- galaxy-user - lists.galaxyproject.org

Viral metagenomics
by Mohammad Mohiuddin 26 Feb '13

26 Feb '13

Hi, Can you please tell me how to work with viral metagenomics in Galaxy? When uploading the data files, there is an option to select the reference genome but in case of viral metagenomics, I can't select any individual genome. What will I do in this step? After uploading and processing the data, I will have to BLAST all my sequences using NCBI BLAST but there is no BLAST option in galaxy. How can I do that? And, is there any way to change the default E-value of Galaxy? Thanks, Mohiuddin

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"join,subtract and group" tools can't be used
by Lu, Mengmeng 26 Feb '13

26 Feb '13

Hi galaxy group, I found the tools of "join,subtract and group" can't be used in the Galaxy main. I am curious when it will come back. Thanks! Mira

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How to create a tool from a script that loads additional source code files?
by Samuel Lampa 25 Feb '13

25 Feb '13

Hi, I have aGalaxy toolwith some R code which is split up into a few files, which are loaded by a "master R script", which orcestrates and executes the whole thing. I realize that when the master script ("run.R" in my case) is run, it will not find the other files, since it is itself moved away to a temporary working directory (something like ".../galaxy/database/job_working_directory/000/165"). Is there any "standard way" of dealing with this, any special toolconfig syntax etc? ... or do I have to just hard code the absolute paths to the extra files in my script? :| Best Regards // Samuel -- Developer at SNIC-UPPMAX www.uppmax.uu.se Developer at Dept of Pharm Biosciences www.farmbio.uu.se

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2013 Galaxy Community Conference (GCC2013) Registration and Abstract Submission are Now Open
by Dave Clements 25 Feb '13

25 Feb '13

Dear Galaxy Community, We are pleased to announce that early registration<http://wiki.galaxyproject.org/Events/GCC2013/Register> and paper and poster abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> are now open for the 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013> . GCC2013 will be held 30 June through July 2 in Oslo Norway, at the University of Oslo <http://uio.no/>. GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference also includes a Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> for the second year in a row, this year with more in-depth topic coverage, more concurrent sessions, and more topics. If you are a biologist or bioinformatician performing or enabling high-throughput biological research, then please consider attending. GCC2013 is aimed at: - Bioinformatics tool developers and data providers - Workflow developers and power bioinformatics users - Sequencing and Bioinformatics core staff - Data archival and analysis reproducibility specialists *Early registration <http://wiki.galaxyproject.org/Events/GCC2013/Register>* *saves up to 75% off regular registration costs,* and is very affordable, with combined registration (Training Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> + main meeting) starting at ~ €95 for post-docs and students. Registering early also assures you a spot in the Training Day workshops you want to attend. Once a Training Day session becomes full, it will be closed to new registrations. Early registration closes 24 May. *Abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> * for oral presentations closes 12 April, and for posters on 3 May. Please consider presenting your work. If you are working with big biological data, then the people at this meeting want to hear about your work. Thanks, and hope to see you in Oslo! The GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers> PS: And please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> ! -- http://galaxyproject.org/GCC2013 <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Installing Galaxy on ARM Architecture
by Shun Liang 21 Feb '13

21 Feb '13

Hi, I am trying to install Galaxy on an ARMV7 architecture Linux server. I ran "run.sh" and failed because some of the python eggs could not be fetched. I then have a look at "http://eggs.galaxyproject.org/" and I have realized there aren't any armv7 builds for those eggs. I then decided to build (or scramble) the eggs on my own. I ran "scripts/scramble.py" and this also failed with the following message (after building a lot of things): scramble(): Copied egg to: /nfs/users/galaxy_dist/eggs/twill-0.9-py2.7.egg Traceback (most recent call last): File "scripts/scramble.py", line 26, in <module> eggs = c.scramble() File "/nfs/users/galaxy_dist/lib/galaxy/eggs/scramble.py", line 242, in scramble raise last_exc # only 1 failure out of the crate, be more informative galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for bx_python 0.7.1 May I ask what may cause this problem? Have I done anything wrong? Or, is it even possible to install Galaxy on ARM architecture Linux? Many thanks, Shun

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History not updating for multiple instances of Galaxy
by Neil.Burdett＠csiro.au 21 Feb '13

21 Feb '13

Hi, I have three instances of galaxy running on the same Linux box. My "/etc/apache2/sites-available/default" is: RewriteEngine on RewriteRule ^/galaxy-csiro$ /galaxy-csiro/ [R] RewriteRule ^/galaxy-csiro/static/style/(.*) /home/galaxy/galaxy-csiro/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-csiro/static/scripts/(.*) /home/galaxy/galaxy-csiro/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-csiro/static/(.*) /home/galaxy/galaxy-csiro/static/$1 [L] RewriteRule ^/galaxy-csiro/favicon.ico /home/galaxy/galaxy-csiro/static/favicon.ico [L] RewriteRule ^/galaxy-csiro/robots.txt /home/galaxy/galaxy-csiro/static/robots.txt [L] RewriteRule ^/galaxy-csiro(.*) http://localhost:9080$1 [P] RewriteRule ^/galaxy-cte$ /galaxy-cte/ [R] RewriteRule ^/galaxy-cte/static/style/(.*) /home/galaxy/galaxy-cte/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-cte/static/scripts/(.*) /home/galaxy/galaxy-cte/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-cte/static/(.*) /home/galaxy/galaxy-cte/static/$1 [L] RewriteRule ^/galaxy-cte/favicon.ico /home/galaxy/galaxy-cte/static/favicon.ico [L] RewriteRule ^/galaxy-cte/robots.txt /home/galaxy/galaxy-cte/static/robots.txt [L] RewriteRule ^/galaxy-cte(.*) http://localhost:9000$1 [P] RewriteRule ^/galaxy-Newcastle$ /galaxy-Newcastle/ [R] RewriteRule ^/galaxy-Newcastle/static/style/(.*) /home/galaxy/galaxy-Newcastle/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy-Newcastle/static/scripts/(.*) /home/galaxy/galaxy-Newcastle/static/scripts/packed/$1 [L] RewriteRule ^/galaxy-Newcastle/static/(.*) /home/galaxy/galaxy-Newcastle/static/$1 [L] RewriteRule ^/galaxy-Newcastle/favicon.ico /home/galaxy/galaxy-Newcastle/static/favicon.ico [L] RewriteRule ^/galaxy-Newcastle/robots.txt /home/galaxy/galaxy-Newcastle/static/robots.txt [L] RewriteRule ^/galaxy-Newcastle(.*) http://localhost:9010$1 [P] I can view all the instances However, when I try and "Get Data" and upload a file the history side panel remains empty. I can see that the files have been uploaded to (for example) % ls -lrt galaxy-Newcastle/database/files/000/ total 22868 -rw-rw-r-- 1 galaxy galaxy 23017819 Feb 21 13:01 dataset_1.dat -rw-rw-r-- 1 galaxy galaxy 187339 Feb 21 13:02 dataset_2.dat -rw-rw-r-- 1 galaxy galaxy 206568 Feb 21 13:03 dataset_3.dat Any ideas much appreciated... The log file state: Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342321 127.0.0.1 - - [21/Feb/2013:13:16:21 +1000] "GET /galaxy-Newcastle/tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/root/tool_menu" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" galaxy.web.framework DEBUG 2013-02-21 13:16:28,630 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,630 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "POST /galaxy-Newcastle/tool_runner/upload_async_create HTTP/1.1" 500 - "http://barium-rbh/galaxy-Newcastle/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342322 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "GET /galaxy-Newcastle/tool_runner/upload_async_message HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "GET /galaxy-Newcastle/history HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_message" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" galaxy.web.framework DEBUG 2013-02-21 13:16:29,261 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/root/user_get_usage 127.0.0.1 - - [21/Feb/2013:13:16:29 +1000] "POST /galaxy-Newcastle/root/user_get_usage HTTP/1.1" 500 - "http://barium-rbh/galaxy-Newcastle/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342323 galaxy.tools.actions.upload_common INFO 2013-02-21 13:16:30,841 tool upload1 created job id 4 127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "POST /galaxy-Newcastle/tool_runner/index HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/tool_runner?tool_id=upload1" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" 127.0.0.1 - - [21/Feb/2013:13:16:30 +1000] "GET /galaxy-Newcastle/history HTTP/1.1" 200 - "http://barium-rbh/galaxy-Newcastle/tool_runner/index" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" galaxy.web.framework DEBUG 2013-02-21 13:16:31,347 Error: this request returned None from get_history(): http://barium-rbh/galaxy-Newcastle/root/user_get_usage 127.0.0.1 - - [21/Feb/2013:13:16:31 +1000] "POST /galaxy-Newcastle/root/user_get_usage HTTP/1.1" 500 - "http://barium-rbh/galaxy-Newcastle/history" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342324 galaxy.jobs.manager DEBUG 2013-02-21 13:16:33,263 (4) Job assigned to handler 'main' galaxy.jobs DEBUG 2013-02-21 13:16:38,574 (4) Working directory for job is: /home/galaxy/galaxy-Newcastle/database/job_working_directory/000/4 galaxy.jobs.handler DEBUG 2013-02-21 13:16:38,574 dispatching job 4 to local runner galaxy.jobs.handler INFO 2013-02-21 13:16:38,837 (4) Job dispatched galaxy.jobs.runners.local DEBUG 2013-02-21 13:16:39,130 executing: python /home/galaxy/galaxy-Newcastle/tools/data_source/upload.py /home/galaxy/galaxy-Newcastle /home/galaxy/galaxy-Newcastle/database/tmp/tmpQK6VjP /home/galaxy/galaxy-Newcastle/database/tmp/tmpD_ySP1 4:/home/galaxy/galaxy-Newcastle/database/job_working_directory/000/4/dataset_4_files:/home/galaxy/galaxy-Newcastle/database/files/000/dataset_4.dat galaxy.jobs.runners.local DEBUG 2013-02-21 13:16:39,549 execution finished: python /home/galaxy/galaxy-Newcastle/tools/data_source/upload.py /home/galaxy/galaxy-Newcastle /home/galaxy/galaxy-Newcastle/database/tmp/tmpQK6VjP /home/galaxy/galaxy-Newcastle/database/tmp/tmpD_ySP1 4:/home/galaxy/galaxy-Newcastle/database/job_working_directory/000/4/dataset_4_files:/home/galaxy/galaxy-Newcastle/database/files/000/dataset_4.dat galaxy.jobs DEBUG 2013-02-21 13:16:39,590 The tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2013-02-21 13:16:39,900 job 4 ended So some reason the history isn't getting updated for multiple instances of Galaxy Thanks Neil

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Re: [galaxy-user] Problem Loading History Pane
by Lizex Husselmann 20 Feb '13

20 Feb '13

Dear all I have in my project single end reads (50 bp) for some samples and paired end reads (100 bp frw and rev) for the other samples. I had to re-sequence some of the samples of which I have paired-end reads. However the re-sequence data I receives is single-end reads of 250 bp. Tophat wont allow mapping single and paired-end reads together. It says the result will look bad. They do mention that you can convert the junctions.bed file (output of Tophat) with bed_to_juncs using the -j option. I quote for TopHat manual "run TopHat on the 2nd set of reads using the -j option to supply the junctions file produced by be_to_juncs in the previous step". This is supposed to work but I didn't get it to work. Any suggestion on how I should go about analyzing this data? Kind regards Lizex >>> Nate Coraor 02/15/13 5:48 PM >>> On Feb 15, 2013, at 10:35 AM, Mike Dufault wrote: > To whom it may concern: > > The History panel on the right side of the Galaxy page is taking a very very long time to load. Also, when it does load, I have tired to save my bam files and the transmissions gets truncated to ~7000kb - 8000kb of data. All of my .bam files are several GB. > > Some times, when I retry tor download the data, it succeeds and other times it is again truncated. The size of the truncation may be different for the same file on the retry attempt. > > Is there a problem with Galaxy? Hi Mike, There are some performance problems with the Main site that we are currently investigating. Thanks for the information and we apologize for the problems. --nate > > Thanks, > Mike > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ This message is confidential and may be covered by legal professional privilege. It must not be read, copied, disclosed or used in any other manner by any person other than the addressee(s). Unauthorised use, disclosure or copying is strictly prohibited and may be unlawful. The views expressed in this email are those of the sender, unless otherwise stated. If you have received this email in error, please contact ARC Service Desk immediately. (mailto:Servicedesk@arc.agric.za) To report incidents of fraud and / or corruption in the ARC use our Ethics Hotline by: Phone number : 0800 000 604 Fax number : 0800 00 7788 Email address : arc(a)tip-offs.com Please Call me : 32840 Website: www.tip-offs.com For more information on the ARC Ethics Hotline, please visit our website at www.arc.agric.za.

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Post Galaxy-ChIP-seq analysis: UCSC Genome browser can't read the wig file
by Bodour Al-Khamees 20 Feb '13

20 Feb '13

Thank you very much Jennifer!

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Post Galaxy-ChIP-seq analysis: UCSC Genome browser can't read the wig file
by Bodour Al-Khamees 20 Feb '13

20 Feb '13

Hello, I am using the Galaxy web tool to analyze ChIP-seq data. By applying MACS algorithm, the Galaxy browser generated bed and wig files. Within the Galaxy browser, the bed file has a link to the UCSC Genome browser whereas the wig file has no link to the UCSC browser. I wonder which file is best to visualize the peaks in the UCSC Genome browser and how? Any experience or just thoughts? Thank you very much in advance!

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Re: [galaxy-user] Welcome to the "galaxy-user" mailing list (Digest mode)
by Bodour Al-Khamees 20 Feb '13

20 Feb '13

Hello, I would like to ask few question. I wonder if I can post in this mailing list. Thank you very much! Bodour On Wed, Feb 20, 2013 at 11:28 AM, <galaxy-user-request(a)lists.bx.psu.edu>wrote: > Welcome to the galaxy-user(a)lists.bx.psu.edu mailing list! The Galaxy > User list is for the discussion of analysis techniques in Galaxy and > use of other features on the public Galaxy server at usegalaxy.org. > For discussion of all topics pertaining to local Galaxy installations > including tool integration, server configuration, and modifications to > the Galaxy source code, please subscribe to the Galaxy Development > list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To post to this list, send your email to: > > galaxy-user(a)lists.bx.psu.edu > > General information about the mailing list is at: > > http://lists.bx.psu.edu/listinfo/galaxy-user > > If you ever want to unsubscribe or change your options (eg, switch to > or from digest mode, change your password, etc.), visit your > subscription page at: > > http://lists.bx.psu.edu/options/galaxy-user/alkhameesbodour%40gmail.com > > > You can also make such adjustments via email by sending a message to: > > galaxy-user-request(a)lists.bx.psu.edu > > with the word `help' in the subject or body (don't include the > quotes), and you will get back a message with instructions. > > You must know your password to change your options (including changing > the password, itself) or to unsubscribe. It is: > > 1234 > > Normally, Mailman will remind you of your lists.bx.psu.edu mailing > list passwords once every month, although you can disable this if you > prefer. This reminder will also include instructions on how to > unsubscribe or change your account options. There is also a button on > your options page that will email your current password to you. >

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