date:20120822

Re: [galaxy-dev] FTP upload - symlink to uploaded data

2012-08-22 Thread Joachim Jacob


Hi Nate,

I have set the new_file_path to the FTP upload directory as you 
suggested.   new_file_path=/mnt/galaxydb/ftp

This did not succeed however: still there is copying to the /tmp directory.

I also see that importing data sets into data libraries from a directory 
of files behaves similarly. I am not a hard-core programmer: but it is 
correct that transferring files from file systems paths and importing 
ftp files are being handled by the same python module? Perhaps you could 
point me to which script this is?



Kind regards, and thanks for the assistance already,

Joachim

PS: I have filed this issue also on bitbucket

Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 08/20/2012 06:13 PM, Nate Coraor wrote:

On Aug 17, 2012, at 3:17 AM, Joachim Jacob wrote:


Hi Nate,

thanks. Do you know what's the reason for using copying first the contents to 
the /tmp directory, before copying it into a the database/files/... Seems 
inefficient to do so, or is this not how it works perhaps?

Hi Joachim,

If you set new_file_path in universe_wsgi.ini to be on the same filesystem as 
your FTP upload directory, there should not be any copying necessary.

Thanks,
--nate


Regards,
Joachim

Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 08/16/2012 05:19 PM, Nate Coraor wrote:

On Aug 16, 2012, at 11:09 AM, Joachim Jacob wrote:


Excuses for the repost, but I really need to solve this.

Uploading with FTP fails on our Galaxy, because the /tmp directory has not 
enough space. How can I hack in the Galaxy code base that the temporary 
directory needs to be /mnt/galaxydb/tmp ? Another solution: how can I provide a 
symlink to our FTP directory?

Hi Joachim,

It's not possible with the FTP upload method, but if you set user_library_import_dir in 
the config file, users can upload files from a server directory and choose the 
link option, just like an admin can.

--nate


Thanks for any hint,

Joachim


Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 08/08/2012 12:12 PM, Joachim Jacob wrote:

Dear devs,

Question about FTP upload: is it correct that Galaxy copies the data from the 
FTP upload directory to galaxy database instead of symlinking? Can I set 
somewhere the option to symlink instead of copying?

I run galaxy in a small virtual machine. The Galaxy database is on a network 
share. With 'get data' - 'Upload file', when importing the files I have 
uploaded with FTP, there is a process filling up the /tmp directory with the 
file I want to import.


Kind regards,
Joachim


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[galaxy-dev] ToolShed enhancement for repository lists

2012-08-22 Thread Peter Cock

Hi all,

This is an idea I mentioned to Dannon (off list during discussion
about moving the NCBI BLAST+ wrappers to the Tool Shed), and
he seemed positive about it.

Currently the left hand pane of the ToolShed (once logged in)
looks like this:

Search
* Search for valid tools
* Search for workflows
Repositories
* Browse by category
* Browse my repositories
* Browse my invalid tools
* Create new repository

I would find it useful to add another entry listing those repositories
where I have contributor rights. This could be included under the
existing Browse my repositories, but perhaps a separate entry
is better - if anyone has a concise description for this (so far
I've not come up with a short way of phrasing this).

Should I file this as an enhancement issue on BitBucket?

Regards,

Peter
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Re: [galaxy-dev] admin_user not being seen

2012-08-22 Thread Paul-Michael Agapow

 A peculiar quirk - I'm configuring a new Galaxy system for production
 use and can't get it to recognise my account as an admin, i.e. the admin
 menu doesn't appear after I've added my email address to the admin_user
 line in the universe file. Of course, I've restarted the instance
 multiple times, checked spelling and so forth. It's just not happening.

 Complication: we're using one Galaxy instance as the webserver with
 another as a job runner. I don't know if this might cause issues.

Thanks to Hans-Rudolf  Peter for possible solutions. The answer actually 
turned out to be my fault - as said, we're running Galaxy as a one db / two 
installation with a webserver/job runner ... and I was putting the admin_user 
in the wrong universe file. Mea culpa, mea maxima culpa.

--
Paul Agapow (paul-michael.aga...@hpa.org.uk)
Bioinformatics, Health Protection Agency (UK)



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[galaxy-dev] missing slash when installing from toolshed?

2012-08-22 Thread Dan Sullivan

Hi, Galaxy Developers,

I have a question that is very similar to the following thread;

http://dev.list.galaxyproject.org/Problem-fetching-updates-to-toolshed-tool-td4353417.html

Basically whenever I try to install a tool from the toolshed, it appears that a 
trailing slash is not appended to the Galaxy URL, which is causing a DNS lookup 
failure.  For example, the URL specified in the attached screenshot should be 
https://crigalaxy.uchicago.edu/admin_toolshed, however it is appearing as 
https://crigalaxy.uchicago.eduadmin_toolshed.Does anybody know if there are 
any known bugs that would cause this behavior?  I might venture down the road 
of modifying lib/galaxy/webapps/community/controllers/repository.py as 
suggested by the thread above, although I would like to avoid doing this if 
possible.  I am seeing experiencing this behavior on the following version of 
Galaxy:

 hg parent
changeset:   7400:ec29ce8e27a1

In addition to this, I feel that its worthwhile to mention that I am using the 
apache proxy balancer with web scaling, however based on what I have seen and 
tested, I do not believe this (apache) to be the root cause of my problem.  The 
URL below is a screenshot of the network debug I am seeing from the firebug 
extension in firefox.

https://webshare.uchicago.edu/users/dansully/Public/Screen%20Shot%202012-08-21%20at%203.22.27%20PM.png

If somebody has seen this, or could offer a suggestion to bring this issue to 
resolve, I would definitely be interested in your strategy.  Thank-you so much 
for your help and for your time.

Dan Sullivan
312-607-3702___
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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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Re: [galaxy-dev] [galaxy-user] LimitInternalRecursion

2012-08-22 Thread Scott McManus

It's the last rewrite rule that's causing the infinite recursion: 
RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] 

Check out this link: 
http://httpd.apache.org/docs/current/mod/mod_rewrite.html#rewriterule 
Look for the table of given rules and resulting substitutions - the proxying 
appears to be supported for other hosts but not the same host. 

-Scott 

- Original Message -

 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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   at usegalaxy.org . Please keep all replies on the list by
 
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Re: [galaxy-dev] [galaxy-user] LimitInternalRecursion

2012-08-22 Thread Nate Coraor

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 ^/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

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

[galaxy-dev] patch for vcf QUAL field with missing value . in lib/galaxy/visualization/tracks/data_providers.py

2012-08-22 Thread Jim Johnson


The VCF format ( 
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
 )
specifies . to represent missing values.

lib/galaxy/visualization/tracks/data_providers.py  throws an float conversion error when 
the qual field of  a vcf file has the missing value:  .

This can be remedied with the following patch,  trackster handles the None  
value when displaying the variant.

diff -r eb542e228a0f lib/galaxy/visualization/tracks/data_providers.py
--- a/lib/galaxy/visualization/tracks/data_providers.py Wed Aug 22 14:56:49 
2012 -0500
+++ b/lib/galaxy/visualization/tracks/data_providers.py Wed Aug 22 14:58:46 
2012 -0500
@@ -634,7 +634,7 @@
 # TODO? VCF does not have strand, so default to 
positive.
 +,
 new_seq,
-float( feature[5] ) ]
+None if feature[5] == '.' else float( feature[5] ) 
]
 rval.append(payload)

 return { 'data': rval, 'message': message }

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Re: [galaxy-dev] [galaxy-user] LimitInternalRecursion

[galaxy-dev] patch for vcf QUAL field with missing value . in lib/galaxy/visualization/tracks/data_providers.py

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