small issue with the black frame around displayed history item
by Hans-Rudolf Hotz
Hi all
I am in the process of updating our galaxy servers (from
"latest_2014.08.11" to "latest_2014.10.06").
As announced in the NewsBriefs
(https://wiki.galaxyproject.org/DevNewsBriefs/2014_10_06), "the
current/active dataset (the dataset being shown/manipulated in the
center panel of 'analyze data') is now highlighted."
This is great and will help our users a lot. Thank you very much for
this new feature!
Unfortunately, I have encountered a small issue: when I hover to
another history item, and click on the 'Visualize' icon. The black frame
switches to that history item - though nothing changes in the center panel
As I said not a big problem, just a little bit confusing...shall I make
Trello card or is there a quick fix possible?
Regards
Hans-Rudolf
--
Hans-Rudolf Hotz, PhD
Bioinformatics Support
Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
5 years, 2 months
Help testing Galaxy - new release is coming soon
by Björn Grüning
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
5 years, 2 months
Deleted tool temp dir
by 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.
5 years, 2 months
Nginx Config
by 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:
"http://127.0.0.1:8084/", 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://127.0.0.1:8085/", 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://127.0.0.1:8086/", 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://127.0.0.1:8087/", 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://127.0.0.1:8088/", host: "localhost"
5 years, 2 months
Galaxy Docker and Tool Shed repository for Chinese researchers?
by Weiyan Shen
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
5 years, 2 months
December 2014 Galaxy Newsletter
by 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
<https://wiki.galaxyproject.org/GalaxyUpdates/2014_12> we say! Highlights
include:
-
Galaxy Day! In Paris! This Wednesday!
<https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Galaxy_Day:_3_Decemb...>
-
Near Richmond, Virginia? There's a Galaxy Workshop at Virginia State U
on December 12
<https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Intro_to_Galaxy_Work...>
.
-
GCC2015 needs sponsors
<https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#GCC2015:_6-8_July.2C...>
!
-
Other upcoming events
<https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Other_Events> on
two continents
-
*96 new papers
<https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#New_Papers>*,
including 6 highlighted papers, referencing, using, extending, and
implementing Galaxy.
-
Job openings at 7+ organizations
<https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Who.27s_Hiring>
-
A new mailing list: Galaxy-Training
<https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#New_Galaxy-Training_...>
-
15 new ToolShed repositories from 10 contributors
<https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#ToolShed_Contributions>
-
And, 10 other juicy
<https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Other_News> (well
maybe not *juicy*, but certainly not *crunchy*) bits of news
<https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Other_News>
Happy December!
Dave Clements and the *crisp* Galaxy Team
<https://wiki.galaxyproject.org/GalaxyTeam>
--
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
5 years, 2 months
