[galaxy-dev] Can't downgrade database.

[Makis Ladoukakis]

Hello everyone,


I tried to download a newer version of Galaxy (I had 15.10 and pulled 16.01 in 
a different directory) and now for some reason in my old working directory I 
get the error:


Your database has version '133' but this code expects version '129'.

Please backup your database and then migrate the schema by running 'sh 
manage_db.sh upgrade'.



when I tried:


sh manage_db.sh downgrade --version=129


I got the error:

Traceback (most recent call last):
  File "./scripts/manage_db.py", line 33, in 
invoke_migrate_main()
  File "./scripts/manage_db.py", line 30, in invoke_migrate_main
main( repository=repo, url=db_url )
  File 
"/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/shell.py",
 line 209, in main
ret = command_func(**kwargs)
  File 
"/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/api.py",
 line 202, in downgrade
return _migrate(url, repository, version, upgrade=False, err=err, **opts)
  File "", line 2, in _migrate
  File 
"/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/util/__init__.py",
 line 160, in with_engine
return f(*a, **kw)
  File 
"/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/api.py",
 line 345, in _migrate
changeset = schema.changeset(version)
  File 
"/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/schema.py",
 line 82, in changeset
changeset = self.repository.changeset(database, start_ver, version)
  File 
"/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/repository.py",
 line 225, in changeset
changes = [self.version(v).script(database, op) for v in versions]
  File 
"/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/repository.py",
 line 189, in version
return self.versions.version(*p, **k)
  File 
"/home/anastasia_dev/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/version.py",
 line 160, in version
return self.versions[VerNum(vernum)]
KeyError: 




I checked earlier posts stating  that i need to remove all .pyc files before 
downgrading. I did just that but nothing worked.


Any ideas?


Thank you in advance,

Efthymios Ladoukakis



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Re: [galaxy-dev] Python script can't can't import BioPython modules in Galaxy 16.01

[Makis Ladoukakis]

Yeah Linda, this was the case for me. When I started the virtual environment I 
reinstalled BioPython and everything worked again. I suggest you do the same to 
any packages you need for your tools.

Makis

To: galaxy-dev@lists.galaxyproject.org
From: linda.bak...@wur.nl
Date: Thu, 3 Mar 2016 14:10:44 +0100
Subject: Re: [galaxy-dev] Python script can't can't import BioPython modules in 
Galaxy 16.01


  

  
  
I guess this relates directly to my
  question as well...

  

  

  

  On 03/03/2016 01:06 PM, Makis Ladoukakis wrote:



  
  
  Hello everyone,



I've recently upgraded to Galaxy 16.01 and i have some issues
with a python wrapper from a tool. When I run it via Galaxy I
get the following error:



Traceback (most recent call last):
  File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", 
line 12, in 
from Bio import SeqIO
ImportError: No module named Bio


However when I click on the "view details" icon to copy the
command from the tool and run it on my command line the tool
works perfectly. In addition this issue occurs while I already
have installed BioPython.



When I type Python and write  "from Bio import SeqIO" I get no
error.



Can this be an issue related to the virtual environment that is
initialized each time Galaxy starts?



Thank you in advance,

Makis Ladoukakis





  
  

  
  

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-- 
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: linda.bak...@wur.nl
  


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[galaxy-dev] Python script can't can't import BioPython modules in Galaxy 16.01

[Makis Ladoukakis]

Hello everyone,

I've recently upgraded to Galaxy 16.01 and i have some issues with a python 
wrapper from a tool. When I run it via Galaxy I get the following error:

Traceback (most recent call last):
  File "/home/galaxy_user/galaxy/tools/myTools/know_parser/know_parser.py", 
line 12, in 
from Bio import SeqIO
ImportError: No module named Bio
However when I click on the "view details" icon to copy the command from the 
tool and run it on my command line the tool works perfectly. In addition this 
issue occurs while I already have installed BioPython.

When I type Python and write  "from Bio import SeqIO" I get no error.

Can this be an issue related to the virtual environment that is initialized 
each time Galaxy starts?

Thank you in advance,
Makis Ladoukakis




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Re: [galaxy-dev] Downgrade tool upload tool

[Makis Ladoukakis]

Thanks a lot Peter and Aysam! The fix worked perfectly!

Regards,
Makis

Date: Mon, 29 Feb 2016 22:18:37 -0500
Subject: Re: [galaxy-dev] Downgrade tool upload tool
From: aysam.guer...@gmail.com
To: p.j.a.c...@googlemail.com
CC: makis4e...@hotmail.com; j...@galaxyproject.org; 
galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org

Thanks Peter. I think you are right and that its a change in Galaxy which 
causes this routing issue. I have prepared a fix for it: 
https://github.com/galaxyproject/galaxy/compare/dev...guerler:fix_upload_link_000?expand=1.
 Ill double check tomorrow with those working on the routing and then issue a 
PR. Thanks a lot for reporting this Makis.

On Mon, Feb 29, 2016 at 8:17 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
Thanks for clarifying Makis,



I think this change is likely due to changes in Galaxy rather than

in the upload tool itself. On our (slightly out of date) Galaxy or the

public server, that URL no longer loads the original tool form -

you get the new drag-and-drop upload interface.



I would guess some of the special case code like this matters:

https://github.com/galaxyproject/galaxy/blob/fe6d22e1a7e4e6d38b15f4128554783765bc69a1/client/galaxy/scripts/mvc/tool/tools.js#L525



Probably Sam (Aysam) can give you more practical advice (CC'd)?



Peter



On Mon, Feb 29, 2016 at 12:29 PM, Makis Ladoukakis

<makis4e...@hotmail.com> wrote:

> I am making some clickable buttons in the home page of my instance through a

> java script that is called from the welcome.html file. These buttons

> correspond to my most used tools. For example I have a section like this:

>

> 

> 

> 

>

> 

>  src="feimg/GetData.gif"/>

> 

>  href="http://myserver/galaxy/tool_runner?tool_id=upload1;

> target="_parent"> height=300%/>

>  href="http://myserver/galaxy/library/browse_libraries; target="_parent"> src="feimg/Libraries.gif" width=250% height=300%/>

> 

> 

> 

> 

>   

>

> indicating two buttons one for the upload tool and one for the libraries.

> The libraries button work but when I click on the button for the upload tool

> the webpage just refreshes instead of opening the tool. This worked

> perfectly with the previous version of the upload tool and I was thinking

> how to get it back.

>

> Thank you,

> Makis

>

>

>> Date: Mon, 29 Feb 2016 11:39:26 +

>> Subject: Re: [galaxy-dev] Downgrade tool upload tool

>> From: p.j.a.c...@googlemail.com

>> To: makis4e...@hotmail.com

>> CC: j...@galaxyproject.org; galaxy-...@lists.bx.psu.edu;

>> galaxy-dev@lists.galaxyproject.org

>

>>

>> Hi Makis,

>>

>> The upload tool is a little special in that it is used internally by

>> Galaxy and doesn't entirely behave like a normal tool.

>>

>> What are you trying to achieve by "downgrading" it?

>>

>> Peter

>>

>> On Mon, Feb 29, 2016 at 11:29 AM, Makis Ladoukakis

>> <makis4e...@hotmail.com> wrote:

>> > What about if I used a second "tool upload" tool? I took the python

>> > script

>> > from an earlier version and named it upload_old.py and did the same for

>> > the

>> > xml file (upload.xml -> upload_old.xml) while changing the latter to

>> > call

>> > the new python script. Nevertheless when I did that and tried to run it

>> > I

>> > got a popup window with the following error:

>> >

>> > Tool request failed

>> >

>> > Uncaught exception in exposed API method:

>> >

>> >

>> > Is there a way to make this work? Or maybe another workaround?

>> >

>> > Thank you in advance,

>> > Makis

>> >

>> >

>> >

>> > 

>> > From: j...@galaxyproject.org

>> > Date: Fri, 26 Feb 2016 10:22:44 -0800

>> > Subject: Re: [galaxy-dev] Downgrade tool upload tool

>> > To: makis4e...@hotmail.com

>> > CC: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org

>> >

>> >

>> > Hello,

>> >

>> > The Upload tool is a direct component of Galaxy. To use an earlier

>> > version

>> > of the tool, I believe that you would have to run an earlier version of

>> > Galaxy.

>> >

>> > Others here can amend this, if they know of an alternative.

>> >

>> > Thanks,

>> >

>> > Jen

>> >

&

Re: [galaxy-dev] Downgrade tool upload tool

[Makis Ladoukakis]

What about if I used a second "tool upload" tool? I took the python script from 
an earlier version and named it upload_old.py and did the same for the xml file 
(upload.xml -> upload_old.xml) while changing the latter to call the new python 
script. Nevertheless when I did that and tried to run it I got a popup window 
with the following error:

Tool request failedUncaught exception in exposed API method:


Is there a way to make this work? Or maybe another workaround?

Thank you in advance,
Makis



From: j...@galaxyproject.org
Date: Fri, 26 Feb 2016 10:22:44 -0800
Subject: Re: [galaxy-dev] Downgrade tool upload tool
To: makis4e...@hotmail.com
CC: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org

Hello,
The Upload tool is a direct component of Galaxy. To use an earlier version of 
the tool, I believe that you would have to run an earlier version of Galaxy. 
Others here can amend this, if they know of an alternative. 
Thanks, Jen
--Jennifer Hillman-JacksonGalaxy Application Supporthttp://usegalaxy.org
http://galaxyproject.org
http://biostar.usegalaxy.org



On Fri, Feb 26, 2016 at 4:01 AM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:



Hello everyone,

I was wondering whether it's possible to downgrade the upload tool to the 
previous version(1.1.4).

I copied the upload.py and upload.xml scripts from a previous galaxy version to 
the tools/data_source/ directory and reloaded the tool as admin but it hasn't 
changed even when I restarted the server. 

Do I have to change something else in addition?

Thank you,
Makis
  

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[galaxy-dev] Downgrade tool upload tool

[Makis Ladoukakis]

Hello everyone,

I was wondering whether it's possible to downgrade the upload tool to the 
previous version(1.1.4).

I copied the upload.py and upload.xml scripts from a previous galaxy version to 
the tools/data_source/ directory and reloaded the tool as admin but it hasn't 
changed even when I restarted the server. 

Do I have to change something else in addition?

Thank you,
Makis
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Re: [galaxy-dev] Galaxy 16.01 Release

[Makis Ladoukakis]

Thanks a lot Nate! You are right!

yum install mariadb-devel

did the trick.

Cheers,
Makis

From: n...@bx.psu.edu
Date: Thu, 25 Feb 2016 10:12:51 -0500
Subject: Re: [galaxy-dev] Galaxy 16.01 Release
To: makis4e...@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org

On Thu, Feb 25, 2016 at 2:49 AM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:



Just upgraded from the last version and after I run the run.sh script I get the 
following error:

mysql_config: command not found
Traceback (most recent call last):
  File "", line 1, in 
  File "/tmp/pip-build-xd3cnM/MySQL-python/setup.py", line 17, in 
metadata, options = get_config()
  File "setup_posix.py", line 43, in get_config
libs = mysql_config("libs_r")
  File "setup_posix.py", line 25, in mysql_config
raise EnvironmentError("%s not found" % (mysql_config.path,))
EnvironmentError: mysql_config not found



Any idea why? 

I am running on CentOS 7.1.1503  with MariaDB installed.

Hi Makis,
Please make sure that you have the -devel package for MariaDB installed. 
MySQL_Python is looking for the `mysql_config` command to be able to build, but 
it's not present on your system.
--nate 

Kind regards,
Makis

From: n...@bx.psu.edu
Date: Wed, 24 Feb 2016 16:56:19 -0500
To: galaxy-annou...@lists.galaxyproject.org; galaxy-dev@lists.galaxyproject.org
CC: galaxy-committ...@lists.galaxyproject.org
Subject: [galaxy-dev] Galaxy 16.01 Release

The Galaxy Committers team is pleased to announce the January 2016 (v16.01) 
release of Galaxy. Galaxy administrators should also be aware of the security 
announcements that I am posting simultaneously with this release announcement. 
The release notes follow.

From: https://docs.galaxyproject.org/en/master/releases/16.01_announce.html


January 2016 Galaxy Release (v 16.01)
Highlights
Interactive Tours
The interactive tours framework allows developers and deployers to build 
interactive tutorials for users superimposed on the actual Galaxy web front 
end. Unlike video tutorials, these will not become stale and are truly 
interactive (allowing users to actually navigate and interact with Galaxy). 
Galaxy 16.01 ships with two example tours and new ones can easily be added by 
creating a small YAML file describing the tour. Try the Galaxy UI tour on Main.
Wheels
Galaxy’s Python dependencies have traditionally been distributed as eggs using 
custom dependency management code to enable Galaxy to distribute binary 
dependencies (enabling quick downloads and minimal system requirements). With 
this release all of that infrastructure has been replaced with a modern Python 
infrastructure based on pip and wheels. Work done as part of this to enable 
binary dependencies on Linux has been included with the recently released pip 8.
Detailed documentation on these changes and their impact under a variety of 
Galaxy deployment scenarios can be found in the Galaxy Framework Dependencies 
section of the Admin documentation.
Nested Workflows
Workflows may now run other workflows as a single abstract step in the parent 
workflow. This allows for reusing or subworkflows in your analyses.
Github
New% git clone -b master https://github.com/galaxyproject/galaxy.gitUpdate to 
latest stable release% git checkout master && pull --ff-only origin 
masterUpdate to exact version% git checkout v16.01
BitBucket
Upgrade% hg pull% hg update latest_16.01
See our wiki for additional details regarding the source code locations.
Deprecation Notices
Barring a strong outcry from deployers, 16.01 will be the last release of 
Galaxy to support Python 2.6. For more information, see Galaxy Github Issue 
#1596.

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Re: [galaxy-dev] Collapse tool panel and history panel

[Makis Ladoukakis]

Just an update/bump of the issue. With the new 16.01 version I made the changes 
in the /client/galaxy/scripts/apps/analysis.js 
b/client/galaxy/scripts/apps/analysis.js file but the none of the panels were 
collapsed even when i restarted my Galaxy instance.

I don't really get the mechanics behind it. Seems like any changes i do either 
in the js files or the mako scripts never take effect in the actual instance. I 
even tried to delete everything in there leaving just a blank file to test my 
theory and after restart the Galaxy instance initializes with no errors at all.

Any ideas?
Makis

From: makis4e...@hotmail.com
To: dannon.ba...@gmail.com
Date: Mon, 22 Feb 2016 13:47:59 +0200
CC: galaxy-...@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Collapse tool panel and history panel




The git log ..origin/master command produced no output so I guess I have the 
latest release (15.10.1 maybe?). The git pull command confirmed that. Should I 
use a release from the dev branch?

Kind regards,
Makis

Date: Fri, 19 Feb 2016 08:39:35 -0500
Subject: Re: [galaxy-dev] Collapse tool panel and history panel
From: dannon.ba...@gmail.com
To: makis4e...@hotmail.com
CC: galaxy-...@lists.bx.psu.edu

Sure, I can help.  Which version of Galaxy are you currently running?  I didn't 
check the history very well and the fix I suggested will work for the 
forthcoming 16.01 release (or current dev branch), but not 15.10.

On Fri, Feb 19, 2016 at 8:32 AM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:



Hello Dannon,

Sorry for asking but can you help me out a little bit with that? I searched in 
my galaxy directory in order to add those two lines you mention in the link but 
there is no galaxy/scripts/apps/analysis.js file and neither any file 
containing the string 'analysisPage.right.historyView'. 

Any advice?

Thank you,
Makis
Date: Mon, 28 Dec 2015 14:30:02 -0500
Subject: Re: [galaxy-dev] Collapse tool panel and history panel
From: dannon.ba...@gmail.com
To: makis4e...@hotmail.com
CC: galaxy-...@lists.bx.psu.edu

Hi Makis,
We've restructured much of the client code fairly recently.  Something like 
this should work for you now:
https://gist.github.com/dannon/bd470d9c70019b07cb8b


Sorry for the slow response!
-Dannon

On Sat, Dec 19, 2015 at 2:57 PM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:



Shamelessly bumping my own question... Does anyone have any ideas about 
collapsing the history and tool panel?

Thank you,
Makis Ladoukakis

From: makis4e...@hotmail.com
To: galaxy-...@lists.bx.psu.edu
Date: Wed, 16 Dec 2015 13:41:19 +0200
Subject: [galaxy-dev] Collapse tool panel and history panel




Hello,

Does anyone know how to start my Galaxy instance with the history panel and 
tool panel collapsed by default?

I used to do it by editing the galaxy/templates/base/base_panels.mako script 
and adding

lp.do_toggle();

and 

rp.do_toggle();

inside the if sections of %if self.has_left_panel: and %if 
self.has_right_panel: respectively but with my new installed instance this 
doesn't seem to work anymore.

Any ideas anyone?

Thank you,
Makis Ladoukakis



  

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Re: [galaxy-dev] Collapse tool panel and history panel

[Makis Ladoukakis]

Hello Dannon,

Sorry for asking but can you help me out a little bit with that? I searched in 
my galaxy directory in order to add those two lines you mention in the link but 
there is no galaxy/scripts/apps/analysis.js file and neither any file 
containing the string 'analysisPage.right.historyView'. 

Any advice?

Thank you,
Makis
Date: Mon, 28 Dec 2015 14:30:02 -0500
Subject: Re: [galaxy-dev] Collapse tool panel and history panel
From: dannon.ba...@gmail.com
To: makis4e...@hotmail.com
CC: galaxy-...@lists.bx.psu.edu

Hi Makis,
We've restructured much of the client code fairly recently.  Something like 
this should work for you now:
https://gist.github.com/dannon/bd470d9c70019b07cb8b


Sorry for the slow response!
-Dannon

On Sat, Dec 19, 2015 at 2:57 PM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:



Shamelessly bumping my own question... Does anyone have any ideas about 
collapsing the history and tool panel?

Thank you,
Makis Ladoukakis

From: makis4e...@hotmail.com
To: galaxy-...@lists.bx.psu.edu
Date: Wed, 16 Dec 2015 13:41:19 +0200
Subject: [galaxy-dev] Collapse tool panel and history panel




Hello,

Does anyone know how to start my Galaxy instance with the history panel and 
tool panel collapsed by default?

I used to do it by editing the galaxy/templates/base/base_panels.mako script 
and adding

lp.do_toggle();

and 

rp.do_toggle();

inside the if sections of %if self.has_left_panel: and %if 
self.has_right_panel: respectively but with my new installed instance this 
doesn't seem to work anymore.

Any ideas anyone?

Thank you,
Makis Ladoukakis



  

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[galaxy-dev] Job is queued for imported dataset in library

[Makis Ladoukakis]

Hello,

I've been trying the newest Galaxy version and there seems to be an issue with 
it. I am importing a dataset via system filepath (through the admin interface) 
in a library but it remains in queued status without ever changing. I can still 
download the dataset though.

Has anyone experienced this before?

Thank you,
Makis Ladoukakis
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Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

[Makis Ladoukakis]

Hello thank you for your reply.

I followed the instructions on your blog together with the Galaxy tutorial and 
even though I changed the port to 127.0.0.1:8091 in supervisord.conf it refuses 
the connection:

supervisorctl status   
http://localhost:9001 refused connection

The port is the wrong one as well!!! It was 8091 the port that I used

ps ax |grep uwsgi doesn't display a working uwsgi service

and sudo lsof -i :4001 returns nothing.

My supervisord.conf file is the following:

[inet_http_server]
port=127.0.0.1:8091

[supervisord]

[supervisorctl]

[program:galaxy_uwsgi]
command = /usr/bin/uwsgi --plugin python --ini-paste 
/home/galaxy/galaxy/config/galaxy.ini
directory   = /home/galaxy/galaxy
umask   = 022
autostart   = true
autorestart = true
startsecs   = 10
user= galaxy
environment = 
PATH=/home/galaxy/galaxy_env:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin,PYTHON_EGG_CACHE=/home/galaxy/galaxy/.python-eggs,PYTHONPATH=/home/galaxy/galaxy/eggs/PasteDeploy-1.5.0-py2.7.egg
numprocs= 1
stopsignal  = INT

[program:handler]
command = /home/galaxy/galaxy_env/bin/python ./scripts/paster.py serve 
config/galaxy.ini --server-name=handler%(process_num)s 
--pid-file=/home/galaxy/galaxy/handler%(process_num)s.pid 
--log-file=/home/galaxy/galaxy/handler%(process_num)s.log
directory   = /home/galaxy/galaxy
process_name= handler%(process_num)s
numprocs= 8
umask   = 022
autostart   = true
autorestart = true
startsecs   = 15
user= galaxy
environment = PYTHON_EGG_CACHE=/home/galaxy/galaxy/.python-eggs
#I didn't include SGE_root as i don't have sge installed

[group:galaxy]
programs = handler, galaxy_uwsgi



Can you help me please?

What am I missing?

Thank you,
Makis


Date: Fri, 4 Dec 2015 17:57:38 +0200
Subject: RE: [galaxy-dev] Multiple web servers and handlers Galaxy failed
From: p...@sanbi.ac.za
To: makis4e...@hotmail.com
CC: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org

I've written up my experiences in a 
blog:http://pvh.wp.sanbi.ac.za/2015/12/04/faster-galaxy-with-uwsgi/The only 
Galaxy side changes were the ones mentioned on the Scaling page. The Bad 
Gateway message means that Apache can't talk to the uWSGI so what is the state 
of uWSGI?
Are you using supervisord? Does supervisorctl show the uWSGI process running? 
Does ps ax |grep uwsgi show it running? What does sudo lsof -i :4001 show is 
listening on port 4001? That would be the starting point of my debugging.
Peter

On 4 Dec 2015 10:57, "Makis Ladoukakis" <makis4e...@hotmail.com> wrote:



It is uwsgi that I am trying but with apache. Could you let me know what 
changes you made to the configuration of Galaxy?

Thank you,
Makis

Date: Fri, 4 Dec 2015 10:01:56 +0200
Subject: Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed
From: p...@sanbi.ac.za
To: makis4e...@hotmail.com
CC: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org

Hi Makis, I recently implemented something like this using uWSGI with a nginx 
frontend. Would you consider using uWSGI instead of your current approach?
On 4 Dec 2015 09:40, "Makis Ladoukakis" <makis4e...@hotmail.com> wrote:



Sorry for bumping my own question but I didn't get any replies. Has anyone 
succesfully installed a production Galaxy instance? 

I could really use some advice.

Thank you,
Makis

From: makis4e...@hotmail.com
To: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
Date: Tue, 1 Dec 2015 18:03:44 +0200
Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed




Hello everyone,

I am trying to setup a Galaxy instance for a multi-user production environment 
and I tried to follow the instructions here:

https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy

but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh 
--daemon) I got the following error in my browser:Bad Gateway
The proxy server received an invalid
response from an upstream server.


I don't get any errors from the paster.log files so I am guessing the error is 
somewhere in my apache configuration although I can't see where it could be.


Has anyone encountered this problem before?

Kind regards,
Makis


P.S. My apache configuration is as follows:

I added that to my apache httpd.conf file:

#for galaxy
#RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) 
/home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*) 
/home/galaxy/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static

Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

[Makis Ladoukakis]

It is uwsgi that I am trying but with apache. Could you let me know what 
changes you made to the configuration of Galaxy?

Thank you,
Makis

Date: Fri, 4 Dec 2015 10:01:56 +0200
Subject: Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed
From: p...@sanbi.ac.za
To: makis4e...@hotmail.com
CC: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org

Hi Makis, I recently implemented something like this using uWSGI with a nginx 
frontend. Would you consider using uWSGI instead of your current approach?
On 4 Dec 2015 09:40, "Makis Ladoukakis" <makis4e...@hotmail.com> wrote:



Sorry for bumping my own question but I didn't get any replies. Has anyone 
succesfully installed a production Galaxy instance? 

I could really use some advice.

Thank you,
Makis

From: makis4e...@hotmail.com
To: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
Date: Tue, 1 Dec 2015 18:03:44 +0200
Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed




Hello everyone,

I am trying to setup a Galaxy instance for a multi-user production environment 
and I tried to follow the instructions here:

https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy

but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh 
--daemon) I got the following error in my browser:Bad Gateway
The proxy server received an invalid
response from an upstream server.


I don't get any errors from the paster.log files so I am guessing the error is 
somewhere in my apache configuration although I can't see where it could be.


Has anyone encountered this problem before?

Kind regards,
Makis


P.S. My apache configuration is as follows:

I added that to my apache httpd.conf file:

#for galaxy
#RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) 
/home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*) 
/home/galaxy/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L]

LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so


Sethandler uwsgi-handler
uWSGISocket 127.0.0.1:4001
uWSGImaxVars 512


I am also attaching my job_conf.xml and galaxy.ini file.

  

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Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

[Makis Ladoukakis]

Sorry for bumping my own question but I didn't get any replies. Has anyone 
succesfully installed a production Galaxy instance? 

I could really use some advice.

Thank you,
Makis

From: makis4e...@hotmail.com
To: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
Date: Tue, 1 Dec 2015 18:03:44 +0200
Subject: [galaxy-dev] Multiple web servers and handlers Galaxy failed




Hello everyone,

I am trying to setup a Galaxy instance for a multi-user production environment 
and I tried to follow the instructions here:

https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy

but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh 
--daemon) I got the following error in my browser:Bad Gateway
The proxy server received an invalid
response from an upstream server.


I don't get any errors from the paster.log files so I am guessing the error is 
somewhere in my apache configuration although I can't see where it could be.


Has anyone encountered this problem before?

Kind regards,
Makis


P.S. My apache configuration is as follows:

I added that to my apache httpd.conf file:

#for galaxy
#RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) 
/home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*) 
/home/galaxy/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L]

LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so


Sethandler uwsgi-handler
uWSGISocket 127.0.0.1:4001
uWSGImaxVars 512


I am also attaching my job_conf.xml and galaxy.ini file.

  

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  http://galaxyproject.org/search/mailinglists/ 
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[galaxy-dev] Multiple web servers and handlers Galaxy failed

[Makis Ladoukakis]

Hello everyone,

I am trying to setup a Galaxy instance for a multi-user production environment 
and I tried to follow the instructions here:

https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy

but when I tried to start my galaxy instance (GALAXY_RUN_ALL=1 sh run.sh 
--daemon) I got the following error in my browser:Bad Gateway
The proxy server received an invalid
response from an upstream server.


I don't get any errors from the paster.log files so I am guessing the error is 
somewhere in my apache configuration although I can't see where it could be.


Has anyone encountered this problem before?

Kind regards,
Makis


P.S. My apache configuration is as follows:

I added that to my apache httpd.conf file:

#for galaxy
#RewriteRule ^/galaxy(.*) http://localhost:8091$1 [P]
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) 
/home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*) 
/home/galaxy/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L]

LoadModule uwsgi_module /etc/httpd/modules/mod_uwsgi.so


Sethandler uwsgi-handler
uWSGISocket 127.0.0.1:4001
uWSGImaxVars 512


I am also attaching my job_conf.xml and galaxy.ini file.

  

galaxy.ini
Description: Binary data


job_conf.xml
Description: XML document
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Re: [galaxy-dev] login problem (redirection to the login page)

[Makis Ladoukakis]

Hello,

I've been struggling with the login issue with Galaxy for a while now. Try to 
use "incognito mode" on your browser when accessing the url for Galaxy and see 
what happens. Also if you don't really need for your users to activate their 
accounts by e-mail set the "user_activation_on=False" in galaxy.ini. You have 
to have set up your smtp server for that which can be a fuss.

Cheers,
Makis

Date: Thu, 5 Nov 2015 18:16:56 +0100
From: floreline.touch...@gmail.com
To: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] login problem (redirection to the login page)

Hi,
I come back to you with some news of my login problem.
I delete my browser cache and cookies with no result. 
I restart all my services (Apache, PostgreSQL, Galaxy) with no more result.
I try to start fresh with my PostgreSQL database cluster (to clear all the user 
information). But it didn't solve the problem. When I register with a user 
name, I get : 
- on the browser side:
"Now logged in as @example.com.
Verification email has been sent to your email address. Please verify it by 
clicking the activation link in the email.
Please check your spam/trash folder in case you cannot find the message.
Return to the home page."
- on the server side :
"galaxy.util ERROR 2015-11-05 17:21:25,394 Mail is not configured for this 
Galaxy instance.
galaxy.util INFO 2015-11-05 17:21:25,394 From nobody Thu Nov  5 17:21:25 2015
Content-Type: text/plain; charset="us-ascii"
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
To: @example.com
From:
Subject: Galaxy Account Activation
Hello ,
In order to complete the activation process for @example.com begun on 
11/05/15 at ip:port, please click on the following link to verify your account:
http://ip:port/activate?email=%40example.com_token=3285151b21c8f85590db0f0c1089110d934f2400
By clicking on the above link and opening a Galaxy account you are also 
confirming that you have read and agreed to Galaxy's Terms and Conditions for 
use of this service (None). This includes a quota limit of one account per 
user. Attempts to subvert this limit by creating multiple accounts or through 
any other method may result in termination of all associated accounts and data.
Please contact us if you need help with your account at: None. You can also 
browse resources available at: None.
More about the Galaxy Project can be found at galaxyproject.org
Your Galaxy Team"

I get a new entry in the galaxy_user table (PostgreSQl table) with "f" in the 
activate field. which I find logical.
If I activate the account with the link, the value becomes "t". Still logical.
But I'm redirected to the welcome page after the login and there's only the 
"login" and "register" options under the user tab.
I have no error on the server log.
For each connection attempt I can see this line : 
"galaxy.auth.providers.localdb DEBUG 2015-11-05 17:31:04,681 User: 
@example.com, LOCALDB: True
10.80.6.195 - - [05/Nov/2015:17:31:04 +0200] "POST /user/login?use_panels=False 
HTTP/1.1" 200 - "http://ip:port/user/login; "Mozilla/5.0 (Windows NT 6.1; 
rv:39.0) Gecko/20100101 Firefox/39.0"
10.80.6.195 - - [05/Nov/2015:17:31:04 +0200] "GET /root HTTP/1.1" 200 - 
"http://ip:port/user/login?use_panels=False; "Mozilla/5.0 (Windows NT 6.1; 
rv:39.0) Gecko/20100101 Firefox/39.0"
10.80.6.195 - - [05/Nov/2015:17:31:05 +0200] "GET /root/welcome HTTP/1.1" 302 - 
"http://ip:port/root; "Mozilla/5.0 (Windows NT 6.1; rv:39.0) Gecko/20100101 
Firefox/39.0"
"
Is it normal ?
My postgreSQl database seems to work fine.
It doesn't come from a browser cache issue (I clear mine and I try to login to 
Galaxy with another computer on the same network).
Or are there other caches I should be aware of ?
Is there another way to get an operational application ? And where did this 
issue come from ? I'm only testing the application but it surprises me since I 
had a working instance for few months. 
Thanks in advance,
F.T


2015-11-04 16:44 GMT+01:00 Floreline TOUCHARD :
Update :When I clic several time on the galaxy name, I got this on the log : 
Exception happened during processing of request from ('127.0.0.1', 45055)
Traceback (most recent call last):
  File path/to/galaxy-master/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", 
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
  File "/usr/lib64/python2.6/SocketServer.py", line 332, in finish_request
self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib64/python2.6/SocketServer.py", line 628, in __init__
self.finish()
  File "/usr/lib64/python2.6/SocketServer.py", line 671, in finish
self.wfile.flush()
  File "/usr/lib64/python2.6/socket.py", line 303, in flush
self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe
 
2015-11-04 15:09 GMT+01:00 Floreline TOUCHARD :
Here is some details :when I enable the access to Galaxy without authentication 
I'm 

Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused

[Makis Ladoukakis]

So yeah you might be on to something here. When I commented the Rewrite rules I 
could access my galaxy instance from myservername:8081 with or without the 
index.html file placed in /var/www/html. When I did place it in the directory 
though and I tried with the rewrite rules my server gave me the following error:

 script not found or unable to stat: /var/www/cgi-bin/common

and once again the galaxy page was blank.

Any ideas why? What is apache's problem with the rewrite rules being there?

thank you,
Makis

Subject: Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused
From: suder...@cs.vassar.edu
Date: Tue, 3 Nov 2015 13:06:03 -0500
CC: federico.zambe...@gmail.com; galaxy-dev@lists.galaxyproject.org
To: makis4e...@hotmail.com

Very odd that you were getting "Address is use" errors then..  What have you 
set the port to in your galaxy.ini file?
The missing index.html/index.php won't make a difference to Galaxy, but it 
might prevent Apache from starting up.  I would put a simple index.html file, 
say:
You should not see this.
in /var/www/html just so Apache is happy and if you see that at least you will 
know Apache is up and running and listening on the correct ports. I would also 
forego the Apache rewrite rules until you know Galaxy is working.
Keith
On Nov 3, 2015, at 12:15 PM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:Νο, no other service is running on 8081. This is the output of netstat 
-tulpn:

tcp0  0 0.0.0.0:33060.0.0.0:*   LISTEN  
-
tcp0  0 0.0.0.0:22  0.0.0.0:*   LISTEN  
-
tcp0  0 127.0.0.1:250.0.0.0:*   LISTEN  
-
tcp6   0  0 :::80   :::*LISTEN  
-
tcp6   0  0 :::22   :::*LISTEN  
-
tcp6   0  0 ::1:25  :::*LISTEN  
-
udp0  0 0.0.0.0:123 0.0.0.0:*   
-
udp0  0 127.0.0.1:323   0.0.0.0:*   
-
udp0  0 0.0.0.0:53530.0.0.0:*   
-
udp0  0 0.0.0.0:33715   0.0.0.0:*   
-
udp6   0  0 :::123  :::*
-
udp6   0  0 ::1:323 :::* 

And no I only have an info.php in that directory. Does that affect Galaxy in 
any way?

Thank you,
Makis

Subject: Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused
From: suder...@cs.vassar.edu
Date: Tue, 3 Nov 2015 12:07:12 -0500
CC: federico.zambe...@gmail.com; galaxy-dev@lists.galaxyproject.org
To: makis4e...@hotmail.com

Do you have another service running on 8081?  I see the server is complaining 
about that address already being in use.  Also, do you have an index.html or 
welcome.html in /var/www/html?
Cheers,Keith
On Nov 3, 2015, at 11:39 AM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:Hello,

Unfortunately I cannot change web servers at the moment. There are a lot of 
applications that I would need to make changes for the nginx configuration plus 
i am not very experienced with nginx (apparently not with apache as well 
outside debian systems).

Thank you,
Makis

> To: galaxy-dev@lists.galaxyproject.org
> From: federico.zambe...@gmail.com
> Date: Tue, 3 Nov 2015 17:19:59 +0100
> Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection
> refused
> 
> Il 03/11/15 11:53, Makis Ladoukakis ha scritto:
> 
> >
> > Nothing seems to work on my server. Is Galaxy even compatible with
> > CentOS? Is there something else that I am missing?
> >
> 
> Hello, I'm running a production Galaxy Server on CentOS and I can assure 
> you it is perfectly feasible. But I'm using NGINX as a web server so I'm 
> not able to help you with Apache configuration, sorry. Did you try to 
> use NGINX instead of Apache in order to see if the problem is Apache 
> related or system related?
> 
> Best,
> Federico Z.
> 
> 
> >
> >
> > 
> > From: david.trudg...@utsouthwestern.edu
> > To: makis4e...@hotmail.com; jcsanch...@gmail.com
> > CC: galaxy-...@lists.bx.psu.edu
> > Date: Fri, 23 Oct 2015 17:30:51 +
> > Subject: RE: [galaxy-dev] FW: Galaxy on Centos via Apache - connection
> > refused
> >
> > SELinux policies are very strict on CentOS by default. Apache isn't
> > allowed to access files outside of its standard directories, nor access
> > network resources. Your local Galaxy apps server is a network resource -
> > even though it's local.
> >
> > If you want to keep SELinux on then use audit2allow to see what policies
> > will enable access:
>

Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

[Makis Ladoukakis]

Also when I tried to run it without the addition of port 8081 in apache 
configuration file (when all I saw was a blank page) the error in 
/var/log/httpd/error_log was the following:

 AH01276: Cannot serve directory /var/www/html/: No matching DirectoryIndex 
(index.html,welcome.html,index.php) found, and server-generated directory index 
forbidden by Options directive


From: makis4e...@hotmail.com
To: david.trudg...@utsouthwestern.edu; jcsanch...@gmail.com; plat...@platyna.org
Date: Tue, 3 Nov 2015 12:53:36 +0200
CC: galaxy-...@lists.bx.psu.edu
Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused




So I disabled SELinux

But that didn't make any difference. While the run.sh runs I still can't see 
anything but a blank page.

When I changed my apache configuration to include port 8081, the script didn't 
even run producing the error:


Traceback (most recent call last):
  File "./scripts/paster.py", line 32, in 
serve.run()
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line 
1052, in run
invoke(command, command_name, options, args[1:])
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line 
1058, in invoke
exit_code = runner.run(args)
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line 
221, in run
result = self.command()
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line 
664, in command
serve()
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line 
648, in serve
server(app)
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 
294, in server_wrapper
**context.local_conf)
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 
99, in fix_call
val = callable(*args, **kw)
  File 
"/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
line 1342, in server_runner
serve(wsgi_app, **kwargs)
  File 
"/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
line 1291, in serve
request_queue_size=request_queue_size)
  File 
"/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
line 1134, in __init__
request_queue_size=request_queue_size)
  File 
"/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
line 1113, in __init__
request_queue_size=request_queue_size)
  File 
"/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
line 328, in __init__
HTTPServer.__init__(self, server_address, RequestHandlerClass)
  File "/usr/lib64/python2.7/SocketServer.py", line 419, in __init__
self.server_bind()
  File "/usr/lib64/python2.7/BaseHTTPServer.py", line 108, in server_bind
SocketServer.TCPServer.server_bind(self)
  File "/usr/lib64/python2.7/SocketServer.py", line 430, in server_bind
self.socket.bind(self.server_address)
  File "/usr/lib64/python2.7/socket.py", line 224, in meth
return getattr(self._sock,name)(*args)
socket.error: [Errno 98] Address already in use

That error was the same when I changed 80 to 8081 and when I added a second 
Listen with 8081.

Nothing seems to work on my server. Is Galaxy even compatible with CentOS? Is 
there something else that I am missing?

Any help would be appreciated. This installation seems impossible.

Thank you,
Makis




From: david.trudg...@utsouthwestern.edu
To: makis4e...@hotmail.com; jcsanch...@gmail.com
CC: galaxy-...@lists.bx.psu.edu
Date: Fri, 23 Oct 2015 17:30:51 +
Subject: RE: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused









SELinux policies are very strict on CentOS by default. Apache isn’t allowed to 
access files outside of its standard directories, nor
 access network resources. Your local Galaxy apps server is a network resource 
– even though it’s local.
 
If you want to keep SELinux on then use audit2allow to see what policies will 
enable access:
 
cat /var/log/audit/audit.log | audit2allow –v
 
Then you can use setsebool (temporary) and setsebool –P (permanent) to enable.
 
 

--

David Trudgian Ph.D.

Computational Scientist, BioHPC

UT Southwestern Medical Center

Dallas, TX 75390-9039

Tel: (214) 648-4833

 


From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org]
On Behalf Of Makis Ladoukakis

Sent: Friday, October 23, 2015 10:30 AM

To: Juan Carlos <jcsanch...@gmail.com>

Cc: galaxy-...@lists.bx.psu.edu

Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused


 

Hello,



That didn't work. The apache restart failed with the following error:



SELinux is preventing /usr/sbin/httpd from name_bind access on the tcp_socket 
port 8081.



Any idea why?



Kind regards,

Makis




Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - 

Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

[Makis Ladoukakis]

So I disabled SELinux

But that didn't make any difference. While the run.sh runs I still can't see 
anything but a blank page.

When I changed my apache configuration to include port 8081, the script didn't 
even run producing the error:


Traceback (most recent call last):
  File "./scripts/paster.py", line 32, in 
serve.run()
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line 
1052, in run
invoke(command, command_name, options, args[1:])
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line 
1058, in invoke
exit_code = runner.run(args)
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line 
221, in run
result = self.command()
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line 
664, in command
serve()
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line 
648, in serve
server(app)
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 
294, in server_wrapper
**context.local_conf)
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 
99, in fix_call
val = callable(*args, **kw)
  File 
"/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
line 1342, in server_runner
serve(wsgi_app, **kwargs)
  File 
"/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
line 1291, in serve
request_queue_size=request_queue_size)
  File 
"/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
line 1134, in __init__
request_queue_size=request_queue_size)
  File 
"/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
line 1113, in __init__
request_queue_size=request_queue_size)
  File 
"/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
line 328, in __init__
HTTPServer.__init__(self, server_address, RequestHandlerClass)
  File "/usr/lib64/python2.7/SocketServer.py", line 419, in __init__
self.server_bind()
  File "/usr/lib64/python2.7/BaseHTTPServer.py", line 108, in server_bind
SocketServer.TCPServer.server_bind(self)
  File "/usr/lib64/python2.7/SocketServer.py", line 430, in server_bind
self.socket.bind(self.server_address)
  File "/usr/lib64/python2.7/socket.py", line 224, in meth
return getattr(self._sock,name)(*args)
socket.error: [Errno 98] Address already in use

That error was the same when I changed 80 to 8081 and when I added a second 
Listen with 8081.

Nothing seems to work on my server. Is Galaxy even compatible with CentOS? Is 
there something else that I am missing?

Any help would be appreciated. This installation seems impossible.

Thank you,
Makis




From: david.trudg...@utsouthwestern.edu
To: makis4e...@hotmail.com; jcsanch...@gmail.com
CC: galaxy-...@lists.bx.psu.edu
Date: Fri, 23 Oct 2015 17:30:51 +
Subject: RE: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused









SELinux policies are very strict on CentOS by default. Apache isn’t allowed to 
access files outside of its standard directories, nor
 access network resources. Your local Galaxy apps server is a network resource 
– even though it’s local.
 
If you want to keep SELinux on then use audit2allow to see what policies will 
enable access:
 
cat /var/log/audit/audit.log | audit2allow –v
 
Then you can use setsebool (temporary) and setsebool –P (permanent) to enable.
 
 

--

David Trudgian Ph.D.

Computational Scientist, BioHPC

UT Southwestern Medical Center

Dallas, TX 75390-9039

Tel: (214) 648-4833

 


From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org]
On Behalf Of Makis Ladoukakis

Sent: Friday, October 23, 2015 10:30 AM

To: Juan Carlos <jcsanch...@gmail.com>

Cc: galaxy-...@lists.bx.psu.edu

Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused


 

Hello,



That didn't work. The apache restart failed with the following error:



SELinux is preventing /usr/sbin/httpd from name_bind access on the tcp_socket 
port 8081.



Any idea why?



Kind regards,

Makis




Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

From: jcsanch...@gmail.com

Date: Tue, 20 Oct 2015 22:25:00 +1030

CC: galaxy-...@lists.bx.psu.edu

To: makis4e...@hotmail.com

 


Hi,


If you have a line in your Apache conf like 


"Listen 80"


change to 


"Listen 8081"


 


 




On 20 Oct 2015, at 21:00, Makis Ladoukakis <makis4e...@hotmail.com> wrote:




Hello,



I am sorry but I have really no experience with setting up the Apache web 
server so I am not really sure how to do that. Can you please help me out with 
it? My apache configuration file is in /etc/httpd/conf/ directory and there are 
no directories such as /sites-

Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

[Makis Ladoukakis]

Hello,

I am sorry but I have really no experience with setting up the Apache web 
server so I am not really sure how to do that. Can you please help me out with 
it? My apache configuration file is in /etc/httpd/conf/ directory and there are 
no directories such as /sites-available/ or /sites-enabled/ (as I would find in 
an ubuntu installation).

What I did already (after some advice from the server admin) is open up the 
8081 port like that:



firewall-cmd
 --permanent  --add-port=8081/tcp

firewall-cmd
 --reload


and then I got another error:



 [cgi:error] [pid
29603] [client 115.230.124.164:4559] script not found or unable to stat:
/var/www/cgi-bin/common

[autoindex:error]
[pid 29716] [client 218.76.28.36:4468] AH01276: Cannot serve directory
/var/www/html/: No matching DirectoryIndex (index.html,index.php) found, and
server-generated directory index forbidden by Options directive


which I tried to solve by adding welcome.html as a recognizable filename in the 
apache configuration:





DirectoryIndex index.html welcome.html




but nothing worked and now the error_log shows the following:

[Tue Oct 20 13:15:23.719295 2015] [mpm_prefork:notice] [pid 29598] AH00170: 
caught SIGWINCH, shutting down gracefully
[Tue Oct 20 13:15:24.810684 2015] [core:notice] [pid 46896] SELinux policy 
enabled; httpd running as context system_u:system_r:httpd_t:s0
[Tue Oct 20 13:15:24.811647 2015] [suexec:notice] [pid 46896] AH01232: suEXEC 
mechanism enabled (wrapper: /usr/sbin/suexec)
[Tue Oct 20 13:15:24.846399 2015] [so:warn] [pid 46896] AH01574: module 
wsgi_module is already loaded, skipping
[Tue Oct 20 13:15:24.847316 2015] [auth_digest:notice] [pid 46896] AH01757: 
generating secret for digest authentication ...
[Tue Oct 20 13:15:24.848294 2015] [lbmethod_heartbeat:notice] [pid 46896] 
AH02282: No slotmem from mod_heartmonitor
[Tue Oct 20 13:15:24.870033 2015] [mpm_prefork:notice] [pid 46896] AH00163: 
Apache/2.4.6 (CentOS) PHP/5.4.16 mod_wsgi/3.4 Python/2.7.5 configured -- 
resuming normal operations
[Tue Oct 20 13:15:24.870075 2015] [core:notice] [pid 46896] AH00094: Command 
line: '/usr/sbin/httpd -D FOREGROUND'

And the webpage that galaxy is supposed to appear is still blank.

Any ideas?

Thank you,
Makis

 

Date: Tue, 20 Oct 2015 11:01:44 +1030
Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused
From: jcsanch...@gmail.com
To: makis4e...@hotmail.com
CC: galaxy-...@lists.bx.psu.edu

hi,
Maybe sounds silly, but have you tried to put the apache configuration in a 
virtual host within the sites-enable site?

cheersjc
On Tue, Oct 20, 2015 at 12:36 AM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:



Forwading to this list too. I am not sure if they are two separate lists.

Makis

From: makis4e...@hotmail.com
To: galaxy-dev@lists.galaxyproject.org
Date: Mon, 19 Oct 2015 17:04:13 +0300
Subject: [galaxy-dev] Galaxy on Centos via Apache -  connection refused




Dear all,

I've been trying to set up a Galaxy instance on my CentOS server but even when 
I manage to run the simplest configuration correctly I can't seem to get it 
right on my browser as the connection is refused.

I have changed the host to 0.0.0.0, the port to 8081 and made the appropriate 
changes in Apache configuration file:

RewriteEngine on
RewriteRule ^/galaxy_test(.*) http://localhost:8081$1 [P]
RewriteRule ^/galaxy_test$ /galaxy_test/ [R]
RewriteRule ^/galaxy_test/static/style/(.*) 
/home/galaxy_test/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy_test/static/scripts/(.*) 
/home/galaxy_test/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy_test/static/(.*) /home/galaxy_test/galaxy/static/$1 [L]
RewriteRule ^/galaxy_test/favicon.ico 
/home/galaxy_test/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy_test/robots.txt /home/galaxy_test/galaxy/static/robots.txt 
[L]

So when I tried to run it the first time I got the "temporarily out of service" 
error on my browser and the following error in apache log:

[Mon Oct 19 05:56:45.308714 2015] [proxy:error] [pid 18505] (13)Permission 
denied: AH00957: HTTP: attempt to connect to 127.0.0.1:8081 (*) failed
[Mon Oct 19 05:56:45.308774 2015] [proxy_http:error] [pid 18505] [client 
185.25.151.159:39629] AH01114: HTTP: failed to make connection to backend: 
localhost

Searching the internet I found the following solution:



/usr/sbin/setsebool
httpd_can_network_connect 1


/usr/sbin/setsebool -P
httpd_can_network_connect 1




but when I restarted my galaxy my browser would now show just a blank page and 
the error log of apache was:

[Mon Oct 19 15:29:09.425120 2015] [proxy:error] [pid 29699] (111)Connection 
refused: AH00957: HTTP: attempt to connect to 127.0.0.1:8081 (*) failed
[Mon Oct 19 15:29:09.425167 2015] [proxy_http:error] [pid 29699] [client 
147.102.86.121:51865] AH01114: HTTP: failed to make connection to backend: 
localhost


Has anyone encountered that?

Kind regards,
Makis






P.S. In case that helps the outpu

[galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

[Makis Ladoukakis]

Forwading to this list too. I am not sure if they are two separate lists.

Makis

From: makis4e...@hotmail.com
To: galaxy-dev@lists.galaxyproject.org
Date: Mon, 19 Oct 2015 17:04:13 +0300
Subject: [galaxy-dev] Galaxy on Centos via Apache -  connection refused




Dear all,

I've been trying to set up a Galaxy instance on my CentOS server but even when 
I manage to run the simplest configuration correctly I can't seem to get it 
right on my browser as the connection is refused.

I have changed the host to 0.0.0.0, the port to 8081 and made the appropriate 
changes in Apache configuration file:

RewriteEngine on
RewriteRule ^/galaxy_test(.*) http://localhost:8081$1 [P]
RewriteRule ^/galaxy_test$ /galaxy_test/ [R]
RewriteRule ^/galaxy_test/static/style/(.*) 
/home/galaxy_test/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy_test/static/scripts/(.*) 
/home/galaxy_test/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy_test/static/(.*) /home/galaxy_test/galaxy/static/$1 [L]
RewriteRule ^/galaxy_test/favicon.ico 
/home/galaxy_test/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy_test/robots.txt /home/galaxy_test/galaxy/static/robots.txt 
[L]

So when I tried to run it the first time I got the "temporarily out of service" 
error on my browser and the following error in apache log:

[Mon Oct 19 05:56:45.308714 2015] [proxy:error] [pid 18505] (13)Permission 
denied: AH00957: HTTP: attempt to connect to 127.0.0.1:8081 (*) failed
[Mon Oct 19 05:56:45.308774 2015] [proxy_http:error] [pid 18505] [client 
185.25.151.159:39629] AH01114: HTTP: failed to make connection to backend: 
localhost

Searching the internet I found the following solution:



/usr/sbin/setsebool
httpd_can_network_connect 1

/usr/sbin/setsebool -P
httpd_can_network_connect 1



but when I restarted my galaxy my browser would now show just a blank page and 
the error log of apache was:

[Mon Oct 19 15:29:09.425120 2015] [proxy:error] [pid 29699] (111)Connection 
refused: AH00957: HTTP: attempt to connect to 127.0.0.1:8081 (*) failed
[Mon Oct 19 15:29:09.425167 2015] [proxy_http:error] [pid 29699] [client 
147.102.86.121:51865] AH01114: HTTP: failed to make connection to backend: 
localhost


Has anyone encountered that?

Kind regards,
Makis






P.S. In case that helps the output of iptables -L is the following:
Chain INPUT (policy ACCEPT)
target prot opt source   destination 
ACCEPT all  --  anywhere anywhere ctstate 
RELATED,ESTABLISHED
ACCEPT all  --  anywhere anywhere
INPUT_direct  all  --  anywhere anywhere
INPUT_ZONES_SOURCE  all  --  anywhere anywhere
INPUT_ZONES  all  --  anywhere anywhere
ACCEPT icmp --  anywhere anywhere
REJECT all  --  anywhere anywhere reject-with 
icmp-host-prohibited

Chain FORWARD (policy ACCEPT)
target prot opt source   destination 
ACCEPT all  --  anywhere anywhere ctstate 
RELATED,ESTABLISHED
ACCEPT all  --  anywhere anywhere
FORWARD_direct  all  --  anywhere anywhere
FORWARD_IN_ZONES_SOURCE  all  --  anywhere anywhere
FORWARD_IN_ZONES  all  --  anywhere anywhere
FORWARD_OUT_ZONES_SOURCE  all  --  anywhere anywhere
FORWARD_OUT_ZONES  all  --  anywhere anywhere
ACCEPT icmp --  anywhere anywhere
REJECT all  --  anywhere anywhere reject-with 
icmp-host-prohibited

Chain OUTPUT (policy ACCEPT)
target prot opt source   destination 
OUTPUT_direct  all  --  anywhere anywhere

Chain FORWARD_IN_ZONES (1 references)
target prot opt source   destination 
FWDI_public  all  --  anywhere anywhere[goto] 
FWDI_public  all  --  anywhere anywhere[goto] 

Chain FORWARD_IN_ZONES_SOURCE (1 references)
target prot opt source   destination 

Chain FORWARD_OUT_ZONES (1 references)
target prot opt source   destination 
FWDO_public  all  --  anywhere anywhere[goto] 
FWDO_public  all  --  anywhere anywhere[goto] 

Chain FORWARD_OUT_ZONES_SOURCE (1 references)
target prot opt source   destination 

Chain FORWARD_direct (1 references)
target prot opt source   destination 

Chain FWDI_public (2 references)
target prot opt source   destination 
FWDI_public_log  all  --  anywhere anywhere
FWDI_public_deny  all  --  anywhere anywhere
FWDI_public_allow  all  --  anywhere anywhere

Chain FWDI_public_allow (1 

[galaxy-dev] Galaxy on Centos via Apache - connection refused

[Makis Ladoukakis]

Dear all,

I've been trying to set up a Galaxy instance on my CentOS server but even when 
I manage to run the simplest configuration correctly I can't seem to get it 
right on my browser as the connection is refused.

I have changed the host to 0.0.0.0, the port to 8081 and made the appropriate 
changes in Apache configuration file:

RewriteEngine on
RewriteRule ^/galaxy_test(.*) http://localhost:8081$1 [P]
RewriteRule ^/galaxy_test$ /galaxy_test/ [R]
RewriteRule ^/galaxy_test/static/style/(.*) 
/home/galaxy_test/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy_test/static/scripts/(.*) 
/home/galaxy_test/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy_test/static/(.*) /home/galaxy_test/galaxy/static/$1 [L]
RewriteRule ^/galaxy_test/favicon.ico 
/home/galaxy_test/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy_test/robots.txt /home/galaxy_test/galaxy/static/robots.txt 
[L]

So when I tried to run it the first time I got the "temporarily out of service" 
error on my browser and the following error in apache log:

[Mon Oct 19 05:56:45.308714 2015] [proxy:error] [pid 18505] (13)Permission 
denied: AH00957: HTTP: attempt to connect to 127.0.0.1:8081 (*) failed
[Mon Oct 19 05:56:45.308774 2015] [proxy_http:error] [pid 18505] [client 
185.25.151.159:39629] AH01114: HTTP: failed to make connection to backend: 
localhost

Searching the internet I found the following solution:



/usr/sbin/setsebool
httpd_can_network_connect 1

/usr/sbin/setsebool -P
httpd_can_network_connect 1



but when I restarted my galaxy my browser would now show just a blank page and 
the error log of apache was:

[Mon Oct 19 15:29:09.425120 2015] [proxy:error] [pid 29699] (111)Connection 
refused: AH00957: HTTP: attempt to connect to 127.0.0.1:8081 (*) failed
[Mon Oct 19 15:29:09.425167 2015] [proxy_http:error] [pid 29699] [client 
147.102.86.121:51865] AH01114: HTTP: failed to make connection to backend: 
localhost


Has anyone encountered that?

Kind regards,
Makis






P.S. In case that helps the output of iptables -L is the following:
Chain INPUT (policy ACCEPT)
target prot opt source   destination 
ACCEPT all  --  anywhere anywhere ctstate 
RELATED,ESTABLISHED
ACCEPT all  --  anywhere anywhere
INPUT_direct  all  --  anywhere anywhere
INPUT_ZONES_SOURCE  all  --  anywhere anywhere
INPUT_ZONES  all  --  anywhere anywhere
ACCEPT icmp --  anywhere anywhere
REJECT all  --  anywhere anywhere reject-with 
icmp-host-prohibited

Chain FORWARD (policy ACCEPT)
target prot opt source   destination 
ACCEPT all  --  anywhere anywhere ctstate 
RELATED,ESTABLISHED
ACCEPT all  --  anywhere anywhere
FORWARD_direct  all  --  anywhere anywhere
FORWARD_IN_ZONES_SOURCE  all  --  anywhere anywhere
FORWARD_IN_ZONES  all  --  anywhere anywhere
FORWARD_OUT_ZONES_SOURCE  all  --  anywhere anywhere
FORWARD_OUT_ZONES  all  --  anywhere anywhere
ACCEPT icmp --  anywhere anywhere
REJECT all  --  anywhere anywhere reject-with 
icmp-host-prohibited

Chain OUTPUT (policy ACCEPT)
target prot opt source   destination 
OUTPUT_direct  all  --  anywhere anywhere

Chain FORWARD_IN_ZONES (1 references)
target prot opt source   destination 
FWDI_public  all  --  anywhere anywhere[goto] 
FWDI_public  all  --  anywhere anywhere[goto] 

Chain FORWARD_IN_ZONES_SOURCE (1 references)
target prot opt source   destination 

Chain FORWARD_OUT_ZONES (1 references)
target prot opt source   destination 
FWDO_public  all  --  anywhere anywhere[goto] 
FWDO_public  all  --  anywhere anywhere[goto] 

Chain FORWARD_OUT_ZONES_SOURCE (1 references)
target prot opt source   destination 

Chain FORWARD_direct (1 references)
target prot opt source   destination 

Chain FWDI_public (2 references)
target prot opt source   destination 
FWDI_public_log  all  --  anywhere anywhere
FWDI_public_deny  all  --  anywhere anywhere
FWDI_public_allow  all  --  anywhere anywhere

Chain FWDI_public_allow (1 references)
target prot opt source   destination 

Chain FWDI_public_deny (1 references)
target prot opt source   destination 

Chain FWDI_public_log (1 references)
target prot opt source   destination 

Re: [galaxy-dev] Galaxy in cluster mode won't start from 0.0.0.0.

[Makis Ladoukakis]

Actually I just fixed that by adding the "host" in each handler  but I get the 
same error as before from the browser when I try to access the webpage:


Bad Gateway
The proxy server received an invalid
response from an upstream server.


My apache configuration settings are the following:

RewriteEngine on
#RewriteRule ^(.*) http://localhost:8080$1 [P]
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) /home/galaxy/galaxy/static/june_2007_sty$
RewriteRule ^/galaxy/static/scripts/(.*) /home/galaxy/galaxy/static/scripts/pac$
RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy/static/robots.txt [L]

LoadModule proxy_uwsgi_module /usr/lib64/httpd/modules/mod_proxy_uwsgi.so
LoadModule uwsgi_module /usr/lib64/httpd/modules/mod_uwsgi.so


Sethandler uwsgi-handler
uWSGISocket 0.0.0.0:4001
uWSGImaxVars 512




From: makis4e...@hotmail.com
To: galaxy-dev@lists.galaxyproject.org
Date: Wed, 14 Oct 2015 12:17:05 +0300
Subject: [galaxy-dev] Galaxy in cluster mode won't start from 0.0.0.0.




Hello everyone,

I am trying to set up a local Galaxy instance publicly available and configured 
via  pbs/torque in order to fully exploit a multi-cpu server.

So I changed my job_conf.xml and my galaxy.ini files (described in the end of 
the e-mail)  according to the istructions on the Galaxy site  but when I tried 
to run the run.sh script:

 GALAXY_RUN_ALL=1 sh run.sh --daemon

all the handlers start from 127.0.0.1 instead of 0.0.0.0.

Has anyone encountered that issue before. Am I missing something?

Thank you,
Makis

The changes in the files:

galaxy.ini

[uwsgi]
processes = 12
stats = 0.0.0.0:9191 # i had this at 127.0.0.1:9191 but with no difference
socket = 0.0.0.0:4001 # I had this at 127.0.0.1:4001 but with no difference
pythonpath = lib
threads = 4
logto = /home/galaxy/uwsgi.log
master = True

[server:handler0]
use = egg:Paste#http
port = 8090
use_threadpool = True
threadpool_workers = 10

[server:handler1]
use = egg:Paste#http
port = 8091
use_threadpool = True
threadpool_workers = 10

[server:handler2]
use = egg:Paste#http
port = 8092
use_threadpool = True
threadpool_workers = 10

[server:handler3]
use = egg:Paste#http
port = 8093
use_threadpool = True
threadpool_workers = 10

[server:handler4]
use = egg:Paste#http
port = 8094
use_threadpool = True
threadpool_workers = 10

[server:handler5]
use = egg:Paste#http
port = 8095
use_threadpool = True
threadpool_workers = 10

# The port on which to listen.
 #port = 8090

# The address on which to listen.  By default, only listen to localhost (Galaxy
# will not be accessible over the network).  Use '0.0.0.0' to listen on all
# available network interfaces.
host = 0.0.0.0


job_conf.xml




















@other.cluster


walltime=72:00:00, nodes=1:ppn=8
128




  

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Re: [galaxy-dev] pbs_python can't be installed via scramble

[Makis Ladoukakis]

Hello Will,

The second command returns the container.hpp inside the directory of the torque 
source which i used to install it:

find / -name container.hpp
/home/user/torque-5.1.1.2-1_18e4a5f1/src/include/container.hpp

I noticed there is also a log.h file there.

the first command doesn't return anything (I've search manually too, nothing 
inside /usr/local/include/).

How do I fix this? Shall I change the export command of PBS_PYTHON_INCLUDEDIR?

Thank you,
Makis



Date: Thu, 24 Sep 2015 08:31:07 -0700
Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble
From: who...@lygos.com
To: makis4e...@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org

And does find /usr/local/include -name container.hppor find / -name 
container.hppreturn torque/src/include/container.hpp ?
My guess is you installed binaries for Torque, but the scrambling requires the 
Torque source (or at least the header files form Torque).
-Will
On Thu, Sep 24, 2015 at 1:16 AM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:



Hello Will,

Thanks again for your reply. Yes I had already tried these but I got the same 
container.hpp error.

The only thing different in my case is that the names of the directories of the 
directories are a bit different:

export PBS_PYTHON_INCLUDEDIR=/usr/local/include/
export PBSCONFIG=/usr/local/bin/pbs-config
export LIBTORQUE_DIR=/usr/local/lib/libtorque.so
python scripts/scramble.py -e pbs_python

Any ideas?

Kind regards,
Makis



Date: Wed, 23 Sep 2015 07:06:32 -0700
Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble
From: who...@lygos.com
To: makis4e...@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org

Hi Makis,
The thread I posted does have the exact same container.hpp error and proposes a 
solution.
Did you try setting your PBS_PYTHON_INCLUDEDIR to point to your torque/include 
directory, as mentioned in that thread?
from the thread:export PBS_PYTHON_INCLUDEDIR=/usr/local/torque/include/
export PBSCONFIG=/usr/local/torque/bin/pbs-config
export LIBTORQUE_DIR=/usr/local/torque/lib/libtorque.so

-Will

On Wed, Sep 23, 2015 at 5:49 AM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:



Hello Will,

Thank you for your reply. I had already checked this thread before as I browsed 
through the mailing list for "pbs_python" issues. It doesn't have the same 
errors (can't locate log.h and when i provide it it wants the container.hpp ) 
and up to one point i've already followed the "rescrambling" of the pbs_python.

Anyone else had any experience with that?

Thank you,
Makis

Date: Tue, 22 Sep 2015 09:35:11 -0700
Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble
From: who...@lygos.com
To: makis4e...@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org

Here is an old thread that looks rather similar to your 
problems:https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/msg00078.html

-Will

On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:



Hello everyone,

I'm trying to set up a Galaxy instance on a multi-core server in my university 
so according to the instructions here:

https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS

I installed Torque, changed the eggs.ini file by adding the 4.4.0. version of 
pbs_python

and tried to setup pbs_python via scramble:

LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python

When I did that I got the error:

Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir via 
PBS_PYTHON_INCLUDEDIR variable)
Traceback (most recent call last):
  File "scripts/scramble.py", line 50, in 
egg.scramble()
  File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in scramble
self.run_scramble_script()
  File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in 
run_scramble_script
raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( 
sys._getframe().f_code.co_name, self.name, self.version ) )
galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed 
for pbs_python 4.4.0

so I did some digging around and found that the file I need is in 

/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/

(please correct me if I am wrong)

So I tried again using:

 
PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/
 LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python

but then I got the error:

In file included from src/C++/pbs_ifl.h:90:0,
 from src/C++/pbs_wrap.cxx:2978:
/usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp: No 
such file or directory
 #include "container.hpp"


Can someone help me please?

Kind regards,
Makis

  

___

Please keep all replies on the list by 

Re: [galaxy-dev] pbs_python can't be installed via scramble

[Makis Ladoukakis]

Hello again,

So I figured out a workaround. I had to downgrade torque to version 4.2.10 
(that is the latest version of torque that doesn't have any compatibility 
issues with pbs_python 4.4.0).

Then i used:

export PBS_PYTHON_INCLUDEDIR=/home/user/torque-4.2.10/src/include/

to include... well... the include directory

So the pbs_python egg for 4.4.0. was created succesfully.

But then after running galaxy:

GALAXY_RUN_ALL=1 sh run.sh --daemon

I got another error:

galaxy.jobs.runners DEBUG 2015-09-25 15:08:22,030 Loading DRMAARunner with 
params: {'invalidjobexception_retries': '0', 'invalidjobexception_state': 'ok', 
'internalexception_retries': '0', 'internalexception_state': 'ok'}
galaxy.jobs.runners.state_handler_factory DEBUG 2015-09-25 15:08:22,030 Loaded 
'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
Traceback (most recent call last):
  File "/home/galaxy/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 51, in 
app_factory
app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs )
  File "/home/galaxy/galaxy/lib/galaxy/app.py", line 142, in __init__
self.job_manager = manager.JobManager( self )
  File "/home/galaxy/galaxy/lib/galaxy/jobs/manager.py", line 23, in __init__
self.job_handler = handler.JobHandler( app )
  File "/home/galaxy/galaxy/lib/galaxy/jobs/handler.py", line 32, in __init__
self.dispatcher = DefaultJobDispatcher( app )
  File "/home/galaxy/galaxy/lib/galaxy/jobs/handler.py", line 722, in __init__
self.job_runners = self.app.job_config.get_job_runner_plugins( 
self.app.config.server_name )
  File "/home/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 667, in 
get_job_runner_plugins
rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 
'kwds', {} ) )
  File "/home/galaxy/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 62, in 
__init__
drmaa = __import__( "drmaa" )
  File "/home/galaxy/galaxy/eggs/drmaa-0.7.6-py2.7.egg/drmaa/__init__.py", line 
48, in 
ZipImportError: bad local file header in 
/home/galaxy/galaxy/eggs/drmaa-0.7.6-py2.7.egg
Removing PID file handler0.pid

Has anyone ever encountered that?

Thank you,
Makis


From: makis4e...@hotmail.com
To: who...@lygos.com
Date: Fri, 25 Sep 2015 12:07:02 +0300
CC: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble





Hello Will,

The second command returns the container.hpp inside the directory of the torque 
source which i used to install it:

find / -name container.hpp
/home/user/torque-5.1.1.2-1_18e4a5f1/src/include/container.hpp

I noticed there is also a log.h file there.

the first command doesn't return anything (I've search manually too, nothing 
inside /usr/local/include/).

How do I fix this? Shall I change the export command of PBS_PYTHON_INCLUDEDIR?

Thank you,
Makis



Date: Thu, 24 Sep 2015 08:31:07 -0700
Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble
From: who...@lygos.com
To: makis4e...@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org

And does find /usr/local/include -name container.hppor find / -name 
container.hppreturn torque/src/include/container.hpp ?
My guess is you installed binaries for Torque, but the scrambling requires the 
Torque source (or at least the header files form Torque).
-Will
On Thu, Sep 24, 2015 at 1:16 AM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:



Hello Will,

Thanks again for your reply. Yes I had already tried these but I got the same 
container.hpp error.

The only thing different in my case is that the names of the directories of the 
directories are a bit different:

export PBS_PYTHON_INCLUDEDIR=/usr/local/include/
export PBSCONFIG=/usr/local/bin/pbs-config
export LIBTORQUE_DIR=/usr/local/lib/libtorque.so
python scripts/scramble.py -e pbs_python

Any ideas?

Kind regards,
Makis



Date: Wed, 23 Sep 2015 07:06:32 -0700
Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble
From: who...@lygos.com
To: makis4e...@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org

Hi Makis,
The thread I posted does have the exact same container.hpp error and proposes a 
solution.
Did you try setting your PBS_PYTHON_INCLUDEDIR to point to your torque/include 
directory, as mentioned in that thread?
from the thread:export PBS_PYTHON_INCLUDEDIR=/usr/local/torque/include/
export PBSCONFIG=/usr/local/torque/bin/pbs-config
export LIBTORQUE_DIR=/usr/local/torque/lib/libtorque.so

-Will

On Wed, Sep 23, 2015 at 5:49 AM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:



Hello Will,

Thank you for your reply. I had already checked this thread before as I browsed 
through the mailing list for "pbs_python" issues. It doesn't have the same 
errors (can't locate log.h and when i provide it it wants the container.hpp ) 
and up to one point i've already followed the "rescrambling" of the pbs_python

Re: [galaxy-dev] pbs_python can't be installed via scramble

[Makis Ladoukakis]

Hello Will,

Thanks again for your reply. Yes I had already tried these but I got the same 
container.hpp error.

The only thing different in my case is that the names of the directories of the 
directories are a bit different:

export PBS_PYTHON_INCLUDEDIR=/usr/local/include/
export PBSCONFIG=/usr/local/bin/pbs-config
export LIBTORQUE_DIR=/usr/local/lib/libtorque.so
python scripts/scramble.py -e pbs_python

Any ideas?

Kind regards,
Makis



Date: Wed, 23 Sep 2015 07:06:32 -0700
Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble
From: who...@lygos.com
To: makis4e...@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org

Hi Makis,
The thread I posted does have the exact same container.hpp error and proposes a 
solution.
Did you try setting your PBS_PYTHON_INCLUDEDIR to point to your torque/include 
directory, as mentioned in that thread?
from the thread:export PBS_PYTHON_INCLUDEDIR=/usr/local/torque/include/
export PBSCONFIG=/usr/local/torque/bin/pbs-config
export LIBTORQUE_DIR=/usr/local/torque/lib/libtorque.so

-Will

On Wed, Sep 23, 2015 at 5:49 AM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:



Hello Will,

Thank you for your reply. I had already checked this thread before as I browsed 
through the mailing list for "pbs_python" issues. It doesn't have the same 
errors (can't locate log.h and when i provide it it wants the container.hpp ) 
and up to one point i've already followed the "rescrambling" of the pbs_python.

Anyone else had any experience with that?

Thank you,
Makis

Date: Tue, 22 Sep 2015 09:35:11 -0700
Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble
From: who...@lygos.com
To: makis4e...@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org

Here is an old thread that looks rather similar to your 
problems:https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/msg00078.html

-Will

On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:



Hello everyone,

I'm trying to set up a Galaxy instance on a multi-core server in my university 
so according to the instructions here:

https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS

I installed Torque, changed the eggs.ini file by adding the 4.4.0. version of 
pbs_python

and tried to setup pbs_python via scramble:

LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python

When I did that I got the error:

Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir via 
PBS_PYTHON_INCLUDEDIR variable)
Traceback (most recent call last):
  File "scripts/scramble.py", line 50, in 
egg.scramble()
  File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in scramble
self.run_scramble_script()
  File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in 
run_scramble_script
raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( 
sys._getframe().f_code.co_name, self.name, self.version ) )
galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed 
for pbs_python 4.4.0

so I did some digging around and found that the file I need is in 

/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/

(please correct me if I am wrong)

So I tried again using:

 
PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/
 LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python

but then I got the error:

In file included from src/C++/pbs_ifl.h:90:0,
 from src/C++/pbs_wrap.cxx:2978:
/usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp: No 
such file or directory
 #include "container.hpp"


Can someone help me please?

Kind regards,
Makis

  

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[galaxy-dev] pbs_python can't be installed via scramble

[Makis Ladoukakis]

Hello everyone,

I'm trying to set up a Galaxy instance on a multi-core server in my university 
so according to the instructions here:

https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS

I installed Torque, changed the eggs.ini file by adding the 4.4.0. version of 
pbs_python

and tried to setup pbs_python via scramble:

LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python

When I did that I got the error:

Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir via 
PBS_PYTHON_INCLUDEDIR variable)
Traceback (most recent call last):
  File "scripts/scramble.py", line 50, in 
egg.scramble()
  File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in scramble
self.run_scramble_script()
  File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in 
run_scramble_script
raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( 
sys._getframe().f_code.co_name, self.name, self.version ) )
galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed 
for pbs_python 4.4.0

so I did some digging around and found that the file I need is in 

/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/

(please correct me if I am wrong)

So I tried again using:

 
PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/
 LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python

but then I got the error:

In file included from src/C++/pbs_ifl.h:90:0,
 from src/C++/pbs_wrap.cxx:2978:
/usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp: No 
such file or directory
 #include "container.hpp"


Can someone help me please?

Kind regards,
Makis

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Re: [galaxy-dev] Login problem with Galaxy instance

[Makis Ladoukakis]

Actually that actually worked. Couldn't see it before.

Thanks Nicola!


From: makis4e...@hotmail.com
To: nsora...@tiscali.it
Date: Wed, 17 Jun 2015 09:06:52 +0300
CC: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Login problem with Galaxy instance




Hi Nicola thanks for the help. Unfortunately that didn't work. I was also 
looking at the Galaxy log and I found this line right next to the login attempt:



galaxy.webapps.galaxy.controllers.user
WARNING 2015-06-16 18:44:33,165 Redirect URL is outside of Galaxy, will
redirect to Galaxy root instead:


I could use any help.

Kind regards,
Efthymios Ladoukakis

Date: Tue, 16 Jun 2015 18:30:12 +0200
From: nsora...@tiscali.it
To: makis4e...@hotmail.com
CC: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Login problem with Galaxy instance



Hi Efthymios,
have you tried to delete the cookies in the browser? That may fix the problem.

Cheers,
Nicola

Il 16.06.2015 17:46 Makis Ladoukakis ha scritto:



Hi I have some experience with setting up Galaxy instances but I came across a 
very peculiar issue when trying to setup the newest version.

While I am able to register as a new user when I try to login I get redirected 
to the home page without being logged in. 

In the galaxy.ini is I disabled user_activation as I don't want a confirmation 
e-mail for new registrations, altered the host to 0.0.0.0 for network use and 
changed the port (which i opened up through the apache webserver)

Am I missing something?

Any help would be appreciated.

Kind regards,
Efthymios Ladoukakis






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E chiami gratis anche i numeri fissi e mobili nel mondo!

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[galaxy-dev] How to hide history and tool panel

[Makis Ladoukakis]

Hi I was wandering how I can make the tool panel and history (left and right 
panels) to be hidden when the Galaxy instance starts. In the older versions you 
had to modify some .mako files but the newest setup has me a little confused.

I'd appreciate any help.

Kind regards,
Efthymios Ladoukakis
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in your mail client.  To manage your subscriptions to this
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  http://galaxyproject.org/search/mailinglists/