Re: [galaxy-dev] ENA SRA data retrieval with Cloudman
Hi Dannon, Thanks for this information. Will the ENA SRA button be enabled on the next update of Cloudman? Is there a protocol (or help page) available for how to re-enable tools in the 'tool_conf.xml'? One of the great things about Galaxy Cloudman is that someone who doesn't know programming (myself and many other biologists and clinicians) can seamlessly use the platform. Unfortunately, when trivial issues arise where the solution is to insert a line or two of code in the universe of Galaxy Cloudman people like me are stymied and really don't even know where to start. I know it requires work at some level, but a tutorial on how to find your 'tool_conf.xml' (or dummies guide to quick Cloudman fixes) would likely be helpful to many end users (including myself). Thanks again, Dannon! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205 On Wed, Apr 2, 2014 at 5:03 PM, Dannon Baker dannon.ba...@gmail.com wrote: Hey Mo, Sorry for the super delayed response here. I can't find a decision to remove it documented anywhere, so my guess is that this tool was unintentionally removed when we last updated the volume. It's actually still available on disk, though, and can be re-enabled in your tool_conf.xml by adding the following back to your Get Data section: tool file=data_source/ebi_sra.xml / -Dannon On Mon, Mar 10, 2014 at 11:53 AM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Hi Cloudman Development Team, I noticed on the most recent Cloudman release (revision 11219:5c789ab4144ahttp://bitbucket.org/galaxy/galaxy-dist/changesets/5c789ab4144a) that there is no option to Get Data from the ENA SRA. We've found that retrieving large (fastq) data sets from public databases into Galaxy/Cloudman is the most convenient from the ENA SRA option in the Get Data menu. Will this option be coming back, or is the ENA SRA option permanently removed? Cheers, Mo Heydarian ___ 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] ENA SRA data retrieval with Cloudman
Hi Dannon, Thanks so much, your protocol was extremely helpful! Thanks for looking into ENA SRA. In our experience, the ENA SRA is the easiest and most reliable way of importing public NGS data into Galaxy. The ENA SRA has an actual button to click that will import your data set of choice into Galaxy, while retaining the data set ID. It is much more straight forward (and reliable) than using any of the NCBI databases. Thanks for your help with all of this, Dannon! Have a great night. Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205 On Wed, Apr 2, 2014 at 6:21 PM, Dannon Baker dannon.ba...@gmail.com wrote: On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Hi Dannon, Thanks for this information. Will the ENA SRA button be enabled on the next update of Cloudman? I'll check to make sure there wasn't a good reason to remove it (couldn't find one in my first pass, and it's available on main, so it should be in the cloud), but yes. Is there a protocol (or help page) available for how to re-enable tools in the 'tool_conf.xml'? With everything headed to the toolshed, hopefully this is a thing of the past very soon. The only documentation I found on the wiki is here: https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial In short, you'll need to: 1) ssh to your cloud galaxy instance 2) navigate to /mnt/galaxy/galaxy-app 3) open tool_conf.xml in your favorite editor, and add the line below, exactly, in the Get Data section (the first one, begins on line 3): tool file=data_source/ebi_sra.xml / 4) Close down ssh, 5) In a web browser, go to the cloud admin panel and click restart for the Galaxy service. One of the great things about Galaxy Cloudman is that someone who doesn't know programming (myself and many other biologists and clinicians) can seamlessly use the platform. Unfortunately, when trivial issues arise where the solution is to insert a line or two of code in the universe of Galaxy Cloudman people like me are stymied and really don't even know where to start. I know it requires work at some level, but a tutorial on how to find your 'tool_conf.xml' (or dummies guide to quick Cloudman fixes) would likely be helpful to many end users (including myself). We definitely do try to make it as ready-to-go out of the box as possible, but that's a great idea. I'll try to document this better. Thanks again, Dannon! Anytime, thanks for your patience and for using Galaxy/Cloudman! ___ 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/
[galaxy-dev] ENA SRA data retrieval with Cloudman
Hi Cloudman Development Team, I noticed on the most recent Cloudman release (revision 11219:5c789ab4144ahttp://bitbucket.org/galaxy/galaxy-dist/changesets/5c789ab4144a) that there is no option to Get Data from the ENA SRA. We've found that retrieving large (fastq) data sets from public databases into Galaxy/Cloudman is the most convenient from the ENA SRA option in the Get Data menu. Will this option be coming back, or is the ENA SRA option permanently removed? Cheers, Mo Heydarian ___ 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] Installing DeepTools on Cloudman 2.0
That did the trick! Thanks, Bjoern! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205 On Tue, Dec 3, 2013 at 5:14 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Am Dienstag, den 03.12.2013, 16:19 -0500 schrieb Mohammad Heydarian: Hi Bjorn, Thanks for the quick response. I am running version: 10201:ebe87051fadf, when I updated to the latest version, I was able to start the install of DeepTools. The tool seemed to be installing but when I went to refresh the page, I was greeted with this message: Initializing repository installation failed. That one should not scare you. Its not an error, I need to fill a trello card about that. But it nothing to worry about. Checking on the progress of the installation with the monitor installing tool shed repositories page, shows that most of the repositories are Installing tool dependencies (yellow box) or Installed, missing both tool and repository dependencies (gray box). This is the case even after ~ two hours. Probably due to the error before. Can you please visit the deepTools repository and choose the 'repair repository' under 'repository actions'. That should fix all previous errors. You can also remove and reinstall deepTools and all packages in the 'Installing' state. Hope that helps! Bjoern I am glad to clarify if my description was unclear, or even share the cloud instance. Thanks in advance for any help! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205 On Tue, Dec 3, 2013 at 1:37 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Mohammed, that seems to be a old Tool Shed bug that is already fixed. Which Galaxy version are you running. Can you update to a more recent version? Thanks for using Galaxy and deepTools, Bjoern Hello, I recently discovered the DeepTools program and have been looking forward to using it with Galaxy Cloudman. Today I attempted to load DeepTools from the Galaxy tool shed on my freshly started Galaxy Cloudman 2.0 instance and got the following error: Internal Server Error Galaxy was unable to sucessfully complete your request URL: http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=8aa7aee9b90e1791changeset_revisions=1ee0b1ecf500 Module galaxy.web.framework.middleware.error:149 in __call__ app_iter = self.application(environ, sr_checker) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:896 in prepare_for_install common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict,includes_tool_dependencies ) Module tool_shed.util.common_install_util:84 in get_dependencies_for_repository installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install(trans, repo_info_tuple ) Module tool_shed.util.common_install_util:190 inget_installed_and_missing_repository_dependencies_for_new_install tool_shed, name, owner, changeset_revision, prior_installation_required =suc.parse_repository_dependency_tuple( rd_tup ) Module tool_shed.util.shed_util_common:1106 in parse_repository_dependency_tuple prior_installation_required = str( prior_installation_required ) UnboundLocalError: local variable 'prior_installation_required' referenced before assignment I got this error when I tried to install either of the three revisions of the tool. Am I doing something wrong? Any guidance is appreciated! Thanks in advance! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School
[galaxy-dev] Installing DeepTools on Cloudman 2.0
Hello, I recently discovered the DeepTools program and have been looking forward to using it with Galaxy Cloudman. Today I attempted to load DeepTools from the Galaxy tool shed on my freshly started Galaxy Cloudman 2.0 instance and got the following error: Internal Server ErrorGalaxy was unable to sucessfully complete your request URL: http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=8aa7aee9b90e1791changeset_revisions=1ee0b1ecf500 Module galaxy.web.framework.middleware.error:*149* in __call__ http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=8aa7aee9b90e1791changeset_revisions=1ee0b1ecf500# app_iter *=* self*.*application*(*environ*,* sr_checker*)* Module paste.recursive:*84* in __call__ http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=8aa7aee9b90e1791changeset_revisions=1ee0b1ecf500# *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=8aa7aee9b90e1791changeset_revisions=1ee0b1ecf500# *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*132* in __call__ http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=8aa7aee9b90e1791changeset_revisions=1ee0b1ecf500# *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*190* in handle_request http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=8aa7aee9b90e1791changeset_revisions=1ee0b1ecf500# body *=* method*(* trans*,* kwargs *)* Module galaxy.web.framework:*221* in decorator http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=8aa7aee9b90e1791changeset_revisions=1ee0b1ecf500# *return* func*(* self*,* trans*,* ***args*,* kwargs *)* Module galaxy.webapps.galaxy.controllers.admin_toolshed:*896* in prepare_for_install http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=8aa7aee9b90e1791changeset_revisions=1ee0b1ecf500# common_install_util*.*get_dependencies_for_repository*(* trans*,* tool_shed_url*,* repo_info_dict*,*includes_tool_dependencies *)* Module tool_shed.util.common_install_util:*84* in get_dependencies_for_repository http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=8aa7aee9b90e1791changeset_revisions=1ee0b1ecf500# installed_rd*,* missing_rd *=* get_installed_and_missing_repository_dependencies_for_new_install*(*trans*,* repo_info_tuple *)* Module tool_shed.util.common_install_util:*190* in get_installed_and_missing_repository_dependencies_for_new_install http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=8aa7aee9b90e1791changeset_revisions=1ee0b1ecf500# tool_shed*,* name*,* owner*,* changeset_revision*,* prior_installation_required *=*suc*.*parse_repository_dependency_tuple*(* rd_tup *)* Module tool_shed.util.shed_util_common:*1106* in parse_repository_dependency_tuple http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=8aa7aee9b90e1791changeset_revisions=1ee0b1ecf500# prior_installation_required *=* str*(* prior_installation_required *)* *UnboundLocalError: local variable 'prior_installation_required' referenced before assignment* I got this error when I tried to install either of the three revisions of the tool. Am I doing something wrong? Any guidance is appreciated! Thanks in advance! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205 ___ 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] Installing DeepTools on Cloudman 2.0
Hi Bjorn, Thanks for the quick response. I am running version: 10201:ebe87051fadf, when I updated to the latest version, I was able to start the install of DeepTools. The tool seemed to be installing but when I went to refresh the page, I was greeted with this message: Initializing repository installation failed. Checking on the progress of the installation with the monitor installing tool shed repositories page, shows that most of the repositories are Installing tool dependencies (yellow box) or Installed, missing both tool and repository dependencies (gray box). This is the case even after ~ two hours. I am glad to clarify if my description was unclear, or even share the cloud instance. Thanks in advance for any help! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205 On Tue, Dec 3, 2013 at 1:37 PM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Mohammed, that seems to be a old Tool Shed bug that is already fixed. Which Galaxy version are you running. Can you update to a more recent version? Thanks for using Galaxy and deepTools, Bjoern Hello, I recently discovered the DeepTools program and have been looking forward to using it with Galaxy Cloudman. Today I attempted to load DeepTools from the Galaxy tool shed on my freshly started Galaxy Cloudman 2.0 instance and got the following error: Internal Server Error Galaxy was unable to sucessfully complete your request URL: http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=8aa7aee9b90e1791changeset_revisions=1ee0b1ecf500 Module galaxy.web.framework.middleware.error:149 in __call__ app_iter = self.application(environ, sr_checker) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request body = method( trans, **kwargs ) Module galaxy.web.framework:221 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:896 in prepare_for_install common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict,includes_tool_dependencies ) Module tool_shed.util.common_install_util:84 in get_dependencies_for_repository installed_rd, missing_rd = get_installed_and_missing_repository_dependencies_for_new_install(trans, repo_info_tuple ) Module tool_shed.util.common_install_util:190 inget_installed_and_missing_repository_dependencies_for_new_install tool_shed, name, owner, changeset_revision, prior_installation_required =suc.parse_repository_dependency_tuple( rd_tup ) Module tool_shed.util.shed_util_common:1106 in parse_repository_dependency_tuple prior_installation_required = str( prior_installation_required ) UnboundLocalError: local variable 'prior_installation_required' referenced before assignment I got this error when I tried to install either of the three revisions of the tool. Am I doing something wrong? Any guidance is appreciated! Thanks in advance! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 402 Biophysics Baltimore, MD 21205 ___ 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/
[galaxy-dev] Cloudman database issue (?)
Hello, I found a couple of issues in using the latest version of Cloudman (revision:10201:ebe87051fadf). The Extract Genomic DNA tool returns an error: No sequences are available for 'mm9', request them by reporting this error. Upon trying to report the error in Galaxy (on the page that comes up when you click the bug icon) I get the error: Mail is not configured for this galaxy instance Any help on fixing the Extract Genomic DNA tool would be great. Thanks. Cheers, Mo Heydarian ___ 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] [galaxy-user] Connecting to new Galaxy Cloudman by FTP
Hey Nate, Thanks for the response and instructions. I understand the last three steps of your protocol, but the first step is difficult for me to understand. I'm guessing that, 1. Set 'use_pbkdf2 = False' in universe_wsgi.ini anywhere in the [app:main] section, is telling me to change a setting of Cloudman by command line. This is generally where we get stuck in using Cloudman, because we aren't familiar with command line (we get cold sweats and light palpitations) and are weary of making changes to the Cloudman code. I would ask our IT guys for help, but their expertise ends at updating Office tools. I would bother a programmer or bioinformatician, but most of them are so busy you need a formal collaboration to get on their radar. I would ask people who vaguely know command line for help, but most of the time their knowledge of command line is just higher than mine and we end up troubleshooting an issue neither of us can really grasp. So, is there a webcast, or video, or slideshow, that can show a newbie how to command line into Cloudman and make the changes you outline in step 1? Cheers, Mo Heydarian On Mon, Jul 15, 2013 at 4:22 PM, Nate Coraor n...@bx.psu.edu wrote: On Jul 8, 2013, at 3:50 PM, Mohammad Heydarian wrote: Hi, I am having trouble setting up a FTP connection with the recently released version of Galaxy Cloudman (ami-118bfc78). I have instantiated the new version of Galaxy Cloudman with CloudLaunch and also through the AWS EC2 wizard (using the same security group settings as the previous versions) and neither instance will connect to my FTP connection. Has anyone else had this problem? Does anyone know what is preventing the FTP connection? Any help would be greatly appreciated. Hey Mo, This may be a case of the new password hashing algorithm's incompatibility with the provided ProFTPD config. Could you try the following: 1. Set 'use_pbkdf2 = False' in universe_wsgi.ini anywhere in the [app:main] section 2. Restart Galaxy 3. Reset your password in the Galaxy UI 4. Test FTP again --nate Cheers, Mo Heydarian ___ 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/ ___ 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/ 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] Galaxy CloudMan release - Tophat does not work
Cufflinks, Cuffcompare, and Cuffdiff are also failing to run because they can not be found. I am using the newly released version of Cloudman 2.0 ( ami-118bfc78). Any help would be appreciated. Cheers, Mo Heydarian On Mon, Jul 8, 2013 at 5:02 PM, Ravpreet Setia ravpreet.se...@oicr.on.cawrote: Some tools (tophat is one) are failing to run because they cannot be found. I have noticed that after launching a new instance with the latest AMI, the package/version/default sym-links under /mnt/galaxy/tools point to a directory in /mnt/galaxyTools, which does not exist since this new AMI merged galaxyTools and galaxyData. Additionally, even after manually fixing the symlink and the path in the env.sh file (it also references galaxyTools), running tophat would fail, although now, at least, it can find the program. This document explains how the default symlink is used by Galaxy: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies Thanks for any suggestions. From: Enis Afgan afg...@gmail.com Date: Sun, 30 Jun 2013 07:37:46 +0200 To: Galaxy-dev galaxy-...@bx.psu.edu Subject: [galaxy-dev] Galaxy CloudMan release *Last night, we released an update to Galaxy CloudMan.* CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration. *IMPORTANT - please read* Any new cluster will automatically start using this version of CloudMan. Existing clusters will be given an option to do an automatic update once the main interface page is refreshed. Note that this upgrade is a major version upgrade and thus the migration is rather complicated. The migration process has been automated but will take a little while to complete. If you have made customizations to your cluster in terms of adding file systems, upgrading the database, or similar, we do not recommend you perform the upgrade. Note that this upgrade comes with (and requires) a new AMI (ami-118bfc78), which will be automatically used if starting an instance via CloudLaunch http://usegalaxy.org/cloudlaunch. *This update brings a large number of updates and new features, the most prominent ones being:* - Unification of *galaxyTools* and *galaxyData* file systems into a single *galaxy* filesystem. This change makes it possible to utilize the Galaxy Tool Shed when installing tools into Galaxy. - Added initial support for Hadoop-type workloads - Added initial support for cluster federation via HTCondor - Added a new file system service for instance's transient storage, allowing it to be used across the cluster over NFS - Added a service for Galaxy Reports webapp - Added optional Loggly (loggly.com) based off-site logging support - Added tags to all resources utilized by CloudMan For more details on the new features, see the the CHANGELOGhttps://bitbucket.org/galaxy/cloudman/src/tip/CHANGELOG.md?at=defaultand for even more details see, all of 291 commit messageshttps://bitbucket.org/galaxy/cloudman/commits/all?search=35baec1%3A8bbae3f from 7 contributors. Enjoy and please let us know what you think, Enis P.S. We also now have a logo for CloudMan [image: Inline image 2] ___ 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/ ___ 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/
[galaxy-dev] Connecting to new Galaxy Cloudman by FTP
Hi, I am having trouble setting up a FTP connection with the recently released version of Galaxy Cloudman (ami-118bfc78). I have instantiated the new version of Galaxy Cloudman with CloudLaunchhttp://usegalaxy.org/cloudlaunch and also through the AWS EC2 wizard (using the same security group settings as the previous versions) and neither instance will connect to my FTP connection. Has anyone else had this problem? Does anyone know what is preventing the FTP connection? Any help would be greatly appreciated. Cheers, Mo Heydarian ___ 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/
[galaxy-dev] Exporting Trackster visualizations.
Hi, Is there a way to export visualizations from Trackster and Sweepster in .pdf or .jpg format? I have been using these fantastic tools to fine tune my parameters and would like to show how I did so in figure format (partially to locally get the word out about these powerful tools). Screenshots often do not suffice (and don't do the tools justice). Any solutions and/or fixes are appreciated! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 ___ 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] Empty TopHat output
Thanks, Jeremy. I updated my instance of Galaxy by the repository you provided ( https://bitbucket.org/galaxy/galaxy-dist/) and re-ran my analysis. I see that TopHat is generating data (by monitoring the disk usage on the Cloudman interface) again, but this time I the output file is in the error state and the message returned is: Job output not returned from cluster. Any thoughts? Thanks in advance! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Wed, Oct 31, 2012 at 9:03 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote: In this case, it's useful to differentiate between (i) the AMI that Galaxy Cloud uses and (ii) the Galaxy code running on the cloud. I suspect that (ii) is out of data for you; this is not (yet) automatically updated, even when starting a new instance. Try using the admin console to update to the most recent Galaxy dist using this URL: https://bitbucket.org/galaxy/galaxy-dist/ (not galaxy-central, as is the default) Best, J. On Oct 31, 2012, at 8:36 PM, Mohammad Heydarian wrote: We are running galaxy-cloudman-2011-03-22 (ami-da58aab3). Our latest instance was loaded up just last week. Thanks! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Wed, Oct 31, 2012 at 8:30 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote: Given that this doesn't seem to be happening on our public server or on local instances, my best guess is that the issue is old code. Are you running the most recent dist? J. On Oct 31, 2012, at 7:37 PM, Mohammad Heydarian wrote: We are still getting empty TopHat output files on our Galaxy instance on the cloud. We see that TopHat is generating data while the tool is running (by monitoring our disk usage on the Amazon cloud), but the output is empty files. Is anyone else having this issue? Does anyone have any suggestions? Many thanks in advance! Cheers, Mo Heydarian On Mon, Oct 15, 2012 at 4:53 AM, Joachim Jacob joachim.ja...@vib.bewrote: The same here. Cheers, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib __**_ 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] Empty TopHat output
We are still getting empty TopHat output files on our Galaxy instance on the cloud. We see that TopHat is generating data while the tool is running (by monitoring our disk usage on the Amazon cloud), but the output is empty files. Is anyone else having this issue? Does anyone have any suggestions? Many thanks in advance! Cheers, Mo Heydarian On Mon, Oct 15, 2012 at 4:53 AM, Joachim Jacob joachim.ja...@vib.be wrote: The same here. Cheers, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib __**_ 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] Empty TopHat output
We have been having also been having this issue, we get empty TopHat output files. This is happening on two instances that were started within the past three weeks on the cloud. Cheers, Mo Heydarian -- Forwarded message -- From: 吳正華 joh...@ibms.sinica.edu.tw Date: Fri, Oct 12, 2012 at 11:12 PM Subject: [galaxy-dev] Empty TopHat output To: galaxy-dev@lists.bx.psu.edu Hi all: ** ** After updating our local galaxy installation to the latest build last week, I found that when tophat finished its execution, all its output files showed empty in the history. ** ** However, I could execute the exact same command via shell and got correct tophat output files. ** ** It seemed that something went wrong when galaxy tried to copy tophat output files to galaxy databases/file. ** ** Did anyone encounter the same problem? How could I fix this problem? ** ** Thanks a lot. ** ** ** ** Best ** ** John Wu - PhD Student Academia Sinica ** ** ___ 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] Blastxml error on Galaxy Cloudman
Hello, I recently updated my instance of Galaxy Cloudman (using Amazon AWS) and I have since not been able to run any jobs. I get the following error: WARNING:galaxy.datatypes.registry:Error loading datatype with extension 'blastxml': 'module' object has no attribute 'BlastXml' WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object has no attribute 'BlastXml' Any help would greatly be appreciated. Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 ___ 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 in loading tools.
Hi Galaxy Community! Hope all is well. I've been trying to install some tools in my Galaxy Cloudman instance (using image: ami-da58aab3 ) from the main toolshed. When I try to install to local Galaxy I get the error: Not Found The resource could not be found. No action for /admin_toolshed/prepare_for_install I have tried to load tools on a couple of different Cloudman instances and tried to load a variety of tools and end up with the same error. Any help would be fantastic. Cheers, Mo Heydarian ___ 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] Trackster - not showing data.
Hi, I have been trying to use trackster on the main Galaxy server for a couple of days now. It was working fine for me early yesterday, I was looking at (larger) BAM files, then it just stopped and would not display the data of the loaded tracks (but did display the track title). I have tried to start Trackster with smaller sized tracks, as well as using another Galaxy account, and still cannot get Trackster to display data (though it will show the track title). Any help would be greatly appreciated! Cheers, Mo Heydarian ___ 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] Can't upload Cuffmerge files to Galaxy Cloudman
Hello, I can not upload Cuffmerge files to Galaxy Cloudman. I can load other .gtf files just fine, but not the merged transcripts.gtf file from Cuffmerge. This is the first time this has happened. After I upload my merged transcripts.gtf file (via ftp) I can not move the file to the history pane. Upon asking Galaxy Cloudman to move the file from the ftp queue to the history pane, I get the error: No data was entered in the upload form, please go back and choose data to upload Even if I try to zip the file to fool Galaxy Cloudman the file still won't load. This may be unrelated, but I have never been able to download Cuffdiff out put files from Galaxy Cloudman directly, I always have to export my history to a file and then rename the files after download. Any help would be great! Cheers, Mo Heydarian ___ 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 upload Cuffmerge files to Galaxy Cloudman
Also, this issue with uploading Cuffmerge files to Galaxy Cloudman is specific to Cuffmerge files I have generated within the last ~24 hours (on Galaxy Main). I can upload these same files to main Galaxy server with no problem. It is specific to Galaxy Cloudman. Thanks for any help! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Thu, May 3, 2012 at 8:19 AM, Mohammad Heydarian mheyd...@jhmi.eduwrote: Hello, I can not upload Cuffmerge files to Galaxy Cloudman. I can load other .gtf files just fine, but not the merged transcripts.gtf file from Cuffmerge. This is the first time this has happened. After I upload my merged transcripts.gtf file (via ftp) I can not move the file to the history pane. Upon asking Galaxy Cloudman to move the file from the ftp queue to the history pane, I get the error: No data was entered in the upload form, please go back and choose data to upload Even if I try to zip the file to fool Galaxy Cloudman the file still won't load. This may be unrelated, but I have never been able to download Cuffdiff out put files from Galaxy Cloudman directly, I always have to export my history to a file and then rename the files after download. Any help would be great! Cheers, Mo Heydarian ___ 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] Increasing EBS storage above 1TB for use with Galaxy cloudman.
Hello, I am performing NGS data analysis using Galaxy cloudman. I am working with very large Fastq files that add up and approach the 1TB limit of the EBS volume when I perform my analysis. Is there a way to use multiple EBS volumes with one EC2 instance of Galaxy cloudman. For example, could I direct which EBS volume holds certain files to prevent reaching the 1 TB limit while still allowing my EC2 instance to access and perform jobs on all files? Many thank in advance! Cheers, Mo Heydarian ___ 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] Private key file format issue (for connecting EC2 instance with EBS volume)
Hello, I am trying to connect an EC2 instance to an EBS volume. I have attached the EBS volume to the EC2 instance (running Galaxy). I now need to mount the EBS volume to the EC2 instance. To do this I will use Putty to make the connection. But first I have to convert the private key from .pem format to .ppk format. I am trying to use Puttygen for the conversion, but the .pem file is not recognized and I get this error message: Could't load private key (key file does not begin with OpenSSH key header) Does anyone have experience with this? BTW, I am using windows. Thanks! Cheers, Mo Heydarian ___ 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] Moving data about the EC2/EBS/S3 spaces on the Amazon cloud.
Hello, I am new to cloud computing and am trying to use the Galaxy cloudman service through Amazon to analyse NGS data. I have a couple of questions regarding data transfer: If I am running an EC2 instance, with an EBS volume attached, how can I retrieve the data from the EBS volume? In addition, how do I view what files are in the EBS volume? Can I send the data to an S3 bucket? And how would I move data from the S3 bucket to a fresh EC2 instance? Assuming I can store my files on EBS (or S3), what is the best way to download them? Can I set up a ftp transfer to (quickly) download my potentially very large files? Many thanks for any insight and direction! Cheers, Mo Heydarian ___ 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] How do you connect existing EBS volumes to a fresh EC2 instance?
Hello, How do you connect existing EBS volumes to a fresh EC2 instance on Amazon? I have been starting the EC2 instance and choosing test cluster where the option to use EBS volume space is given (when the Galaxy cloud console starts up), since there is no place to insert my EBS volume address. This leads to Galaxy starting one 15 GB EBS volume (the other two, 10 Gb and 700 Gb, EBS volumes are not started) and I then manually tell my desired EBS volume to connect to the fresh EC2 instance. The EBS volume says it is attached to the EC2 instance, but the Galaxy cloud console shows no linkage to any data (in the service status row) and the disk status is 0 \ 0 (0%). Help would greatly be appreciated. Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 ___ 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/
