env=RU
 /Location

/VirtualHost



   9. Re: [galaxy-user] LimitInternalRecursion (Nate Coraor)

--

 Message: 9
 Date: Wed, 22 Aug 2012 10:46:30 -0400
 From: Nate Coraor n...@bx.psu.edu
 To: azn...@gmail.com
 Cc: galaxy-dev@lists.bx.psu.edu
 Subject: Re: [galaxy-dev] [galaxy-user] LimitInternalRecursion
 Message-ID: bd7e4946-0184-4887-9e3d-17946adce...@bx.psu.edu
 Content-Type: text/plain; charset=iso-8859-1

 On Aug 21, 2012, at 4:44 PM, Adhemar wrote:

  Hi,
  There's this error message in my apache log:
 
   [error] Request exceeded the limit of 10 subrequest nesting levels due
 to probable confguration error. Use 'LimitInternalRecursion' to increase
 the limit if necessary. Use 'LogLevel debug' to get a backtrace., referer:
 ...
 
 
  When I turn the apache debug log on it also shows:
 
 
  [debug] core.c(3072):  r-uri = /galaxy/proxy:
 http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/root/history_item_updates,
 referer: ...
 
 
  It seems like mod_rewrite is somehow misconfigured, but I couldb't
 figure out what it is.
 
  Here is my httpd.con mod_rewrite conf:
 
 
 RewriteEngine on
 RewriteRule ^/galaxy$ /galaxy/ [R]
 RewriteRule ^/galaxy/static/style/(.*)
 /opt/bioinformatics/share/galaxy-central/static/june_2007_style/blue/$1 [L]
 RewriteRule ^/galaxy/static/scripts/(.*)
 /opt/bioinformatics/share/galaxy-central/static/scripts/packed/$1 [L]
 RewriteRule ^/galaxy/static/(.*)
 /opt/bioinformatics/share/galaxy-central/static/$1 [L]
 RewriteRule ^/galaxy/favicon.ico
 /opt/bioinformatics/share/galaxy-central/static/favicon.ico [L]
 RewriteRule ^/galaxy/robots.txt
 /opt/bioinformatics/share/galaxy-central/static/robots.txt [L]
 RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]

 Hi Adhemar,

 I've moved this over to the galaxy-dev list since it's concerning a local
 installation.

 Are there any other RewriteRules defined?  Are these directives inside
 another block, or just inside a VirtualHost?  It would be useful to see
 your entire VirtualHost config.

 --nate

 
 
  Could you please help me to debug this?
 
  Thank you,
  Adhemar
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Re: [galaxy-dev] [galaxy-user] LimitInternalRecursion

2012-08-22 Thread Adhemar 
Here is a copy of the whole VirtualHost section.
Thanks,
Adhemar



VirtualHost lbas046.cnptia.embrapa.br:443

ServerName lbas046.cnptia.embrapa.br
ErrorLog logs/galaxy_ssl_error_log
TransferLog logs/galaxy_ssl_access_log
LogLevel warn

SSLEngine on

SSLCertificateFile /etc/pki/tls/certs/lbas046.cnptia.embrapa.br.crt
SSLCertificateKeyFile
/etc/pki/tls/private/lbas046.cnptia.embrapa.br.key.insecure
SSLCACertificateFile /etc/pki/tls/certs/cacert.pem



   RewriteEngine on
   RewriteRule ^/galaxy$ /galaxy/ [R]
   RewriteRule ^/galaxy/static/style/(.*)
/opt/bioinformatics/share/galaxy-central/static/june_2007_style/blue/$1 [L]
   RewriteRule ^/galaxy/static/scripts/(.*)
/opt/bioinformatics/share/galaxy-central/static/scripts/packed/$1 [L]
   RewriteRule ^/galaxy/static/(.*)
/opt/bioinformatics/share/galaxy-central/static/$1 [L]
   RewriteRule ^/galaxy/favicon.ico
/opt/bioinformatics/share/galaxy-central/static/favicon.ico [L]
   RewriteRule ^/galaxy/robots.txt
/opt/bioinformatics/share/galaxy-central/static/robots.txt [L]
   RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]


 Location /galaxy
   AuthType Basic
   AuthName Galaxy_pam
   AuthPAM_Enabled on
   Require valid-user

RewriteEngine On
RewriteCond %{LA-U:REMOTE_USER} (.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER %{RU}e env=RU
 /Location

/VirtualHost


2012/8/22 Nate Coraor n...@bx.psu.edu

 On Aug 21, 2012, at 4:44 PM, Adhemar wrote:

  Hi,
  There's this error message in my apache log:
 
   [error] Request exceeded the limit of 10 subrequest nesting levels due
 to probable confguration error. Use 'LimitInternalRecursion' to increase
 the limit if necessary. Use 'LogLevel debug' to get a backtrace., referer:
 ...
 
 
  When I turn the apache debug log on it also shows:
 
 
  [debug] core.c(3072):  r-uri = /galaxy/proxy:
 http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/root/history_item_updates,
 referer: ...
 
 
  It seems like mod_rewrite is somehow misconfigured, but I couldb't
 figure out what it is.
 
  Here is my httpd.con mod_rewrite conf:
 
 
 RewriteEngine on
 RewriteRule ^/galaxy$ /galaxy/ [R]
 RewriteRule ^/galaxy/static/style/(.*)
 /opt/bioinformatics/share/galaxy-central/static/june_2007_style/blue/$1 [L]
 RewriteRule ^/galaxy/static/scripts/(.*)
 /opt/bioinformatics/share/galaxy-central/static/scripts/packed/$1 [L]
 RewriteRule ^/galaxy/static/(.*)
 /opt/bioinformatics/share/galaxy-central/static/$1 [L]
 RewriteRule ^/galaxy/favicon.ico
 /opt/bioinformatics/share/galaxy-central/static/favicon.ico [L]
 RewriteRule ^/galaxy/robots.txt
 /opt/bioinformatics/share/galaxy-central/static/robots.txt [L]
 RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]

 Hi Adhemar,

 I've moved this over to the galaxy-dev list since it's concerning a local
 installation.

 Are there any other RewriteRules defined?  Are these directives inside
 another block, or just inside a VirtualHost?  It would be useful to see
 your entire VirtualHost config.

 --nate

 
 
  Could you please help me to debug this?
 
  Thank you,
  Adhemar
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  please use the interface at:
 
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Re: [galaxy-dev] [galaxy-user] LimitInternalRecursion

2012-08-22 Thread Adhemar 
Hi Nate!
That line really solved the problem.

RewriteCond %{IS_SUBREQ} ^false$

No more errors in my log!
Thank you, I really appreciate it.
Adhemar




2012/8/22 Nate Coraor n...@bx.psu.edu

 Hi Adhemar,

 Could you try the following?:

 VirtualHost lbas046.cnptia.embrapa.br:443

 ServerName lbas046.cnptia.embrapa.br
 ErrorLog logs/galaxy_ssl_error_log
 TransferLog logs/galaxy_ssl_access_log
 LogLevel warn

 SSLEngine on

 SSLCertificateFile /etc/pki/tls/certs/lbas046.cnptia.embrapa.br.crt
 SSLCertificateKeyFile
 /etc/pki/tls/private/lbas046.cnptia.embrapa.br.key.insecure
 SSLCACertificateFile /etc/pki/tls/certs/cacert.pem

 Proxy http://localhost:8080
 Order deny,allow
 Allow from all
 /Proxy

 RewriteEngine on

 Location /galaxy
 AuthType Basic
 AuthName Galaxy_pam
 AuthPAM_Enabled on
 Require valid-user

 RewriteCond %{IS_SUBREQ} ^false$
 RewriteCond %{LA-U:REMOTE_USER} (.+)
 RewriteRule . - [E=RU:%1]
 RequestHeader set REMOTE_USER %{RU}e env=RU
 /Location

 RewriteRule ^/galaxy$ /galaxy/ [R]
 RewriteRule ^/galaxy/static/style/(.*)
 /opt/bioinformatics/share/galaxy-central/static/june_2007_style/blue/$1 [L]
 RewriteRule ^/galaxy/static/scripts/(.*)
 /opt/bioinformatics/share/galaxy-central/static/scripts/packed/$1 [L]
 RewriteRule ^/galaxy/static/(.*)
 /opt/bioinformatics/share/galaxy-central/static/$1 [L]
 RewriteRule ^/galaxy/favicon.ico
 /opt/bioinformatics/share/galaxy-central/static/favicon.ico [L]
 RewriteRule ^/galaxy/robots.txt
 /opt/bioinformatics/share/galaxy-central/static/robots.txt [L]
 RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]

 /VirtualHost

 On Aug 22, 2012, at 12:38 PM, Adhemar wrote:

  Here is a copy of the whole VirtualHost section.
  Thanks,
  Adhemar
 
 
 
  VirtualHost lbas046.cnptia.embrapa.br:443
 
  ServerName lbas046.cnptia.embrapa.br
  ErrorLog logs/galaxy_ssl_error_log
  TransferLog logs/galaxy_ssl_access_log
  LogLevel warn
 
  SSLEngine on
 
  SSLCertificateFile /etc/pki/tls/certs/lbas046.cnptia.embrapa.br.crt
  SSLCertificateKeyFile
 /etc/pki/tls/private/lbas046.cnptia.embrapa.br.key.insecure
  SSLCACertificateFile /etc/pki/tls/certs/cacert.pem
 
 
 
 RewriteEngine on
 RewriteRule ^/galaxy$ /galaxy/ [R]
 RewriteRule ^/galaxy/static/style/(.*)
 /opt/bioinformatics/share/galaxy-central/static/june_2007_style/blue/$1 [L]
 RewriteRule ^/galaxy/static/scripts/(.*)
 /opt/bioinformatics/share/galaxy-central/static/scripts/packed/$1 [L]
 RewriteRule ^/galaxy/static/(.*)
 /opt/bioinformatics/share/galaxy-central/static/$1 [L]
 RewriteRule ^/galaxy/favicon.ico
 /opt/bioinformatics/share/galaxy-central/static/favicon.ico [L]
 RewriteRule ^/galaxy/robots.txt
 /opt/bioinformatics/share/galaxy-central/static/robots.txt [L]
 RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
 
 
   Location /galaxy
 AuthType Basic
 AuthName Galaxy_pam
 AuthPAM_Enabled on
 Require valid-user
 
  RewriteEngine On
  RewriteCond %{LA-U:REMOTE_USER} (.+)
  RewriteRule . - [E=RU:%1]
  RequestHeader set REMOTE_USER %{RU}e env=RU
   /Location
 
  /VirtualHost
 
 
  2012/8/22 Nate Coraor n...@bx.psu.edu
  On Aug 21, 2012, at 4:44 PM, Adhemar wrote:
 
   Hi,
   There's this error message in my apache log:
  
[error] Request exceeded the limit of 10 subrequest nesting levels
 due to probable confguration error. Use 'LimitInternalRecursion' to
 increase the limit if necessary. Use 'LogLevel debug' to get a backtrace.,
 referer: ...
  
  
   When I turn the apache debug log on it also shows:
  
  
   [debug] core.c(3072):  r-uri = /galaxy/proxy:
 http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/root/history_item_updates,
 referer: ...
  
  
   It seems like mod_rewrite is somehow misconfigured, but I couldb't
 figure out what it is.
  
   Here is my httpd.con mod_rewrite conf:
  
  
  RewriteEngine on
  RewriteRule ^/galaxy$ /galaxy/ [R]
  RewriteRule ^/galaxy/static/style/(.*)
 /opt/bioinformatics/share/galaxy-central/static/june_2007_style/blue/$1 [L]
  RewriteRule ^/galaxy/static/scripts/(.*)
 /opt/bioinformatics/share/galaxy-central/static/scripts/packed/$1 [L]
  RewriteRule ^/galaxy/static/(.*)
 /opt/bioinformatics/share/galaxy-central/static/$1 [L]
  RewriteRule ^/galaxy/favicon.ico
 /opt/bioinformatics/share/galaxy-central/static/favicon.ico [L]
  RewriteRule