Re: [galaxy-dev] unexpanded macros

2015-12-10 Thread John Chilton 
Hey Brad,

  What version of Galaxy are you on? Parameterized macros are pretty
new and will not work on older Galaxies.

-John

On Fri, Dec 4, 2015 at 3:36 AM, Langhorst, Brad  wrote:
> Hi:
> I just installed hisat2 and the data manager from the toolshed ….
>
> Some macros seem not to be expanded when I load the tool in the UI (even
> across galaxy restarts)
> e.g. I see @FTYPE@ instead of fastqsanger
>
> the data manager produces this error:
>
> Fatal error: Exit code 1 ()
> Traceback (most recent call last):
>   File
> "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py",
> line 85, in 
> main()
>   File
> "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py",
> line 79, in main
> build_hisat_index( data_manager_dict, options, params, sequence_id,
> sequence_name )
>   File
> "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py",
> line 41, in build_hisat_index
> proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
>   File "/mnt/galaxy/data/galaxy/sw/lib/python2.7/subprocess.py", line 710,
> in __init__
> errread, errwrite)
>   File "/mnt/galaxy/data/galaxy/sw/lib/python2.7/subprocess.py", line 1327,
> in _execute_child
> raise child_exception
> OSError: [Errno 13] Permission denied
>
>
> that seems to be a result of a missing execute bit for the binaries in
>
> tool-deps/hisat/2.0/iuc/package_hisat_2_0/c65f00072e57/bin
>
>
>
> Should I file issues, or did my installation go wrong?
>
> Any hints to get this running?
>
>
> Brad
>
>
>
> --
> Brad Langhorst, Ph.D.
> Development Scientist
> New England Biolabs
>
>
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Re: [galaxy-dev] AssertionError: ID tag is required for a Display Application

2015-12-10 Thread John Chilton 
Despite sounding very similar, visualizations and display applications
are different things - display applications for the most part send or
expose Galaxy data to outside sources, visualizations run on the
Galaxy server and the client side.

It seems like you are trying to configure a visualization as a display
application. I would figure out which you need and base your example
plugin on an existing type of that.

More information @

https://wiki.galaxyproject.org/Admin/Tools/External%20Display%20Applications%20Tutorial
https://wiki.galaxyproject.org/Learn/Visualization

-John



On Thu, Dec 10, 2015 at 9:32 PM,   wrote:
> Dear Galaxy Team,
> I am trying to create my own visualization for a unique datatype but I
> cannot get past this error in the load.  Where is the ID tag assigned for my
> visualization?
> Thanks
> Bob
>
> galaxy.datatypes.registry ERROR 2015-12-10 15:10:13,440 Error loading
> display application
> (/home/HM_galaxy/config/plugins/visualizations/heatmap/config/heatmap.xml):
> ID tag is required for a Display Application
> Traceback (most recent call last):
> File "/home/HM_galaxy/lib/galaxy/datatypes/registry.py", line 563, in
> load_display_applications
> display_app = DisplayApplication.from_file( config_path, app )
> File
> "/home/rbrown/HM_galaxy/lib/galaxy/datatypes/display_applications/application.py",
> line 253, in from_file
> return cls.from_elem( parse_xml( filename ).getroot(), app,
> filename=filename )
> File
> "/home/rbrown/HM_galaxy/lib/galaxy/datatypes/display_applications/application.py",
> line 257, in from_elem
> att_dict = cls._get_attributes_from_elem( elem )
> File
> "/home/rbrown/HM_galaxy/lib/galaxy/datatypes/display_applications/application.py",
> line 265, in _get_attributes_from_elem
> assert display_id, “ID tag is required for a Display Application”
> AssertionError: ID tag is required for a Display Application
>
> The  /visualizations/heatmap/config/heatmap.xml  file it is complaining
> about is below and I have a template under /templates
>
> 
> 
> 
> 
> 
> HistoryDatasetAssociation
>  result_type="datatype">text.chm
> dataset_id
> 
> 
> 
>  required="true">dataset_id
> 
> heatmap.mako
> 
>
>
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Re: [galaxy-dev] unexpanded macros

2015-12-10 Thread John Chilton 
Yeah - those wrappers are not going to work with 15.05. Parameterized
XML macros were added in 15.07 it looks like
(http://galaxy.readthedocs.org/en/master/releases/15.07_announce.html).

-John

On Thu, Dec 10, 2015 at 10:28 PM, Langhorst, Brad  wrote:
> Hi:
>
> I’m at release_15.05
>
> Some of this was just wrapper bugs (missing @xxx@) looks like dave already
> fixed this...
> I don’t know about this @FTYPE@ stuff though.
>
>
> it’s working for me like this:
>
>
> diff -r 6d4d39720545 hisat2.xml
> --- a/hisat2.xml Sat Oct 10 16:24:47 2015 -0400
> +++ b/hisat2.xml Thu Dec 10 17:07:38 2015 -0500
> @@ -193,7 +193,7 @@
>  First Strand (R/RF)
>  Second Strand (F/FR)
>  
> - name="ignore_quals" type="boolean" truevalue="--no-spliced-alignment"
> falsevalue="" label="Disable spliced alignment" />
> + name="no_spliced_alignment" type="boolean"
> truevalue="--no-spliced-alignment" falsevalue="" label="Disable spliced
> alignment" />
>  
>  
>  Use default reporting.
> diff -r 6d4d39720545 hisat2_macros.xml
> --- a/hisat2_macros.xml Sat Oct 10 16:24:47 2015 -0400
> +++ b/hisat2_macros.xml Thu Dec 10 17:07:38 2015 -0500
> @@ -25,12 +25,12 @@
>  
>  
>  
> - multiple="true" name="reads_f" type="data" />
> - multiple="true" name="reads_r" type="data" />
> + multiple="true" name="reads_f" type="data" />
> + multiple="true" name="reads_r" type="data" />
>  
>  
>  
> - name="reads" type="data" />
> + name="reads" type="data" />
>  
>  
>  
> @@ -56,7 +56,7 @@
>  ${input_format.paired.paired_end_options.no_discordant}
>  #end if
>  
> -
> +
>  #if str($spliced_options.spliced_options_selector) == "advanced":
>  #if str($spliced_options.rna_strandness).strip() != '':
>  --rna-strandness $spliced_options.rna_strandness
> —
> Brad Langhorst, Ph.D.
> Development Scientist
> New England Biolabs
>
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Re: [galaxy-dev] Multiple web servers and handlers Galaxy failed

2015-12-10 Thread 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"  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"  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