Re: [galaxy-dev] 回复： Help testing Galaxy - new release is coming soon

2014-12-01 Thread Martin Čech 
Hello,

you might want to look at
https://github.com/bgruening/docker-galaxy-stable/blob/master/galaxy/Dockerfile
and other Bjoern's docker recipes:
https://github.com/bgruening/docker-recipes

M.

On Mon, Dec 1, 2014 at 8:45 PM, Weiyan Shen  wrote:

> Hi bjoern.gruening‍,
> It is great that galaxy work on http://localhost:8080‍ by "docker run -p
> 8080:80 -p 8800:8800 --privileged bgruening/galaxy-stable:dev‍". Is there
> Dockerfile about bgruening/galaxy-stable:dev‍ we may get?Thank you very
> much.
>
> --
> 沈维燕 | Steven Shen
> China National GeneBank Mobile +86 186 8228 6556
> Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen China
>
>
>
> -- 原始邮件 --
> *发件人:* "bjoern.gruening";;
> *发送时间:* 2014年11月29日(星期六) 凌晨2:46
> *收件人:* "galaxy-...@lists.bx.psu.edu";
> *主题:* [galaxy-dev] Help testing Galaxy - new release is coming soon
>
> Hi!
>
> As far as I know the Galaxy team is preparing a new release for next
> week with a ton of great new features, like Interactive Environments,
> multiple History view, Dataset collections and many more ...
>
> If you want to help testing, trying out the latest features or just give
> feedback we have put together a Galaxy Docker Image with all this stuff
> included.
>
> Install Docker, run the following command and report any issues!
>
> docker run -p 8080:80 -p 8800:8800 --privileged bgruening/galaxy-stable:dev
>
> Happy testing and Thanksgiving to everyone!
> The Galaxy Docker Team
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
> --
> 沈维燕 | Steven Shen
> China National GeneBank Mobile +86 186 8228 6556
> Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen China
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
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>
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[galaxy-dev] 回复： Help testing Galaxy - new release is coming soon

2014-12-01 Thread Weiyan Shen 
Hi bjoern.gruening‍,
It is great that galaxy work on http://localhost:8080‍ by "docker run -p 
8080:80 -p 8800:8800 --privileged bgruening/galaxy-stable:dev‍". Is there 
Dockerfile about bgruening/galaxy-stable:dev‍ we may get?Thank you very much.

--
 沈维燕 | Steven Shen


China National GeneBank Mobile +86 186 8228 6556
Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen China


 




-- 原始邮件 --
发件人: "bjoern.gruening";;
发送时间: 2014年11月29日(星期六) 凌晨2:46
收件人: "galaxy-...@lists.bx.psu.edu"; 

主题: [galaxy-dev] Help testing Galaxy - new release is coming soon



Hi!

As far as I know the Galaxy team is preparing a new release for next
week with a ton of great new features, like Interactive Environments,
multiple History view, Dataset collections and many more ...

If you want to help testing, trying out the latest features or just give
feedback we have put together a Galaxy Docker Image with all this stuff
included.

Install Docker, run the following command and report any issues!

docker run -p 8080:80 -p 8800:8800 --privileged bgruening/galaxy-stable:dev

Happy testing and Thanksgiving to everyone!
The Galaxy Docker Team
___
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  https://lists.galaxyproject.org/

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  http://galaxyproject.org/search/mailinglists/
--
 沈维燕 | Steven Shen


China National GeneBank Mobile +86 186 8228 6556
Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen China___
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Re: [galaxy-dev] Trimmomatic wrapper for Galaxy

2014-12-01 Thread Michael R. Crusoe 
Simon and I worked on https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/
trimmomatic_032  during the BOSC 2014 Codefest to add compatibility for
sets of pairs of input files via the then-new dataset collections feature.

I'm not seeing support for that in Peter Briggs version though I am no
expert and happy to be corrected. Hopefully the two will be merged so we
don't lose the enhancements that both bring.

On Mon Dec 01 2014 at 10:52:03 AM Peter Cock 
wrote:

> Hello all,
>
> I've not heard back from Simon yet (it was the weekend), but in
> the meantime there is a new alternative wrapper from Peter Briggs
> which has skipped the Test Tool Shed and gone straight to the
> main Tool Shed:
>
> https://toolshed.g2.bx.psu.edu/view/pjbriggs/trimmomatic
>
> This one knows Trimmomatic now bundles the Illumina adatpers,
> and has tests too (fingers crossed the Tool Shed tests work
> tonight) :)
>
> @PeterB - My only immediate feedback on scanning the repository
> is to try renaming README.markdown to README.md as currently
> the Tool Shed has not spotted and shown the README file.
>
> Regards
>
> PeterC
>
> On Fri, Nov 28, 2014 at 2:31 PM, Peter Cock 
> wrote:
> > Hi Simon,
> >
> > I was looking for a Trimmomatic wrapper for Galaxy (which I have thus
> > far only used at the command line outside of Galaxy), and while there
> > does not seem to be one in the main Tool Shed, I see you have been
> > working on this over on the Test Tool Shed:
> >
> > https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_0_22
> > https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_032
> >
> > Note that according to http://www.usadellab.org/cms/?page=trimmomatic
> > the Trimmomatic authors have been given permission to redistribute
> > the Illumina adapter sequences now :)
> >
> > It would be nice to have functional tests, but other than that, what
> > status is the wrapper? Are there some issues blocking releasing this
> > via the main Tool Shed for wider use?
> >
> > Thanks,
> >
> > Peter
> ___
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Re: [galaxy-dev] Trimmomatic wrapper for Galaxy

2014-12-01 Thread Peter Cock 
Hello all,

I've not heard back from Simon yet (it was the weekend), but in
the meantime there is a new alternative wrapper from Peter Briggs
which has skipped the Test Tool Shed and gone straight to the
main Tool Shed:

https://toolshed.g2.bx.psu.edu/view/pjbriggs/trimmomatic

This one knows Trimmomatic now bundles the Illumina adatpers,
and has tests too (fingers crossed the Tool Shed tests work
tonight) :)

@PeterB - My only immediate feedback on scanning the repository
is to try renaming README.markdown to README.md as currently
the Tool Shed has not spotted and shown the README file.

Regards

PeterC

On Fri, Nov 28, 2014 at 2:31 PM, Peter Cock  wrote:
> Hi Simon,
>
> I was looking for a Trimmomatic wrapper for Galaxy (which I have thus
> far only used at the command line outside of Galaxy), and while there
> does not seem to be one in the main Tool Shed, I see you have been
> working on this over on the Test Tool Shed:
>
> https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_0_22
> https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_032
>
> Note that according to http://www.usadellab.org/cms/?page=trimmomatic
> the Trimmomatic authors have been given permission to redistribute
> the Illumina adapter sequences now :)
>
> It would be nice to have functional tests, but other than that, what
> status is the wrapper? Are there some issues blocking releasing this
> via the main Tool Shed for wider use?
>
> Thanks,
>
> Peter
___
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Re: [galaxy-dev] Deleted tool temp dir

2014-12-01 Thread John Chilton 
That Galaxy version is quite old at this point. There were a couple
fixes for the cleanup_job config handling over the last year that may
have fixed the problem. I run with this option enabled daily and I
have not seen any problems in months. If you can confirm this is still
a problem with latest stable Galaxy instance - I would be definitely
be eager to address any bugs.

-John

On Sun, Nov 30, 2014 at 5:43 PM, Pandori n  wrote:
> Hi all.
> Config:
> - galaxy-dist stable (changeset:   11247:a9a0ac9c1afa) [Dec/18/2013]
> - NFS
> - Cluster (torque)
>
> When i start my WF,  on step 2, in 'job_working_directory' created temp
> (intermediate) dir (for tool step 3). But when step 2 is completed, temp dir
> (in  'job_working_directory') removed(via galaxy) and step 3 failed. In
> 'universe_wsgi.ini'  'cleanup_job = never'. Why galaxy.jobs deleted temp
> dir?
>
> Any help is appreciated. Thanks.
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
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>   http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] Nginx Config

2014-12-01 Thread Dannon Baker 
And can you verify that the galaxy server is actually currently running and
using those ports (from the box, something like 'curl http://127.0.0.1:8080'
)?

On Mon, Dec 1, 2014 at 5:42 AM, Peter van Heusden  wrote:

> Wow that's a lot of upstreams... what is your Galaxy configuration?
>
> On 26 November 2014 at 20:26, Nicholas Kline  wrote:
>
>> Hi,
>>
>> I am trying to setup a local production Galaxy running on Ubuntu,
>> Nginx, PostgreSQL, and ProFTD.
>>
>> When visiting http://localhost, "502 Bad Gateway" is returned.
>> Visiting https://localhost returns "unable to connect". I was
>> expecting to see the Galaxy website instead.
>>
>> My Nginx configuration file is included below. Thank you for your help.
>>
>>
>>
>> ###
>> # /etc/nginx/nginx.conf
>> ###
>>
>> user www-data;
>> worker_processes 4;
>> pid /run/nginx.pid;
>>
>> events {
>> worker_connections 768;
>> # multi_accept on;
>> }
>>
>> http {
>>
>> ##
>> # Basic Settings
>> ##
>>
>> sendfile on;
>> tcp_nopush on;
>> tcp_nodelay on;
>> keepalive_timeout 65;
>> types_hash_max_size 2048;
>> # server_tokens off;
>>
>> # server_names_hash_bucket_size 64;
>> # server_name_in_redirect off;
>>
>> include /etc/nginx/mime.types;
>> default_type application/octet-stream;
>>
>> ##
>> # Logging Settings
>> ##
>>
>> access_log /var/log/nginx/access.log;
>> error_log /var/log/nginx/error.log;
>>
>> ##
>> # Gzip Settings
>> ##
>>
>> gzip on;
>> gzip_http_version 1.1;
>> gzip_vary on;
>> gzip_comp_level 4;
>> gzip_proxied any;
>> gzip_types text/plain text/css application/x-javascript text/xml
>> application/xml text/javascript application/json;
>> gzip_buffers 16 8k;
>> gzip_disable "MSIE [1-6].(?!.*SV1)";
>>
>> ##
>> # nginx-naxsi config
>> ##
>> # Uncomment it if you installed nginx-naxsi
>> ##
>>
>> #include /etc/nginx/naxsi_core.rules;
>>
>> ##
>> # nginx-passenger config
>> ##
>> # Uncomment it if you installed nginx-passenger
>> ##
>>
>> #passenger_root /usr;
>> #passenger_ruby /usr/bin/ruby;
>>
>> ##
>> # Virtual Host Configs
>> ##
>>
>> include /etc/nginx/conf.d/*.conf;
>> #include /etc/nginx/sites-enabled/*;
>>
>> ##
>> # Galaxy
>> ##
>>
>> upstream galaxy_app {
>> # As defined in galaxy config file universe_wsgi.ini
>> server localhost:8080;
>> server localhost:8081;
>> server localhost:8082;
>> server localhost:8083;
>> server localhost:8084;
>> server localhost:8085;
>> server localhost:8086;
>> server localhost:8087;
>> server localhost:8088;
>> server localhost:8089;
>> }
>>
>> server {
>> # Maximum upload size that can be handled by POST requests
>> through nginx.
>> # Disabled because using FTP instead of web interface.
>> #client_max_body_size 10G;
>>
>> location / {
>> proxy_pass   http://galaxy_app;
>> proxy_set_header   X-Forwarded-Host $host;
>> proxy_set_header   X-Forwarded-For
>> $proxy_add_x_forwarded_for;
>> # If using SSL, makes Galaxy aware of what type of URL it
>> should generate for external sites like Biomart.
>> proxy_set_header   X-URL-SCHEME https;
>> }
>>
>> # nginx is more efficient at serving static content.
>> # expires 24h is for caching purposes.
>> location /static {
>> alias /home/galaxy/galaxy-dist/static;
>> expires 24h;
>> }
>> location /static/style {
>> alias /home/galaxy/galaxy-dist/static/june_2007_style/blue;
>> expires 24h;
>> }
>> location /static/scripts {
>> alias /home/galaxy/galaxy-dist/static/scripts/packed;
>> }
>> location /favicon.ico {
>> alias /home/galaxy/galaxy-dist/static/favicon.ico;
>> }
>> location /robots.txt {
>> alias /home/galaxy/galaxy-dist/static/robots.txt;
>> }
>>
>> # Use nginx to send files (downloads) instead of Galaxy.
>> location /_x_accel_redirect/ {
>> internal;
>> alias /;
>> }
>> }
>> }
>>
>>
>>
>> ###
>> # /var/log/nginx/error.log
>> ###
>>
>> 2014/11/25 15:43:21 [error] 56433#0: *23 connect() failed (111:
>> Connection refused) while connecting to upstream, client: 127.0.0.1,
>> server: , request: "GET / HTTP/1.1", upstream:
>> "http://127.0.0.1:8089/";, host: "localhost"
>> 2014/11/25 15:43:21 [error] 56433#0: *23 connect() failed (111:
>> Connection refused) while connecting to upstream, client: 127.0.0.1,
>> server: , request: "GET / HTTP/1.1", upstream:
>> "http://127.0.0.1:8080/";, host: "localhost"
>> 2014/11/25 15:43:21 [error] 56433#0: *23 conne

Re: [galaxy-dev] Galaxy Docker and Tool Shed repository for Chinese researchers?

2014-12-01 Thread Dannon Baker 
Hi Steven,

Using Docker can simplify deployment, enhance reproducibility, and enhance
security with the eventual goal of allowing users to run untrusted code on
the shared Galaxy infrastructure, to name a few reasons.

For details on how to set up your own tool shed, this page should help you
out:  https://wiki.galaxyproject.org/HostingALocalToolShed

Let me know if you have any other questions, good luck!

-Dannon

On Mon, Dec 1, 2014 at 2:02 AM, Weiyan Shen  wrote:

> Galaxy developers,
> I am programmer from BGI-Shenzhen,China.And I came accross some problems
> in the Galaxy docker and I need your advices.
> As we known,Galaxy supports running tools within Docker containers since
> August 2014 release.I don't clear know why we need to develop the galaxy
> docker and what will improve by running galaxy tools whitin docker.Are
> there any details about that ?
> ‍We also want to make a Galaxy Tool Shed repository for Chinese
> biomedicine researchers,can us get the Galaxy Tool Shed repository‍ from
> https://toolshed.g2.bx.psu.edu/
> ? And how to make it ?
> Thank you very much.
> ‍‍
> Best regards
> Steven Shen
> --
> 沈维燕 | Steven Shen
> China National GeneBank Mobile +86 186 8228 6556
> Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen China
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
___
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Re: [galaxy-dev] Nginx Config

2014-12-01 Thread Peter van Heusden 
Wow that's a lot of upstreams... what is your Galaxy configuration?

On 26 November 2014 at 20:26, Nicholas Kline  wrote:

> Hi,
>
> I am trying to setup a local production Galaxy running on Ubuntu,
> Nginx, PostgreSQL, and ProFTD.
>
> When visiting http://localhost, "502 Bad Gateway" is returned.
> Visiting https://localhost returns "unable to connect". I was
> expecting to see the Galaxy website instead.
>
> My Nginx configuration file is included below. Thank you for your help.
>
>
>
> ###
> # /etc/nginx/nginx.conf
> ###
>
> user www-data;
> worker_processes 4;
> pid /run/nginx.pid;
>
> events {
> worker_connections 768;
> # multi_accept on;
> }
>
> http {
>
> ##
> # Basic Settings
> ##
>
> sendfile on;
> tcp_nopush on;
> tcp_nodelay on;
> keepalive_timeout 65;
> types_hash_max_size 2048;
> # server_tokens off;
>
> # server_names_hash_bucket_size 64;
> # server_name_in_redirect off;
>
> include /etc/nginx/mime.types;
> default_type application/octet-stream;
>
> ##
> # Logging Settings
> ##
>
> access_log /var/log/nginx/access.log;
> error_log /var/log/nginx/error.log;
>
> ##
> # Gzip Settings
> ##
>
> gzip on;
> gzip_http_version 1.1;
> gzip_vary on;
> gzip_comp_level 4;
> gzip_proxied any;
> gzip_types text/plain text/css application/x-javascript text/xml
> application/xml text/javascript application/json;
> gzip_buffers 16 8k;
> gzip_disable "MSIE [1-6].(?!.*SV1)";
>
> ##
> # nginx-naxsi config
> ##
> # Uncomment it if you installed nginx-naxsi
> ##
>
> #include /etc/nginx/naxsi_core.rules;
>
> ##
> # nginx-passenger config
> ##
> # Uncomment it if you installed nginx-passenger
> ##
>
> #passenger_root /usr;
> #passenger_ruby /usr/bin/ruby;
>
> ##
> # Virtual Host Configs
> ##
>
> include /etc/nginx/conf.d/*.conf;
> #include /etc/nginx/sites-enabled/*;
>
> ##
> # Galaxy
> ##
>
> upstream galaxy_app {
> # As defined in galaxy config file universe_wsgi.ini
> server localhost:8080;
> server localhost:8081;
> server localhost:8082;
> server localhost:8083;
> server localhost:8084;
> server localhost:8085;
> server localhost:8086;
> server localhost:8087;
> server localhost:8088;
> server localhost:8089;
> }
>
> server {
> # Maximum upload size that can be handled by POST requests
> through nginx.
> # Disabled because using FTP instead of web interface.
> #client_max_body_size 10G;
>
> location / {
> proxy_pass   http://galaxy_app;
> proxy_set_header   X-Forwarded-Host $host;
> proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
> # If using SSL, makes Galaxy aware of what type of URL it
> should generate for external sites like Biomart.
> proxy_set_header   X-URL-SCHEME https;
> }
>
> # nginx is more efficient at serving static content.
> # expires 24h is for caching purposes.
> location /static {
> alias /home/galaxy/galaxy-dist/static;
> expires 24h;
> }
> location /static/style {
> alias /home/galaxy/galaxy-dist/static/june_2007_style/blue;
> expires 24h;
> }
> location /static/scripts {
> alias /home/galaxy/galaxy-dist/static/scripts/packed;
> }
> location /favicon.ico {
> alias /home/galaxy/galaxy-dist/static/favicon.ico;
> }
> location /robots.txt {
> alias /home/galaxy/galaxy-dist/static/robots.txt;
> }
>
> # Use nginx to send files (downloads) instead of Galaxy.
> location /_x_accel_redirect/ {
> internal;
> alias /;
> }
> }
> }
>
>
>
> ###
> # /var/log/nginx/error.log
> ###
>
> 2014/11/25 15:43:21 [error] 56433#0: *23 connect() failed (111:
> Connection refused) while connecting to upstream, client: 127.0.0.1,
> server: , request: "GET / HTTP/1.1", upstream:
> "http://127.0.0.1:8089/";, host: "localhost"
> 2014/11/25 15:43:21 [error] 56433#0: *23 connect() failed (111:
> Connection refused) while connecting to upstream, client: 127.0.0.1,
> server: , request: "GET / HTTP/1.1", upstream:
> "http://127.0.0.1:8080/";, host: "localhost"
> 2014/11/25 15:43:21 [error] 56433#0: *23 connect() failed (111:
> Connection refused) while connecting to upstream, client: 127.0.0.1,
> server: , request: "GET / HTTP/1.1", upstream:
> "http://127.0.0.1:8081/";, host: "localhost"
> 2014/11/25 15:43:21 [error] 56433#0: *23 connect() failed (111:
> Connection refused) while connecting to upstream, client: 127.0.0.1,
> server: , request: "GET / HTTP/1.1", upstream:
> "http://127.0.0.1

[galaxy-dev] Deleted tool temp dir

2014-12-01 Thread Pandori n 
Hi all.
Config:
- galaxy-dist stable (changeset:   11247:a9a0ac9c1afa) [Dec/18/2013]
- NFS
- Cluster (torque)

When i start my WF,  on step 2, in 'job_working_directory' created temp
(intermediate) dir (for tool step 3). But when step 2 is completed, temp
dir (in  'job_working_directory') removed(via galaxy) and step 3 failed. In
'universe_wsgi.ini'  'cleanup_job = never'. Why galaxy.jobs deleted temp
dir?

Any help is appreciated. Thanks.
___
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[galaxy-dev] Nginx Config

2014-12-01 Thread Nicholas Kline 
Hi,

I am trying to setup a local production Galaxy running on Ubuntu,
Nginx, PostgreSQL, and ProFTD.

When visiting http://localhost, "502 Bad Gateway" is returned.
Visiting https://localhost returns "unable to connect". I was
expecting to see the Galaxy website instead.

My Nginx configuration file is included below. Thank you for your help.



###
# /etc/nginx/nginx.conf
###

user www-data;
worker_processes 4;
pid /run/nginx.pid;

events {
worker_connections 768;
# multi_accept on;
}

http {

##
# Basic Settings
##

sendfile on;
tcp_nopush on;
tcp_nodelay on;
keepalive_timeout 65;
types_hash_max_size 2048;
# server_tokens off;

# server_names_hash_bucket_size 64;
# server_name_in_redirect off;

include /etc/nginx/mime.types;
default_type application/octet-stream;

##
# Logging Settings
##

access_log /var/log/nginx/access.log;
error_log /var/log/nginx/error.log;

##
# Gzip Settings
##

gzip on;
gzip_http_version 1.1;
gzip_vary on;
gzip_comp_level 4;
gzip_proxied any;
gzip_types text/plain text/css application/x-javascript text/xml
application/xml text/javascript application/json;
gzip_buffers 16 8k;
gzip_disable "MSIE [1-6].(?!.*SV1)";

##
# nginx-naxsi config
##
# Uncomment it if you installed nginx-naxsi
##

#include /etc/nginx/naxsi_core.rules;

##
# nginx-passenger config
##
# Uncomment it if you installed nginx-passenger
##

#passenger_root /usr;
#passenger_ruby /usr/bin/ruby;

##
# Virtual Host Configs
##

include /etc/nginx/conf.d/*.conf;
#include /etc/nginx/sites-enabled/*;

##
# Galaxy
##

upstream galaxy_app {
# As defined in galaxy config file universe_wsgi.ini
server localhost:8080;
server localhost:8081;
server localhost:8082;
server localhost:8083;
server localhost:8084;
server localhost:8085;
server localhost:8086;
server localhost:8087;
server localhost:8088;
server localhost:8089;
}

server {
# Maximum upload size that can be handled by POST requests
through nginx.
# Disabled because using FTP instead of web interface.
#client_max_body_size 10G;

location / {
proxy_pass   http://galaxy_app;
proxy_set_header   X-Forwarded-Host $host;
proxy_set_header   X-Forwarded-For  $proxy_add_x_forwarded_for;
# If using SSL, makes Galaxy aware of what type of URL it
should generate for external sites like Biomart.
proxy_set_header   X-URL-SCHEME https;
}

# nginx is more efficient at serving static content.
# expires 24h is for caching purposes.
location /static {
alias /home/galaxy/galaxy-dist/static;
expires 24h;
}
location /static/style {
alias /home/galaxy/galaxy-dist/static/june_2007_style/blue;
expires 24h;
}
location /static/scripts {
alias /home/galaxy/galaxy-dist/static/scripts/packed;
}
location /favicon.ico {
alias /home/galaxy/galaxy-dist/static/favicon.ico;
}
location /robots.txt {
alias /home/galaxy/galaxy-dist/static/robots.txt;
}

# Use nginx to send files (downloads) instead of Galaxy.
location /_x_accel_redirect/ {
internal;
alias /;
}
}
}



###
# /var/log/nginx/error.log
###

2014/11/25 15:43:21 [error] 56433#0: *23 connect() failed (111:
Connection refused) while connecting to upstream, client: 127.0.0.1,
server: , request: "GET / HTTP/1.1", upstream:
"http://127.0.0.1:8089/";, host: "localhost"
2014/11/25 15:43:21 [error] 56433#0: *23 connect() failed (111:
Connection refused) while connecting to upstream, client: 127.0.0.1,
server: , request: "GET / HTTP/1.1", upstream:
"http://127.0.0.1:8080/";, host: "localhost"
2014/11/25 15:43:21 [error] 56433#0: *23 connect() failed (111:
Connection refused) while connecting to upstream, client: 127.0.0.1,
server: , request: "GET / HTTP/1.1", upstream:
"http://127.0.0.1:8081/";, host: "localhost"
2014/11/25 15:43:21 [error] 56433#0: *23 connect() failed (111:
Connection refused) while connecting to upstream, client: 127.0.0.1,
server: , request: "GET / HTTP/1.1", upstream:
"http://127.0.0.1:8082/";, host: "localhost"
2014/11/25 15:43:21 [error] 56433#0: *23 connect() failed (111:
Connection refused) while connecting to upstream, client: 127.0.0.1,
server: , request: "GET / HTTP/1.1", upstream:
"http://127.0.0.1:8083/";, host: "localhost"
2014/11/25 15:43:21 [error] 56433#0: *23 connect() failed (111:
Connection refused) while connecting to upstream, client: 127.0.0.1,
server: , request: "GET / HTTP/1.1", upstream:
"ht

Re: [galaxy-dev] galaxy with torque

2014-12-01 Thread Fernandez Edgar 
Hi John,

First, thank you very much for your prompt answer.
It's extremely appreciated.

Secondly, I have some other questions: whatever answers you can provide me 
with, will be greatly helpful.
Please, forgive my beginner level understanding of an DRM system.

1. Once I compile, make and install the Torque Submit Node code against the 
server running Galaxy, what exactly is the purpose for an DRMAA ?

2. What is exactly the PBS step describe here: 
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster 
galaxy_user@galaxy_server% LIBTORQUE_DIR=/path/to/libtorque python 
scripts/scramble.py -e pbs_python
What does it do exactly ?

3. All servers which includes my torque server, torque compute nodes and torque 
submit node (a.k.a galaxy server) have the galaxy user defines and its home 
shared on all of them. This means all of them have access (via NFS) of the 
installation directory of galaxy. But what about the MySQL server access. Does 
the torque server or the compute nodes need access to that service? 

I hope I'm not sending too many emails/questions...
Thank you very much!

Cordialement / Regards, 
Edgar Fernandez

-Message d'origine-
De : John Chilton [mailto:jmchil...@gmail.com] 
Envoyé : November-25-14 12:07 PM
À : Fernandez Edgar
Cc : galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] galaxy with torque

I am not sure we have a walkthrough for Torque specifically - but if you have 
Galaxy up and running and you can qsub commands to torque - hopefully you have 
done all of the hard parts.

You will need a DRMAA library for your torque setup - 
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
suggests compiling pbs_drmaa and outlines how to set it up. After that you just 
need to add a plugin and default destination to your job_conf.xml file - also 
outlined on that wiki page.

Other good resources to consult if you are scaling up your Galaxy this way are:
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay/AdminWalkthrough

Good luck and let us know if you encounter any problems.

-John

On Fri, Nov 21, 2014 at 2:30 PM, Fernandez Edgar  
wrote:
> Hello all,
>
>
>
> My name is Edgar Fernandez. I’m a sys. admin. at University of Montreal.
>
> I’ve contacted you a while back about installing galaxy and I’ve 
> successfully done it on a redhat 6 server.
>
>
>
> I see myself in a situation where I need to utilise all my redhat 
> servers (who are identical to the server running the galaxy website).
>
>
>
> I’ve also successfully installed a server torque with compute notes 
> and clients nodes.
>
>
>
> What are the last step to make the link between galaxy and torque?
>
> Also, once that connection is made, how will galaxy keep track of the 
> jobs sent?
>
> I mean who will it know this job that just finished is for this user 
> and not another ?
>
>
>
> Also, my torque installation is so that my server running galaxy is a 
> submit node and a client node.
>
> I hope this is not a problem.
>
>
>
> Please help!
>
>
>
> Cordialement / Regards,
>
>
>
> Edgar Fernandez
>
> System Administrator (Linux)
>
> Direction Générale des Technologies de l'Information et de la 
> Communication
>
> (  Bur. : 1-514-343-6111 poste 16568
>
>
>
> Université de Montréal
>
> PAVILLON ROGER-GAUDRY, bureau X-218
>
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this and other 
> Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
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>   http://galaxyproject.org/search/mailinglists/
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Re: [galaxy-dev] Problem with LWR (input size limitation)

2014-12-01 Thread Misharl Monsoor 

Hi John,

I can confirm you that your advice putting "LWR_CURL_TRANSPORT=1" works 
very fine, thanks a lot! Sorry, i haven't expressed myself correctly for 
my second question, thanks for answering, it helps me.
I have another problem with LWR, when executing the jobs on the Windows 
Server, i have the following bug (it happens a lot of time, and i must 
restart the LWR server in order for it to works):


 File "C:\Python2764\lib\site-packages\paste-1.7.5.1-py2.7.egg\paste\httpserver
py", line 287, in wsgi_execute
   self.wsgi_start_response)
 File "C:\Desktop\lwr_master\lwr\web\framework.py", l
ne 37, in __call__
   return controller(environ, start_response, **request_args)
 File "C:\Desktop\lwr_master\lwr\web\framework.py", l
ne 141, in controller_replacement
   resp = self.__build_response(result)
 File "C:\Desktop\lwr_master\lwr\web\framework.py", l
ne 129, in __build_response
   resp = Response(body=self.body(result))
 File "C:\Desktop\lwr_master\lwr\web\framework.py", l
ne 155, in body
   body = dumps(result)
 File "C:\Python2764\lib\json\__init__.py", line 243, in dumps
   return _default_encoder.encode(obj)
 File "C:\Python2764\lib\json\encoder.py", line 207, in encode
   chunks = self.iterencode(o, _one_shot=True)
 File "C:\Python2764\lib\json\encoder.py", line 270, in iterencode
   return _iterencode(o, 0)
nicodeDecodeError: 'utf8' codec can't decode byte 0x92 in position 718: invalid
start byte


Bests regards and thank you very much for your help,

Misharl Monsoor.



Le 21/11/2014 17:44, John Chilton a écrit :

On Wed, Nov 19, 2014 at 12:58 PM, Misharl Monsoor
 wrote:

Hi John ,

First all, thank you very much for your quick reply. I will test your
suggestion about pycurl,  and tell you if it has worked. For the second
question, i was wondering if it is possible with LWR to define a path (where
are located the inputs) as an input (string input in the wrapper xml).

Still not certain I understand - but I do not believe this is possible
for datasets - this is something that must be configured for the LWR
itself. If you have inputs to the tool that are not datasets - such as
reference or index data - those could potentially be specified this
way as just 
Thank you again for your help,

Misharl Monsoor.





Le 19/11/2014 15:30, John Chilton a écrit :


If you install pycurl (globally or in a Galaxy's virtualenv) and set
LWR_CURL_TRANSPORT=1 in Galaxy's environment than the LWR will stream
large files with CURL instead of the mmap hack.

I don't understand your second question - the LWR should stream
whatever data inputs are selected by the user. If you want the tool to
be able to take many inputs you can use multiple="true" on your data
parameter or use a repeat block.
(https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax).

Hope this helps,
-John


On Mon, Nov 17, 2014 at 3:04 AM, Misharl Monsoor 
wrote:

Hi everybody,

In our lab, we are trying to connect our Galaxy instance to a Windows 7
64
bits server, in order to executes programs that need to be run within
Windows. However we have a problem concerning the size of the input that
is
uploaded to the Windows server, it doesn't accept inputs with a size >
1.3
Gb ? We have the following problem with mmap function:

data = mmap.mmap(input.fileno(), 0, access=mmap.ACCESS_READ)
error: [Errno 12] Cannot allocate memory


I have another question concerning the inputs, is there a way to use
several
inputs that be uploaded to a Windows Server?

Thank you very much in advance,

Bests regards,

Cheers,

Misharl Monsoor
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[galaxy-dev] December 2014 Galaxy Newsletter

2014-12-01 Thread Dave Clements 
Hello all,

As always there's a lot going on in the Galaxy this month. "Like what?" you
say. Well, read the dang December Galaxy Newsletter
 we say! Highlights
include:


   -

   Galaxy Day! In Paris! This Wednesday!
   

   -

   Near Richmond, Virginia? There's a Galaxy Workshop at Virginia State U
   on December 12
   

   .
   -

   GCC2015 needs sponsors
   

   !
   -

   Other upcoming events
    on
   two continents
   -

   *96 new papers
   *,
   including 6 highlighted papers, referencing, using, extending, and
   implementing Galaxy.
   -

   Job openings at 7+ organizations
   
   -

   A new mailing list: Galaxy-Training
   

   -

   15 new ToolShed repositories from 10 contributors
   
   -

   And, 10 other juicy
    (well
   maybe not *juicy*, but certainly not *crunchy*) bits of news
   

Happy December!

Dave Clements and the *crisp* Galaxy Team


-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
___
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