- galaxy-user - lists.galaxyproject.org

How do I add Ray to Galaxy Central in the tool shed ?
by Sébastien Boisvert 13 Jun '13

13 Jun '13

Hello, I want to add Ray (a scalable de novo assembler for genomes and metagenomes) to Galaxy. Ray is GPLv3 [1]. I have read http://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial and I understand that I have to write a Tool Definition File in XML. I also visited the source code here: https://bitbucket.org/galaxy/galaxy-central/src/5de636ce68faededc52d7b0c161… I will also have to write a wrapper for Ray to prepare the command line from the options provided by the Galaxy API. But where is stored the executable (in my case, where is sdtored Ray) ? Does Galaxy include the specs to build all the tools available in Galaxy-Central ? --- [1] http://denovoassembler.sourceforge.net/

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FTP upload problem
by Delong, Zhou 12 Jun '13

12 Jun '13

Hello, I was using the ftp uploading via filezilla. It worked perfectly this morning, but after a disconnection of the internet I can no longer upload any file. This is the message I got: 530 Sorry, the maximum number of clients (3) for this user are already connected I restarted my computer and shut down the program for 30 minutes hoping the server will reset the connection but it didnt work. I've done some search on the internet but nothing helped. I noticed that this problem has already been mentioned on the ML but the solution was not given. Anyone could help please? Thanks Delong

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Upload files to Galaxy via FTP
by Hoang, Thanh 11 Jun '13

11 Jun '13

Hi, I have been trying to upload my RNA-seq data files (~20 Gb total) via FTP using my account in Galaxy. But I could not connect to the server. The following message showed up: *"Error: Critical error* *Error: Could not connect to server"* Could you suggest any idea to overcome this problem? Thank you so much Thanh * *

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problem with custom database build
by Ann Holtz-Morris, M.S. 11 Jun '13

11 Jun '13

Hi, I'm trying to create a new custom build . I keep getting GURU MEDITATION: #aa96a62c69784be49b7864f6ef42ddc6 I've been trying 1 or 2 times a day for the last 3 days. Thanks Ann CONFIDENTIALITY NOTICE: This electronic message is intended to be for the use only of the named recipient, and may contain information that is confidential or privileged. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is strictly prohibited. If you have received this message in error or are not the named recipient, please notify us immediately by contacting the sender at the electronic mail address noted above, and delete and destroy all copies of this message. Thank you.

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Tophat problem on a new local instance
by Elwood Linney 11 Jun '13

11 Jun '13

Hello, I will try this again without attachments and hope it gets on the list. I have installed a local instance of Galaxy as a one user in a Mac Pro desktop. I got some valuable help from Dannon Baker regarding how to load large datasets into it. However I noticed that the Upload file for this instance would only go up to the Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) version of the zebrafish assembly while where as the online version went up to the newer assembly zebrafish assembly Jul. 2010 (Zv9/danRER7) While I could download newer reference genome in the program from UCSC Main table browser whenever the local instance offered alternatives for genomes it only went up the earlier version (Zv8/danRer6) (danRer6) . I went ahead anyway, groomed 4 x 16gb datasets but when it came to Tophat, An error occurred with this dataset: Could not determine Tophat version /bin/sh: tophat: command not found Error indexing reference sequence /bin/sh: bowtie-build: command not found So minimally I have two problems that may or may not be related: 1)The Galaxy-dist that I just installed into a Mac pro does not have the latest zebrafish assembly 2) but more importantly when I try to process groomed datasets through Tophat and "Use a built-in genome" as reference it does not allow me an option for the reference genome AND if I try to use a reference genome from the UCSC download, it won't allow that. So right now I am stymied--any advice? Elwood Linney Duke University Medical Center

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Tophat problem on a new local instance
by Elwood Linney 09 Jun '13

09 Jun '13

I have installed a local instance of Galaxy as a one user in a Mac Pro desktop. I got some valuable help from Dannon Baker regarding how to load large datasets into it. However I noticed that the Upload file for this instance would only go up to the Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) version of the zebrafish assembly while where as the online version went up to the newer assembly zebrafish assembly Jul. 2010 (Zv9/danRER7) While I could download newer reference genome in the program from UCSC Main table browser whenever the local instance offered alternatives for genomes it only went up the earlier version (Zv8/danRer6) (danRer6) . I went ahead anyway, groomed 4 x 16gb datasets but when it came to Tophat, An error occurred with this dataset: Could not determine Tophat version /bin/sh: tophat: command not found Error indexing reference sequence /bin/sh: bowtie-build: command not found Also, when I download from UCSC the most updated zebrafish genome reference sequence and use it for Tophat, I get the following error signal: I don't know if this issue of assembly version is associated with my Tophat problem--the two Tophat screens I get from either the main Galaxy or my instance are attached for comparison: my local instance does not give me a "Use built-in genome option" while the main Galaxy does Any advice? Elwood Linney DUMC

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Galaxy Error
by Delong, Zhou 07 Jun '13

07 Jun '13

Hello, I'm using the main galaxy server to analyse some data and then I got this messege: An error occurred while getting updates from the server. Please contact a Galaxy administrator if the problem persists. I was uploading data from my computer since yesterday morning and it seems to take forever to accomplish. After one of my reads is uploaded I used the groomer tool on this dataset and then I got this messege. I tried the reflesh bottom on the right pannal severial times and I got the same messege each time. You can access to my history here: https://main.g2.bx.psu.edu/u/zhoud/h/knockdown Besides, is it possible to show the grade of progress of uploading? Thanks, Delong ZHOU

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GCC2013 Regular Registration closes June 14
by Dave Clements 04 Jun '13

04 Jun '13

Hello all, This is a reminder that registration<http://wiki.galaxyproject.org/Events/GCC2013/Register>for the 2013 Galaxy Community Conference (GCC2013<http://wiki.galaxyproject.org/Events/GCC2013>) closes June 14*, just ten days from today. *Registering now<http://wiki.galaxyproject.org/Events/GCC2013/Register>avoids the 100% late registration surcharges, and guarantees you a spot in the Training Day sessions<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay>you want to take. *Registration is still a bargain with the full 3-day registration starting at ~ €165 for post-docs and students (that is just €55 per day). The program <http://wiki.galaxyproject.org/Events/GCC2013/Program> features 15 Training Day sessions<http://wiki.galaxyproject.org/Events/GCC2013/Program#Day_0:_Training_Day.2C…> in 5 tracks on 12 different topics, 25 Talks<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Talk_Abstracts> on topics ranging from Reproducibility<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FA…> to Exploiting Galaxy<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FA…> , 23 Posters<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Poster_Abstracts> (and counting), 2 Lightning Talk sessions, and a end-of-conference event at an historic venue high above Oslo. GCC2013 is a great opportunity to share best practices from and network with other researchers also facing the challenges of data-intensive biology. Ser frem til å se deg i Oslo! GCC2013 Organizing Committee PS: and please help get the word out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion> . * Not June 7, as had been stated earlier in several places. -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Re: [galaxy-user] galaxy on the cloud
by Colaneri, Alejandro Cesar 04 Jun '13

04 Jun '13

Hi Dannon It does show up. I you see at my screen capture you can see the name (highlighted in blue) that is associated to the ami-da58aab3. However it does not look to be the latest version of the ami name. At least it does not work when I copy and paste in the searching box for all AMI images. Then I tried to follow the link that you provide in this email but unfortunately did not accept my AWS credentials. Also notice that the provided AMI name is dated march 2013, it is that ok? Is really the latest? Dr. Alejandro Colaneri Departments of Biology University of North Carolina at Chapel Hill 310 Coker Hall, CB# 3280 120 South Road Chapel Hill, NC 27599-3280 Tel: 919-962-2273 fax: 919- 962-1625 From: Dannon Baker <dannon.baker(a)gmail.com<mailto:dannon.baker@gmail.com>> Date: Monday, June 3, 2013 5:18 PM To: "Colaneri, Alejandro Cesar" <colaneri(a)email.unc.edu<mailto:colaneri@email.unc.edu>> Cc: "galaxy-user(a)list.bx.psu.edu<mailto:galaxy-user@list.bx.psu.edu>" <galaxy-user(a)bx.psu.edu<mailto:galaxy-user@bx.psu.edu>> Subject: Re: [galaxy-user] galaxy on the cloud Hi Alejandro, It should show up if you search for the AMI ID, which is ami-da58aab3. That said, the easiest way to launch a galaxy cloud cluster if you're not already familiar with EC2 is probably using usegalaxy.org/cloudlaunch<http://usegalaxy.org/cloudlaunch>. This interface will guide you through the launch process without any extra input on your part other than providing your AWS keys. -Dannon On Mon, Jun 3, 2013 at 1:51 PM, Colaneri, Alejandro Cesar <colaneri(a)email.unc.edu<mailto:colaneri@email.unc.edu>> wrote: Hello, I'm trying to start an instance of galaxy in the cloud (AMAZON) I'm following the screencast but when I copy the AMI name form the wiki site [cid:8F29F430-A843-4C52-8A1B-3DACF9E074A5] And paste in the Community AMIs search box , it does not work. Can you please tell me which is the lastest AMI name? Thank you Alejandro [cid:4C28C476-6FFD-45DD-9B06-795A2C46266C] Dr. Alejandro Colaneri Departments of Biology University of North Carolina at Chapel Hill 310 Coker Hall, CB# 3280 120 South Road Chapel Hill, NC 27599-3280 Tel: 919-962-2273 fax: 919- 962-1625 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org<http://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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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How to share an history with a SPECIFIC user ?
by Sarah Maman 04 Jun '13

04 Jun '13

Hello, My question is about sharing histories _with a specific user._ The share is not effective for a specific one but for all users logged in our local instance. Could you please help me ? Thank you in advance, Sarah -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*--

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