Re: [galaxy-dev] Multicore
Hi Alexander, There is a -t for PeakRanger to indicate the number of threads. I don't think macs14 or macs2 can run on mutltiple cores - I am cc'ing Tao Lui, the author of macs, who can confirm this. Thanks, Q On Tue, Mar 26, 2013 at 6:15 AM, Alexander Kurze alexander.ku...@gmail.com wrote: Hi there, we have a 32 core server but I realised that a lot of programs are only using a fraction of that. I was able to adjust bowtie, bowtie2 and Tophat to use all of the cores but couldn't find an thread/core option for Macs14, Macs2 or PeakRanger. Does anyone know if these programs are capable of multi threading? If yes, where do I adjust it? Would be nice to have some global parameter set in the universewgsi.ini file. Thanks, Alex ___ Please keep all replies on the list by using reply all in your mail client. 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/ ___ Please keep all replies on the list by using reply all in your mail client. 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/
Re: [galaxy-dev] error installing BWA from toolshed
Hi Greg, Works. Thanks. Is it possible to create a branch call 'latest_stable', which always points to the latest stable release so then on our end, we can always do 'hg update latest_stable' in one of our scripts to update rather using 'release_2013.02.08'? Thanks, On Mon, Feb 25, 2013 at 8:52 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Quang, It looks like you are attempting to install from the main Galaxy tool shed into a Galaxy instance that is older than the December 20, 2012 Galaxy release. You have to be using that release or newer (up to the current stable branch) to use the main Galaxy tool shed. To get the latest stable branch, you can do this: hg update release_2013.02.08 Then to get all updates to the stable branch, you can: hg pull -b stable https://bitbucket.org/galaxy/galaxy-central followed by: hg update Greg Von Kuster On Feb 25, 2013, at 8:35 AM, Quang Trinh wrote: Hi dev, I am trying to install bwa from toolshed on my Galaxy instance on Amazon just now and get this error ( please see below). Installing bwa worked for me before. URL: http://xxx.xxx.xxx.xxx/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=25bdd3c7f0d57b06changeset_revisions=ffa8aaa14f7c Module paste.exceptions.errormiddleware:143 in __call__ app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.web.framework:206 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:1199 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple ValueError: too many values to unpack Thanks, Q ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] error installing BWA from toolshed
Hi dev, I am trying to install bwa from toolshed on my Galaxy instance on Amazon just now and get this error ( please see below). Installing bwa worked for me before. URL: http://xxx.xxx.xxx.xxx/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=25bdd3c7f0d57b06changeset_revisions=ffa8aaa14f7c Module paste.exceptions.errormiddleware:143 in __call__ app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.web.framework:206 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:1199 in prepare_for_install description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple ValueError: too many values to unpack Thanks, Q ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] can't run instance for CloudMan
Hi Stefano, Can you try out what we put together: https://github.com/modENCODE-DCC/Galaxy Thanks, Q On Thu, Feb 14, 2013 at 8:28 PM, stefano cardinale s.cardin...@berkeley.edu wrote: Hi, I am having a problem with running galaxy on the Amazon cloud. I have tried this several times over the past few days, I followed the list and it seems my instance is up and running. However, when I type the DNS in any browser it can't connect to it. I am kind of aiming in the dark now because I don't know where the problem is, anyone can help? thanks! stefano ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] ce10
Hello Alfonso, You can do this by yourself in your own Galaxy instance by clicking on Get Data, Upload File, and either select your ce10 genome from your local machine or cut and paste the ce10 genome URL from somewhere into the URL/Textbox. Then click on Execute. You are welcome to use our ce10 genome from http://data.modencode.org/modENCODE_Galaxy/Test_Data/fasta/WS220.fasta Q On Fri, Jan 25, 2013 at 4:12 PM, Alfonso Garrido-Lecca alfonso.garrido-le...@colorado.edu wrote: Hello, Could somebody please help me uploading the C. elegans genome (Ce10) into galaxy on the cloud? thanks alfonso ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy Main cloudlaunch stall
Hi Matthew, Would you like to try out what we put together for modENCODE DCC? Please see the README file in the docs folder at https://github.com/modENCODE-DCC/Galaxy Thanks, Q On Fri, Jan 18, 2013 at 10:17 AM, Dannon Baker dannonba...@me.com wrote: Cloudlaunch on the main public instance is fully supported and should work fine -- I use it regularly for launching instances without issue. There was a brief EC2 API outage yesterday (on the Amazon end) that caused intermittent errors to all users of the API (including cloudlaunch), but that should be resolved now. Creating security groups and selecting (or creating, if necessary) an access key should be possible -- since it's not even getting that far I'm wondering if there isn't a Javascript error or something preventing the form submission. What browser are you using, and do you see any errors? -Dannon On Jan 17, 2013, at 5:11 PM, Matthew Shirley mshir...@jhmi.edu wrote: I've searched the list to see if anyone specifically mentions not being able to use the cloud launch feature on the main public instance, but no one seems to address it. I have no trouble launching Galaxy-cloudman using an AMI and pasting in my own user data. However, I can't successfully use the cloud launch page to do the same. I've tried letting it create a new security group as well as using a pre-existing security group. Also, I've then deleted all security groups to see if it would create one, which it did not. Similarly, I tried creating a new access key pair, with no further success. I make it through the process of entering the key ID and secret key, it pulls existing security group information into the drop-down selector, and I give a cluster name and password and submit the form. Then it just stalls forever. No new security groups and no EC2 instances launched. What is the state of this tool? Thanks. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] macs error for chipseq data
Hi James, Yes, we will be putting everything on toolshed shortly. Arthur ( cc'ed ), my student from OICR, will be taking lead on this. Thanks, Q On Wed, Jan 16, 2013 at 11:06 AM, James Taylor ja...@jamestaylor.org wrote: This is great. For the Galaxy tools, will you be able to submit wrappers to the toolshed? This should make it easier for users to install into their local Galaxy instances. Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, Jan 16, 2013 at 8:38 AM, Quang Trinh quang.tr...@gmail.com wrote: Hi Kathryn, We at the modENCODE DCC ( http://www.modencode.org/ ) have been setting up a suite of 3rd party tools for calling peaks ( i.e., macs2, spp, PeakRanger ) using Galaxy on Amazon Cloud the last little while. Please have a look at the README files in the docs folder on our github at https://github.com/modENCODE-DCC/Galaxy Please give it a try and send us your comments/questions to h...@modencode.org. Thanks, Q On Fri, Jan 11, 2013 at 10:59 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Kathryn, I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility. Thanks! Jen Galaxy team On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote: Hi Jen, Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out. It seems to me that MACS was installed…. What is the issue? Thank you very much, Kathryn On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote: Hi Jennifer, Thanks for the information on MACS tools. Yes, I forgot to mention that I used bowtie mapped files as the input. Thank you very much, Kathryn From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Friday, January 11, 2013 3:48 AM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: [External] Re: [galaxy-user] macs error for chipseq data Hello Kathryn, This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 If you need more help with your local install, directing questions to the galaxy-...@bx.psu.edu mailing list would be best, Thanks! Jen Galaxy team On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote: Dear galaxy users, I’ve encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error An error occurred running this job: /bin/sh: macs: not found Anybody can kindly provide some hints? Thanks, Kathryn ___ 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/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] missing BWA tools on AWS AMI
Hi dev, I launched an instance of Galaxy on Amazon ( AMI ami-da58aab3 ) this morning and noticed bwa is no longer available. Is this temporary or if we want to use bwa, we have to add the bwa ourselves? Thanks, Q ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] refresh user history
Hi dev, We have a script that download a number of files from an external site, however, only the first file shows up in the user history once the downloads are complete. The rest of the files show up when we click on the refresh user history button. Is there a way to refresh the user history in our script when all the files are downloaded? THanks, Q ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] adding IDR to Galaxy
Hi dev, Just wondering if there is plan to add IDR ( please see the link below ) to Galaxy Amazon AMI? https://sites.google.com/site/anshulkundaje/projects/idr IDR is being used by both modENCODE and ENCODE projects for ChiP-seq analysis. Thanks, Q ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] adding IDR to Amazon AMI
Hi dev, Just wondering if there is plan to add IDR ( please see the link below ) to Galaxy Amazon AMI? https://sites.google.com/site/anshulkundaje/projects/idr IDR is being used by both modENCODE and ENCODE projects for ChiP-seq analysis. Thanks, Q ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
