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Building reference genome with Data Manager socket.error: [Errno 110] Connection timed out
by Vova Korniychuk 03 Dec '14

03 Dec '14

Hello, I am a new Galaxy learner. I try to master data managers. I have tried to create sacCer2 reference genome following instruction on video http://vimeo.com/74265510. In Data Manager History, it gives a following error: Traceback (most recent call last): File "/home/uladzimir/shed_tools/ toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2e…", line 350, in <module> if __name__ == "__main__": main() File "/home/uladzimir/shed_tools/ toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2e…", line 345, in main REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name ) File "/home/uladzimir/shed_tools/ toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2e…", line 182, in download_from_ucsc ftp = FTP( UCSC_FTP_SERVER ) File "/usr/lib/python2.7/ftplib.py", line 120, in __init__ self.connect(host) File "/usr/lib/python2.7/ftplib.py", line 135, in connect self.sock = socket.create_connection((self.host, self.port), self.timeout) File "/usr/lib/python2.7/socket.py", line 571, in create_connection raise err socket.error: [Errno 110] Connection timed out Can you please help me? Thanks Uladzimir

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no reference genome list in variant_selector tool
by Evan Bollig PhD 03 Dec '14

03 Dec '14

Devteam: The "cached" reference genome option on the variant_selector tool (Main Toolshed) does not properly load reference options into the drop down. Please comment out the following line to get it to work (the same edit was already done in Unified Genotyper tool): ########### diff -r 135e8721ffc5 variant_select.xml --- a/variant_select.xml Tue Apr 01 10:49:48 2014 -0400 +++ b/variant_select.xml Wed Dec 03 13:53:46 2014 +0000 @@ -106,7 +106,7 @@ <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &lt;variant&gt;" /> <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> <options from_data_table="gatk_picard_indexes"> - <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> +  </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> ########### Can I rely on one of you folks in devteam to post a new revision of the tool? I'd rather not maintain a full fork. Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

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Page generated by a Galaxy behind HTTPS(Nginx) makes HTTP calls
by Maxime Lévesque 03 Dec '14

03 Dec '14

I have followed the instructions here : https://wiki.galaxyproject.org/Admin/Config/nginxProxy to run a Galaxy behind an NGinx proxy under with HTTPS, The relevant part of my NGinx config has : proxy_set_header REMOTE_USER "$loginOnHost"; proxy_set_header X-Forwarded-Host $host; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; proxy_set_header X-URL-SCHEME https; it is working well, with the exception that some pages are making external calls to http://genome.ucsc.edu, and not https://genome.ucsc.edu . I get a "mixed content" error (in chrome) : I verified that the URL that the page is trying to access *does* exist under HTTPS, so it's just a matter of telling galaxy to generate HTTPS links. I would have thought that this is what "proxy_set_header X-URL-SCHEME https;" did... https://galaxy-1hge11q-uvd.udes.genap.ca/' was loaded over HTTPS, but requested an insecure resource ' http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//galaxy-1hge11q…'. This request has been blocked; the content must be served over HTTPS. Thanks !

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Hovering over a history dataset lights up the other datasets....?
by Hans-Rudolf Hotz 02 Dec '14

02 Dec '14

Hi all and just as a follow up to my previous mail: If I continue reading the NewsBrief, it says: "Hovering over a history dataset lights up the other datasets from which it was derived." This doesn't wotk for me. I also tried it on 'main' without success. Is there a special trick I need to do? Thanks for your help Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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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

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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

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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

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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.

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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"

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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

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