Re: [galaxy-dev] galaxy with torque
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 edgar.fernan...@umontreal.ca 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/
[galaxy-dev] Deleted tool temp dir
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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Nginx Config
Wow that's a lot of upstreams... what is your Galaxy configuration?
On 26 November 2014 at 20:26, Nicholas Kline nx...@case.edu 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://127.0.0.1:8082/;, 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 /
Re: [galaxy-dev] Galaxy Docker and Tool Shed repository for Chinese researchers?
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 shenw...@gmail.com 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/ https://toolshed.g2.bx.psu.edu/repos/crs4/edena? 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/ ___ 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/
Re: [galaxy-dev] 回复： Help testing Galaxy - new release is coming soon
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 shenw...@gmail.com 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;bjoern.gruen...@gmail.com; *发送时间:* 2014年11月29日(星期六) 凌晨2:46 *收件人:* galaxy-...@lists.bx.psu.edugalaxy-...@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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/
