December 2014 - galaxy-dev - lists.galaxyproject.org

small issue with the black frame around displayed history item
by Hans-Rudolf Hotz 02 Dec '14

02 Dec '14

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

2 1

Help testing Galaxy - new release is coming soon
by Björn Grüning 02 Dec '14

02 Dec '14

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

3 2

Trimmomatic wrapper for Galaxy
by Peter Cock 01 Dec '14

01 Dec '14

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

2 2

Deleted tool temp dir
by Pandori n 01 Dec '14

01 Dec '14

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.

2 1

Nginx Config
by Nicholas Kline 01 Dec '14

01 Dec '14

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"

3 2

Galaxy Docker and Tool Shed repository for Chinese researchers?
by Weiyan Shen 01 Dec '14

01 Dec '14

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

2 1

December 2014 Galaxy Newsletter
by Dave Clements 01 Dec '14

01 Dec '14

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_December…> - 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_Worksh…> . - GCC2015 needs sponsors <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#GCC2015:_6-8_July.2C_N…> ! - 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_Ma…> - 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/

1 0