Re: [galaxy-dev] Forward of moderated message
Hi, I am posting my findings so that this may be useful for some body. I found a way to specify our own toolshed mentioned herehttps://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#Installing_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance. Toggle line numbershttps://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy# 1 https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#CA-04ee43fe2d1b2f55f5601ee1f9d4664b167450aa_1 ?xml version=1.0? 2 https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#CA-04ee43fe2d1b2f55f5601ee1f9d4664b167450aa_2 tool_sheds 3 https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#CA-04ee43fe2d1b2f55f5601ee1f9d4664b167450aa_3 tool_shed name=Bx tool shed url=http://someserver.bx.psu.edu:9009// 4 https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#CA-04ee43fe2d1b2f55f5601ee1f9d4664b167450aa_4 tool_shed name=Galaxy main tool shed url=http://toolshed.g2.bx.psu.edu// 5 https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#CA-04ee43fe2d1b2f55f5601ee1f9d4664b167450aa_5 tool_shed name=Galaxy test tool shed url=http://testtoolshed.g2.bx.psu.edu// 6 https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#CA-04ee43fe2d1b2f55f5601ee1f9d4664b167450aa_6 /tool_sheds We can run a toolshed and specify that multiple galaxy instances can access our own toolshed. Thanks, JanakiRam On Tue, Mar 25, 2014 at 7:51 AM, galaxy-user-boun...@lists.bx.psu.eduwrote: ___ 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/ -- Forwarded message -- From: Janaki Rama Rao Gollapudi janakiram.gollap...@india.semanticbits.com To: galaxy-u...@lists.bx.psu.edu Cc: Date: Mon, 24 Mar 2014 20:49:15 +0530 Subject: Reg: Creating a private repository for ToolShed Hi All, I setup galaxy in my local system successfully and I was able to install tools from ToolShed. My requirement: Assume that multiple galaxy instances are running on different systems. Both the ToolShed will be able to access a private repository(with custom/installed tools) which setup in any one of the system. Basically I want to setup a central repository accessed by the multiple ToolShed. Can you please provide me resources to achieve this. Thanks, JanakiRam ___ 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] Finding cruft in database/files/?
Hi Brian It is difficult to imagine where such files are coming from. As each file in ~/database/files/*/ has a corresponding entry in the 'dataset' table. If you have such files, then something went horribly wrong, eg by using two different databases on the same files system. To double check manually compare the list of files on the file system, with the contents of the 'dataset' table. Also, have a look at the ~/database/job_working_directory/ and ~/database/tmp/ directories. You might have some old, big files there using a lot of space. Regards, Hans-Rudolf On Mar 24, 2014, at 12:43 AM, Brian Claywell wrote: Daniel, I've been using the purge scripts in cron jobs for a long time now; unless I missed something on that page, what I'm looking for is something slightly different -- rather than purging datasets marked as old/deleted/whatever in the Galaxy db, I want to find files that *aren't* in the Galaxy db but still exist on the filesystem. On Sun, Mar 23, 2014 at 12:39 PM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Brian, Have a look at purging histories and datasets: https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets Thanks for using Galaxy, Dan On Mar 22, 2014, at 9:24 PM, Brian Claywell bclay...@fhcrc.org wrote: Is there an existing method for finding files in $GALAXY_DIR/database/files that have been orphaned due to errors, or leftover from testing, etc? I'm pretty sure ours is bigger than it ought to be, and I'd really like to look at a little audit of the files there vs the ones registered in Galaxy. Thanks! -- Brian Claywell, Systems Analyst/Programmer Fred Hutchinson Cancer Research Center bclay...@fhcrc.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Brian Claywell, Systems Analyst/Programmer Fred Hutchinson Cancer Research Center bclay...@fhcrc.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/ 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] Finding cruft in database/files/?
On Tue, Mar 25, 2014 at 11:42 AM, Hans-Rudolf Hotz wrote: Hi Brian It is difficult to imagine where such files are coming from. As each file in ~/database/files/*/ has a corresponding entry in the 'dataset' table. If you have such files, then something went horribly wrong, eg by using two different databases on the same files system. To double check manually compare the list of files on the file system, with the contents of the 'dataset' table. Also, have a look at the ~/database/job_working_directory/ and ~/database/tmp/ directories. You might have some old, big files there using a lot of space. Regards, Hans-Rudolf I think Brian is right - there is nothing to stop tools writing temp files under ~/database/files/*/ - the most obvious examples would be any index file named after the input dataset it is indexing (e.g. like *.bai and *.fai files normally next to a *.bam or *.fasta). Similarly file format conversions may also be generated next to the input file (although here using $TMP seems preferable). Tool/wrappers may or may not clean up this sort of thing, and in the event of a job failure, stray files are more likely to remain. So I agree, it would be good to have a script audit what Galaxy thinks is under ~/database/files/*/ tracked in its database, and what extra files have appeared. Regards, Peter ___ 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] Question concerning the xml file for local tools with multiple output files.
Hi Lifeng The easiest way to execute your script will be to provide a wrapper script (written in your preferred language, eg Python, perl, etc). Call the wrapper script like this: commandwrapper $input $output1 $output2/command and define $output1 $output2 according to your needs: format=fasta, format=txt the wrapper will call your script and rename/move the output. Hope this helps, Regards, Hans-Rudolf On Mar 25, 2014, at 3:23 AM, galaxy-user-boun...@lists.bx.psu.edu galaxy-user-boun...@lists.bx.psu.edu wrote: From: Lifeng Lin linlif...@gmail.com Date: March 25, 2014 12:58:52 AM GMT+01:00 To: galaxy-u...@lists.bx.psu.edu Subject: Question concerning the xml file for local tools with multiple output files. Hi folks, I am trying to integrate some of my local Perl scripts into a downloaded instance of Galaxy. So far the script with a simple in_file to out_file format worked great, but I am having problems understanding how to treat scripts with multiple output files that share the same input argv. for example: the script run like this in command line: script name input_name output_name_base and two files are generated from this script: output_name_base.fasta and output_name_base.txt. I am at a loss of how these parameter should be represented in the xml format, especially how the outputs data name= tag should be filled, since in the command tag, there is only one $output. Any suggestions? thanks! #GalaxyNoobie ___ 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] tool_dependencies.xml Environmental Variable Question
Michael, I've tested your tool_dependencies.xml definition locally, and verified that the JAVA_HOME variable is available within the virtualenv it sets up. In order to help narrow down the source of this issue, could you provide 5 lines before and after the following line in your paster log, when attempting to run a tool that uses this tool dependency? galaxy.tools.deps DEBUG 2014-03-25 08:52:54,953 Building dependency shell command for dependency 'wsextensions_deps' --Dave B. On 03/21/2014 01:22 PM, Michael E. Cotterell wrote: Is the expected behavior that environmental variables setup in a tool’s tool_dependencies.xml file are not available in the tool’s python virtualenv during runtime? It’s seems odd that we can specify modules (installable from pip) that are available during runtime, but that the environmental variables are not available during runtime. Thanks! Sincerely, Michael E. Cotterell Ph.D. Student in Computer Science, University of Georgia Instructor of Record, Graduate RA TA, University of Georgia Department Liaison, CS Graduate Student Association, University of Georgia mepcotter...@gmail.com (mailto:mepcotter...@gmail.com) mepc...@uga.edu (mailto:mepc...@uga.edu) m...@cs.uga.edu (mailto:m...@cs.uga.edu) http://michaelcotterell.com/ ___ 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] prims workflows
Hello Pieter, When you install a repository into Galaxy that contains workflows, you can import the workflow into Galaxy. At the time the workflow is imported, the import process checks to see if all required tools are available in Galaxy. If not, a page is displayed with links to accessible Tool Sheds allowing the user to search for missing required tools. I believe this still works, although there have been some changes to the workflow framework over the past several months, and I have not checked to see if this is still available. See https://wiki.galaxyproject.org/ToolShedWorkflowSharing for more details. This approach is basically a hack that I implemented several years ago. A much better approach would be to enhance the workflow UI to include a feature allowing the user to search Tool Sheds to discover and install missing tools required by any workflow currently abvailable in the Galaxy instance. Hopefully at some point soon something like this will be introduced. Greg Von Kuster On Mar 25, 2014, at 6:47 AM, Lukasse, Pieter pieter.luka...@wur.nl wrote: Hi Bjoern, I think you may have misunderstood me. What I mean is : instead of me having to add a tool_dependencies or repository_dependencies.xml to the workflows package, let Galaxy Tool Shed find these dependencies based on metadata available in the workflow itself. Best regards, Pieter. -Original Message- From: Björn Grüning [mailto:bjoern.gruen...@gmail.com] Sent: dinsdag 25 maart 2014 11:43 To: Lukasse, Pieter; Greg Von Kuster (g...@bx.psu.edu) Subject: Re: FW: prims workflows Hi Pieter, if I'm not misunderstood you, thats already possible: Have a look at: https://github.com/bgruening/galaxytools/tree/master/workflows/glimmer3 For an example. Cheers, Bjoern Am 25.03.2014 11:08, schrieb Lukasse, Pieter: Hi Greg, Do you have any plans of resolving the dependencies automatically when it comes to workflows? E.g. I have a Tool Shed repository where I would like to add workflows that are constructed using tools from different repositories. It would be nice if you could let Tool Shed install the tools automatically upon installation of the workflow. Any plans? Best regards, Pieter -Original Message- From: Björn Grüning [mailto:bjoern.gruen...@gmail.com] Sent: zaterdag 22 maart 2014 16:25 To: Lukasse, Pieter Subject: prims workflows Hi Pieter, thanks for your prims Galaxy contributions. Any chance to add a repository_dependencies.xml file to the workflow repository? Thanks, Bjoern ___ 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] tophat2 install
If you installe dit from the main Tool Shed, then this repository has the recipe for installing the package. http://toolshed.g2.bx.psu.edu/view/devteam/package_tophat2_2_0_9 Greg Von Kuster On Mar 25, 2014, at 9:25 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca wrote: Hi, Not sure if you saw my last email. Updating to the latest patch version doesn't seem to help. I was wondering where I could get the galaxy package version of tophat2 and put it where it needs to be manually. Then I could try the uninstall/install and see if that helps. Thanks! -Sheldon -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon Sent: Thursday, March 20, 2014 3:11 PM To: 'Greg Von Kuster' Cc: galaxy-dev@lists.bx.psu.edu Dev Subject: Re: [galaxy-dev] tophat2 install No difference. Same error -Original Message- From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Thursday, March 20, 2014 2:56 PM To: Briand, Sheldon Cc: galaxy-dev@lists.bx.psu.edu Dev Subject: Re: [galaxy-dev] tophat2 install Sorry, should have advised this: hg pull https://bitbucket.org/galaxy/galaxy-central#stable hg update stable See the end ot this thread: http://dev.list.galaxyproject.org/Persistent-jobs-in-cluster-queue-even-after-canceling-job-in-galaxy-td4663719.html On Mar 20, 2014, at 1:51 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi, you need to track galaxy-central to make use of the patches that are applied as bugfixes after the release. You can do that easily with changing the path in .hg/hgrc ... but I do not know if that is the right way to do ;) For me it worked. Cheers, Bjoern Am 20.03.2014 18:46, schrieb Briand, Sheldon: pulling from https://bitbucket.org/galaxy/galaxy-dist searching for changes no changes found From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Thursday, March 20, 2014 2:36 PM To: Briand, Sheldon Cc: 'galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] tophat2 install There have been several fixes released to the stable branch that you do not have in 12441. I would recommend doing the following: hg pull hg update stable Then uninstall the tophat2 repository and reinstall it. See if that makes a difference. On Mar 20, 2014, at 1:30 PM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.camailto:sheldon.bri...@ssc-spc.gc.ca wrote: $ hg summary parent: 12441:dc067a95261d From the tool_dependencies.xml: package name=tophat2 version=2.0.9 repository changeset_revision=8549fd545473 name=package_tophat2_2_0_9 owner=devteam prior_installation_required=False toolshed =http://toolshed.g2.bx.psu.edu; / From: Greg Von Kuster [mailto:g...@bx.psu.eduhttp://bx.psu.edu] Sent: Thursday, March 20, 2014 2:23 PM To: Briand, Sheldon Cc: 'galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] tophat2 install What version of Galaxy are you running? You want to look in the tophat2 repository directory, not its package dependency. There should be a tool_dependencies.xml file in the tophat2's installation directory hierarchy somewhere. On Mar 20, 2014, at 1:12 PM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.camailto:sheldon.bri...@ssc-spc.gc.ca wrote: Hi, dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473 contains only: env.sh If that isn't the right place to look let me know. -Sheldon From: Greg Von Kuster [mailto:g...@bx.psu.eduhttp://bx.psu.edu] Sent: Thursday, March 20, 2014 2:04 PM To: Briand, Sheldon Cc: 'galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] tophat2 install It looks like your database and file system are out of sync. Your database seems to think you have an installed repository but your file system does not seem to have the repository's installation directory. Can you confirm that this is the case? On Mar 20, 2014, at 11:53 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.camailto:sheldon.bri...@ssc-spc.gc.ca wrote: Hi, Here is the error from the paster.log: Traceback (most recent call last): File /BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py, line 496, in handle_tool_dependencies from_install_manager=from_install_manager ) File /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py, line 318, in install_package from_install_manager=from_install_manager ) File /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py, line 245, in handle_complex_repository_d ependency_for_package tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' ) File /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py,
Re: [galaxy-dev] I can't impersonate an user
It isn't in galaxy-dist (yet), but it is in the stable branch of
galaxy-central, which is safe to pull into a galaxy-dist based repository.
-Dannon
On Tue, Mar 25, 2014 at 10:13 AM, Eric Kuyt erick...@gmail.com wrote:
Hi Dannon,
could this still be existent in galaxy-dist?
Impersonate.makohttps://bitbucket.org/galaxy/galaxy-dist/src/29ce93a13ac7c4a5d2b54e5e2c10960f30a350b3/templates/admin/impersonate.mako?at=default
doesn't seem to have ${h.url_for(controller=/api/users,
action=index)} in its source and tries to find /api/user on the server
root.
Thanks,
Eric
On 17 March 2014 16:31, Dannon Baker dannon.ba...@gmail.com wrote:
694411e94d9a
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Re: [galaxy-dev] tophat2 install
Hi, Not sure if you saw my last email. Updating to the latest patch version doesn't seem to help. I was wondering where I could get the galaxy package version of tophat2 and put it where it needs to be manually. Then I could try the uninstall/install and see if that helps. Thanks! -Sheldon -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon Sent: Thursday, March 20, 2014 3:11 PM To: 'Greg Von Kuster' Cc: galaxy-dev@lists.bx.psu.edu Dev Subject: Re: [galaxy-dev] tophat2 install No difference. Same error -Original Message- From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Thursday, March 20, 2014 2:56 PM To: Briand, Sheldon Cc: galaxy-dev@lists.bx.psu.edu Dev Subject: Re: [galaxy-dev] tophat2 install Sorry, should have advised this: hg pull https://bitbucket.org/galaxy/galaxy-central#stable hg update stable See the end ot this thread: http://dev.list.galaxyproject.org/Persistent-jobs-in-cluster-queue-even-after-canceling-job-in-galaxy-td4663719.html On Mar 20, 2014, at 1:51 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi, you need to track galaxy-central to make use of the patches that are applied as bugfixes after the release. You can do that easily with changing the path in .hg/hgrc ... but I do not know if that is the right way to do ;) For me it worked. Cheers, Bjoern Am 20.03.2014 18:46, schrieb Briand, Sheldon: pulling from https://bitbucket.org/galaxy/galaxy-dist searching for changes no changes found From: Greg Von Kuster [mailto:g...@bx.psu.edu] Sent: Thursday, March 20, 2014 2:36 PM To: Briand, Sheldon Cc: 'galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] tophat2 install There have been several fixes released to the stable branch that you do not have in 12441. I would recommend doing the following: hg pull hg update stable Then uninstall the tophat2 repository and reinstall it. See if that makes a difference. On Mar 20, 2014, at 1:30 PM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.camailto:sheldon.bri...@ssc-spc.gc.ca wrote: $ hg summary parent: 12441:dc067a95261d From the tool_dependencies.xml: package name=tophat2 version=2.0.9 repository changeset_revision=8549fd545473 name=package_tophat2_2_0_9 owner=devteam prior_installation_required=False toolshed =http://toolshed.g2.bx.psu.edu; / From: Greg Von Kuster [mailto:g...@bx.psu.eduhttp://bx.psu.edu] Sent: Thursday, March 20, 2014 2:23 PM To: Briand, Sheldon Cc: 'galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] tophat2 install What version of Galaxy are you running? You want to look in the tophat2 repository directory, not its package dependency. There should be a tool_dependencies.xml file in the tophat2's installation directory hierarchy somewhere. On Mar 20, 2014, at 1:12 PM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.camailto:sheldon.bri...@ssc-spc.gc.ca wrote: Hi, dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473 contains only: env.sh If that isn't the right place to look let me know. -Sheldon From: Greg Von Kuster [mailto:g...@bx.psu.eduhttp://bx.psu.edu] Sent: Thursday, March 20, 2014 2:04 PM To: Briand, Sheldon Cc: 'galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu' Subject: Re: [galaxy-dev] tophat2 install It looks like your database and file system are out of sync. Your database seems to think you have an installed repository but your file system does not seem to have the repository's installation directory. Can you confirm that this is the case? On Mar 20, 2014, at 11:53 AM, Briand, Sheldon sheldon.bri...@ssc-spc.gc.camailto:sheldon.bri...@ssc-spc.gc.ca wrote: Hi, Here is the error from the paster.log: Traceback (most recent call last): File /BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py, line 496, in handle_tool_dependencies from_install_manager=from_install_manager ) File /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py, line 318, in install_package from_install_manager=from_install_manager ) File /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py, line 245, in handle_complex_repository_d ependency_for_package tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' ) File /BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py, line 126, in get_absolute_path_to_file_i n_repository for root, dirs, files in os.walk( repo_files_dir ): File /opt/local/python-2.7.5/lib/python2.7/os.py, line 276, in walk names = listdir(top) TypeError: coercing to Unicode: need string or buffer, NoneType found -Sheldon From:
Re: [galaxy-dev] create local galaxy in mac os
Hi, for installing tools into Galaxy please see the full guide: https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy for adding custom tools please see: https://wiki.galaxyproject.org/Admin/Tools and https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial Martin On Tue, Mar 25, 2014 at 9:51 AM, Chunjiang He camel...@gmail.com wrote: I am adding tools to local galaxy and encountered some problems. when I install samtools from Tool Shed, it stays on installing dependent tools for long time. I am not sure where is the problem. Anyone can help. Or I would like to create XML myself for downloaded packages. How to do that? Thanks, Cam ___ 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] Galaxy startup takes very long. Normal?
Dear all, I'm wondering if the following behaviour is normal. Since I reinstalled the latest galaxy distribution, every restart hangs/loads for up to 10 minutes at the following lines: galaxy.model.migrate.check INFO 2014-03-25 15:56:57,965 At database version 118 tool_shed.galaxy_install.migrate.check INFO 2014-03-25 15:56:58,477 At migrate_tools version 9 galaxy.config INFO 2014-03-25 15:56:58,694 Install database targetting Galaxy's database configuration. After several minutes of no heavy processing (cpu/database is almost idle), the startup continues. Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer ___ 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] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7
Providing some additional information will help diagnose the problem: *are you running galaxy-dist? If so, have you manually pulled and applied commits from galaxy-central? If so, which ones? *which Web browser are you using? *can you please open the JavaScript console in your browser and provide any errors that you see? Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 24, 2014, at 11:38 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi all, We have recently updated our local Galaxy installation to vrelease_2014.02.10--2--29ce93a13ac7 (database version is 118). I found that the Trackster is not working. I have checked the latest commits related to Trackster bugs. So i have updated theses files: ./static/scripts/viz/trackster.js (commits date: 2014-02-28) ./static/scripts/viz/trackster_ui.js (commits date: 2014-02-28) ./static/scripts/viz/trackster/tracks.js (commits date: 2014-03-16) ./static/scripts/utils/utils.js (commits date: 2014-03-19) ./static/scripts/utils/config.js (commits date: 2014-03-15) But, it is still not working. I have tried different format…bam, bed, sam….all are not working. I looked into all possible files I can think about that might cause the problems but still don't have any clues. I also looked into the log, and there is no error, but i noticed that there is difference from the log where the trackster was working in previous installation. The log where the trackster is not working: 1. GET /galaxy-dev/visualization/trackster?dataset_id=f04ecb1d3d259245hda_ldda=hda The log where the trackster is working (from the old installation): 1. GET /galaxy/visualization/trackster?dataset_id=5d38b380cba2f4a6hda_ldda=hda…… 2. GET /galaxy/api/datasets/5d38b380cba2f4a6?hda_ldda=hdadata_type=converted_datasets_state…. 3. GET /galaxy/api/datasets/5d38b380cba2f4a6?data_type=datachrom=chr2L….. It looks like that the trackster in new version of Galaxy does not execute the second and the third steps. Here is the screen shot when i clicked View in new visualization (there is nothing shown up---blank) Any ideas or suggestions are appreciated. Thank you very much. Best, Shu-Yi PastedGraphic-1.tiff ___ 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] read_bits64 error when loading large genomes/data into trackster
Jeremy, I uploaded my dataset to the main galaxy site and the visualization failed. Here is the link to the history: https://usegalaxy.org/u/raj-a-n/h/amborella-viz-test I used the same genome and a cufflinks gtf file instead of the bam file (Bam is too big to load). I am seeing the same problem on both main and my local galaxy instances (local is tracking latest galaxy-dist). Thanks, -Raj On Wednesday, March 05, 2014 11:25:26 AM, Raj Ayyampalayam wrote: I checked the version of bx-python egg and confirmed that it is bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg. I will upload the dataset to the public server and try it over there and report. Thanks, -Raj On Wednesday, March 05, 2014 11:21:56 AM, Jeremy Goecks wrote: Would it be possible that you have an old copy of the bx-python egg? You should have bx-python 0.7.1 If you check your eggs directory and you see version 0.7.1, then there may be something wrong with bx-python. In this case, please upload your build and bam to our public server and try again; if it fails on our public server, share the datasets with me and I'll take a look. Thanks, J. -- Jeremy Goecks Assistant Professor, Computational Biology Institute George Washington University On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam ra...@uga.edu mailto:ra...@uga.edu wrote: Hello, I am trying to visualize a large genome (Large number of scaffolds) and a large (bam file) in trackster on our local galaxy instance (running release_2014.02.10). When ever I try to do the above I see the following error in the logs: File bbi_file.pyx, line 215, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5596) File bbi_file.pyx, line 222, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5210) File bbi_file.pyx, line 183, in bx.bbi.bbi_file.BBIFile.summarize (lib/bx/bbi/bbi_file.c:4475) File bbi_file.pyx, line 248, in bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) File bpt_file.pyx, line 76, in bx.bbi.bpt_file.BPTFile.find (lib/bx/bbi/bpt_file.c:1388) File bpt_file.pyx, line 55, in bx.bbi.bpt_file.BPTFile.r_find (lib/bx/bbi/bpt_file.c:1154) AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' Trackster works OK when I load smaller data sets. It seems that there was a fix for this in bx-python code, as per mail from Jeremy (http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664p4662672.html). How do I get the fixed code into my galaxy instance? Thanks, -Raj ___ 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/
Re: [galaxy-dev] Question concerning the xml file for local tools with multiple output files.
Hi Lifeng I am glad to hear it works WRT your thoughts about using a wrapper script for each tool: I agree it might help you to standardize your tools, however it also introduces an extra step, which needs to be taken care of if you want to change/upgrade your tool. Personally, I would only use a wrapper if it is necessary or it adds some benefits for the tool. Others on the list might have a different opinion? Hans-Rudolf On Mar 25, 2014, at 3:13 PM, Lifeng Lin wrote: works like a charm. Thank you! I start to wonder if i should use this wrapper approach on all scripts regardless of the original input-output format for standardized integration, and possible automated integrations in the future. On Tue, Mar 25, 2014 at 6:53 AM, Hans-Rudolf Hotz hansrudolf.h...@fmi.ch wrote: Hi Lifeng The easiest way to execute your script will be to provide a wrapper script (written in your preferred language, eg Python, perl, etc). Call the wrapper script like this: commandwrapper $input $output1 $output2/command and define $output1 $output2 according to your needs: format=fasta, format=txt the wrapper will call your script and rename/move the output. Hope this helps, Regards, Hans-Rudolf On Mar 25, 2014, at 3:23 AM, galaxy-user-boun...@lists.bx.psu.edu galaxy-user-boun...@lists.bx.psu.edu wrote: From: Lifeng Lin linlif...@gmail.com Date: March 25, 2014 12:58:52 AM GMT+01:00 To: galaxy-u...@lists.bx.psu.edu Subject: Question concerning the xml file for local tools with multiple output files. Hi folks, I am trying to integrate some of my local Perl scripts into a downloaded instance of Galaxy. So far the script with a simple in_file to out_file format worked great, but I am having problems understanding how to treat scripts with multiple output files that share the same input argv. for example: the script run like this in command line: script name input_name output_name_base and two files are generated from this script: output_name_base.fasta and output_name_base.txt. I am at a loss of how these parameter should be represented in the xml format, especially how the outputs data name= tag should be filled, since in the command tag, there is only one $output. Any suggestions? thanks! #GalaxyNoobie ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Strange issue with datatypes in Galaxy version of last week
Hi,
Apparently a new datatypes bug has been introduced in the Galaxy version of
last week:
I have a tool that generates a csv file. Tool configuration is like this:
outputs
data name=simOut format=msclust.csv label=${tool.name} on ${on_string}
- SIM file/
The datatypes has this entry:
datatype extension=msclust.csv type=galaxy.datatypes.tabular:Tabular
mimetype=text/csv display_in_upload=true subclass=true/
At first Galaxy output seems fine:
[cid:image001.png@01CF4847.DE4A1A70]
But when I download the file, the downloaded file name will be :
Galaxy40-[MsClust_on_data_1_-_SIM_file]-
When I go to edit attributes and just click save, then upon downloading
again, the file name is correct...
Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv .
Anyone faced this issue?
Thanks and regards,
Pieter.
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317481122; skype: pieter.lukasse.wur
http://www.pri.wur.nlhttp://www.pri.wur.nl/
inline: image001.png___
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Re: [galaxy-dev] apache setting
On Monday, March 24, 2014, Jun Fan j@qmul.ac.uk wrote: RewriteEngine on RewriteRule ^(.*) http://localhost:8080$1 [P] I tried to add them to 1) the main conf file: apache2.conf, 2) newly generated httpd.conf by myself under /etc/apache2 folder and 3) newly generated .htaccess file under /etc/apache2/conf.d folder, and none of them gave me the luck. This thread might help you: http://dev.list.galaxyproject.org/Running-Galaxy-behind-apache2-td4624545.html --Carlos ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Strange issue with datatypes in Galaxy version of last week
Pieter,
I just experienced the same with another generic tabular .tab file output. It
broke the filename at dash without any extension.
The file itself was ok, just the name.
Alex
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Lukasse, Pieter
Verzonden: dinsdag 25 maart 2014 16:33
Aan: galaxy-dev@lists.bx.psu.edu
Onderwerp: [galaxy-dev] Strange issue with datatypes in Galaxy version of last
week
Hi,
Apparently a new datatypes bug has been introduced in the Galaxy version of
last week:
I have a tool that generates a csv file. Tool configuration is like this:
outputs
data name=simOut format=msclust.csv label=${tool.name} on ${on_string}
- SIM file/
The datatypes has this entry:
datatype extension=msclust.csv type=galaxy.datatypes.tabular:Tabular
mimetype=text/csv display_in_upload=true subclass=true/
At first Galaxy output seems fine:
[cid:image001.png@01CF484A.88C64A30]
But when I download the file, the downloaded file name will be :
Galaxy40-[MsClust_on_data_1_-_SIM_file]-
When I go to edit attributes and just click save, then upon downloading
again, the file name is correct...
Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv .
Anyone faced this issue?
Thanks and regards,
Pieter.
Pieter Lukasse
Wageningen UR, Plant Research International
Departments of Bioscience and Bioinformatics
Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands
+31-317481122; skype: pieter.lukasse.wur
http://www.pri.wur.nlhttp://www.pri.wur.nl/
inline: image001.png___
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and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] I can't impersonate an user
Hi Dannon,
could this still be existent in galaxy-dist?
Impersonate.makohttps://bitbucket.org/galaxy/galaxy-dist/src/29ce93a13ac7c4a5d2b54e5e2c10960f30a350b3/templates/admin/impersonate.mako?at=default
doesn't seem to have ${h.url_for(controller=/api/users, action=index)} in
its source and tries to find /api/user on the server root.
Thanks,
Eric
On 17 March 2014 16:31, Dannon Baker dannon.ba...@gmail.com wrote:
694411e94d9a
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Re: [galaxy-dev] Question concerning the xml file for local tools with multiple output files.
works like a charm. Thank you! I start to wonder if i should use this wrapper approach on all scripts regardless of the original input-output format for standardized integration, and possible automated integrations in the future. On Tue, Mar 25, 2014 at 6:53 AM, Hans-Rudolf Hotz hansrudolf.h...@fmi.chwrote: Hi Lifeng The easiest way to execute your script will be to provide a wrapper script (written in your preferred language, eg Python, perl, etc). Call the wrapper script like this: commandwrapper $input $output1 $output2/command and define $output1 $output2 according to your needs: format=fasta, format=txt the wrapper will call your script and rename/move the output. Hope this helps, Regards, Hans-Rudolf On Mar 25, 2014, at 3:23 AM, galaxy-user-boun...@lists.bx.psu.edu galaxy-user-boun...@lists.bx.psu.edu wrote: From: Lifeng Lin linlif...@gmail.com Date: March 25, 2014 12:58:52 AM GMT+01:00 To: galaxy-u...@lists.bx.psu.edu Subject: Question concerning the xml file for local tools with multiple output files. Hi folks, I am trying to integrate some of my local Perl scripts into a downloaded instance of Galaxy. So far the script with a simple in_file to out_file format worked great, but I am having problems understanding how to treat scripts with multiple output files that share the same input argv. for example: the script run like this in command line: script name input_name output_name_base and two files are generated from this script: output_name_base.fasta and output_name_base.txt. I am at a loss of how these parameter should be represented in the xml format, especially how the outputs data name= tag should be filled, since in the command tag, there is only one $output. Any suggestions? thanks! #GalaxyNoobie ___ 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] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7
Hi Jeremy, Thank you very much for the reply. Yes, we are running on galaxy-dist, and manually pulled to update our installation. The release version is vrelease_2014.02.10--2--29ce93a13ac7. I have tried safari and firefox. Both are not working. Here is the error massage from console: [Error] Failed to load resource: the server responded with a status of 404 (Not Found) (backbone-relational.js, line 0) [Error] Failed to load resource: the server responded with a status of 404 (Not Found) (galaxy.utils.js, line 0) [Error] Error: Script error for: libs/backbone/backbone-relational http://requirejs.org/docs/errors.html#scripterror defaultOnError (require.js, line 1) onError (require.js, line 1) onScriptError (require.js, line 1) [Error] Error: Script error for: utils/galaxy.utils http://requirejs.org/docs/errors.html#scripterror defaultOnError (require.js, line 1) onError (require.js, line 1) onScriptError (require.js, line 1);;; We are also wondering if there is anything we didn't set up probably for our universe_wsgi.ini file. Thank you. Best, Shu-Yi On Mar 25, 2014, at 4:05 PM, Jeremy Goecks wrote: Providing some additional information will help diagnose the problem: *are you running galaxy-dist? If so, have you manually pulled and applied commits from galaxy-central? If so, which ones? *which Web browser are you using? *can you please open the JavaScript console in your browser and provide any errors that you see? Thanks, J. -- Jeremy Goecks Assistant Professor of Computational Biology George Washington University On Mar 24, 2014, at 11:38 AM, Shu-Yi Su shu-yi...@embl.de wrote: Hi all, We have recently updated our local Galaxy installation to vrelease_2014.02.10--2--29ce93a13ac7 (database version is 118). I found that the Trackster is not working. I have checked the latest commits related to Trackster bugs. So i have updated theses files: ./static/scripts/viz/trackster.js (commits date: 2014-02-28) ./static/scripts/viz/trackster_ui.js (commits date: 2014-02-28) ./static/scripts/viz/trackster/tracks.js (commits date: 2014-03-16) ./static/scripts/utils/utils.js (commits date: 2014-03-19) ./static/scripts/utils/config.js (commits date: 2014-03-15) But, it is still not working. I have tried different format…bam, bed, sam….all are not working. I looked into all possible files I can think about that might cause the problems but still don't have any clues. I also looked into the log, and there is no error, but i noticed that there is difference from the log where the trackster was working in previous installation. The log where the trackster is not working: 1. GET /galaxy-dev/visualization/trackster?dataset_id=f04ecb1d3d259245hda_ldda=hda The log where the trackster is working (from the old installation): 1. GET /galaxy/visualization/trackster?dataset_id=5d38b380cba2f4a6hda_ldda=hda…… 2. GET /galaxy/api/datasets/5d38b380cba2f4a6?hda_ldda=hdadata_type=converted_datasets_state…. 3. GET /galaxy/api/datasets/5d38b380cba2f4a6?data_type=datachrom=chr2L….. It looks like that the trackster in new version of Galaxy does not execute the second and the third steps. Here is the screen shot when i clicked View in new visualization (there is nothing shown up---blank) Any ideas or suggestions are appreciated. Thank you very much. Best, Shu-Yi PastedGraphic-1.tiff ___ 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] Errors loading data into IGV from Galaxy
Dear Galaxy Team, I have already contacted IgV about this issue and they say that I needed to contact you. I have had and instance of IgV shared with me for some time and it has worked as recently as last week. However, even last week the data was only loading approximately 25% of the time and now will not load at all. Could you please explain the error that I am getting below and what can be done to correct them. Unfortunately the individual who created and shared these files is no longer in the lab so I do not have direct access to the data. Any help would be greatly appreciated. Sincerely, -Paul Hillman- Errors were encountered loading the session: https://main.g2.bx.psu.edu/display_application/b35f82886ba2954e/igv_bam/web_link_main/99234cff5c86008d/data/galaxy_b35f82886ba2954e.bam nbs;p org.broad.igv.exceptions.DataLoadException: HTTP access error (status code 500) https://main.g2.bx.psu.edu/display_application/70deaaa1fc17635d/igv_bam/web_link_main/39ca6e346e73f08a/data/galaxy_70deaaa1fc17635d.bam nbs;p org.broad.igv.exceptions.DataLoadException: HTTP access error (status code 500) ___ 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 startup takes very long. Normal?
Hello Geert, Do you have a lot of repositories installed from the Tool Shed into you Galaxy instance? if so, the time you're experience may be due to loading the in-memory installed repository registry. Using this registry is optional, but the default configuration setting is to use it. You can set the following to entry to False in your universe_wsgi.ini file and restart your Galaxy server to see if that is the problem. This registry is not currently used by anythin except to display the set of dependent repositories that will be affected if a repository is uninstalled. If this is ot what is causing the slow statup, then I'm not sure where else to look. # Enable use of an in-memory registry with bi-directional relationships # between repositories (i.e., in addition to lists of dependencies for a # repository, keep an in-memory registry of dependent items for each repository. #manage_dependency_relationships = True Greg Von Kuster On Mar 25, 2014, at 11:08 AM, Geert Vandeweyer geert.vandewey...@uantwerpen.be wrote: Dear all, I'm wondering if the following behaviour is normal. Since I reinstalled the latest galaxy distribution, every restart hangs/loads for up to 10 minutes at the following lines: galaxy.model.migrate.check INFO 2014-03-25 15:56:57,965 At database version 118 tool_shed.galaxy_install.migrate.check INFO 2014-03-25 15:56:58,477 At migrate_tools version 9 galaxy.config INFO 2014-03-25 15:56:58,694 Install database targetting Galaxy's database configuration. After several minutes of no heavy processing (cpu/database is almost idle), the startup continues. Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer ___ 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] GCC2014 Early Registration and Abstract Submission are now OPEN!
Hello all, This is just a reminder that *abstract submission for oral presentations at GCC2014 closes April 4*, ten days from now. This is a great opportunity to present your work. See https://wiki.galaxyproject.org/Events/GCC2014/Abstracts for details and how to submit. Thanks, Dave C On Fri, Feb 14, 2014 at 1:33 PM, Dave Clements cleme...@galaxyproject.orgwrote: Hello all, *We are pleased to announce that Early Registration https://wiki.galaxyproject.org/Events/GCC2014/Register and Talk and Poster Abstract Submission https://wiki.galaxyproject.org/Events/GCC2014/Abstracts are now open for the 2014 Galaxy Community Conference (GCC2014) https://wiki.galaxyproject.org/Events/GCC2014.* GCC2014 https://wiki.galaxyproject.org/Events/GCC2014 will be held at the Homewood Campushttp://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/of Johns Hopkins University http://jhu.edu, in Baltimore, Marylandhttp://visitors.baltimorecity.gov/, United States, from June 30 through July 2, 2014. GCC2014https://wiki.galaxyproject.org/Events/GCC2014starts with a Training Day https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay featuring four *five* parallel tracks, each with three, two and half hour long workshops. There are 13 different topics spanning the full Galactic spectrum of topics. Take a look!https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay *Early registration https://wiki.galaxyproject.org/Events/GCC2014/Register* is now open. Register early and *avoid paying 70% more for regular registration costs.* Early registration is very affordable, with combined registration (Training Day https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay + main meeting) starting at $140 for post-docs and students. Registration is capped this year at 250 participants, *and we expect to hit that limit*. Registering early assures you a place at the conference and also a spot in the Training Day workshops you want to attend. You can also book affordable conference housing at the same time you register. See the conference Logistics pagehttps://wiki.galaxyproject.org/Events/GCC2014/Logisticsfor details on this and other housing options. *Abstract submission https://wiki.galaxyproject.org/Events/GCC2014/Abstracts* for both oral presentations and posters is also open. Abstract submission for oral presentations closes April 4, while poster submission closes April 25. Poster authors will be notified of acceptance status within two weeks of submission, while presentation authors will be notified no later than May2. *Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.* The *GigaScience http://www.gigasciencejournal.com/* Galaxy: Data Intensive and Reproducible Research series announced for the last conference has published its first papershttp://www.gigasciencejournal.com/series/Galaxy, *and is continuing to take submissions for this year's meeting and beyond*. BGI is also continuing to cover the article processing charges until the end of the year, and for more information see their latest updatehttp://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibility-first-papers-in-our-galaxy-series-utilizing-our-gigagalaxy-platform/. Thanks, and hope to see you in Baltimore! The GCC2014 Organizing Committeehttps://wiki.galaxyproject.org/Events/GCC2014/Organizers -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Dealing with qiime output
Hello galaxy devs, I installed qiime-galaxy to my local galaxy (running jobs on a cluster). The split_libraries.py tool outputs a dir of files. How do I go about displaying these files in the history panel after the tool finishes running? I have been trying to look at the composite datatypes guide, but I really am having a hard time wrapping my head around it. Should I be creating a new composite datatype for any tool that outputs directories (each with diff files to display). Is there anyway to have galaxy automatically unzip output directories to history? Thanks Ravi ___ 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] Recovery of lost DRMAA job?
We're having a slight issue with some of the jobs our Galaxy instance is submitting to the cluster via the DRMAA runner. Our cluster admin thinks it's not Galaxy's fault, but the problem results in some odd behavior in Galaxy, as follows. From galaxy.log: galaxy.jobs.runners.drmaa INFO 2014-03-25 12:17:46,950 (1667/5806401) job left DRM queue with following message: code 1: slurm_load_jobs error: Socket timed out on send/recv operation,job_id: 5806401 galaxy.jobs.runners ERROR 2014-03-25 12:17:50,272 (1667/5806401) Job output not returned from cluster: [Errno 2] No such file or directory: '/galaxy/database/job_working_directory/001/ 1667/galaxy_1667.o' galaxy.jobs.output_checker INFO 2014-03-25 12:17:50,379 Job 1667: Log: tool progress galaxy.jobs.output_checker INFO 2014-03-25 12:17:50,379 Job 1667: Log: tool progress galaxy.jobs DEBUG 2014-03-25 12:17:51,123 job 1667 ended 1. As best we can tell, for some reason the socket Galaxy's using to keep track of the job times out (this is the part we don't think is Galaxy's fault). The job continues to run on the cluster, but: 2. When the socket times out, Galaxy checks to see if the redirected stdout file exists, but since the job's still running, it doesn't exist, and so it throws an error... 3. ... and eventually Galaxy just gives up on the job entirely. This seems strange, considering Galaxy so gracefully recovers jobs when it's restarted; I admit I'm not familiar with the mechanics of tracking a job, but would a few retries spaced out over a few minutes be appropriate here, if that's possible? Failing that, is there a way to manually recover it, or could such a way be added? This job will probably run for days, and it would be nice not to have to manually collect the outputs and send them back to the user! What ends up happening in the Galaxy interface is that the history items turn green as if they completed successfully, but of course they're completely empty, which was a bit of a confusing thing for the user that was having this problem. Thanks! -- Brian Claywell, Systems Analyst/Programmer Fred Hutchinson Cancer Research Center bclay...@fhcrc.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] [CONTENT] Re: Re: Unable to remove old datasets
I have now been able to successfully remove datasets from disk. After deleting the dataset or history from the front-end interface (as the user), I then run the cleanup scripts as admin: python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 0 -1 $@ ./scripts/cleanup_datasets/delete_userless_histories.log python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 0 -2 -r $@ ./scripts/cleanup_datasets/purge_histories.log python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 0 -3 -r $@ ./scripts/cleanup_datasets/purge_datasets.log python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 0 -5 -r $@ ./scripts/cleanup_datasets/purge_folders.log python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 0 -4 -r $@ ./scripts/cleanup_datasets/purge_libraries.log python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 0 -6 -r $@ ./scripts/cleanup_datasets/delete_datasets.log However, my final goal is to have a process that can remove old datasets from disk regardless of whether or not the users have deleted them at the front-end (and then automate said process via cronjob). This will be essentially in a situation where users are likely to leave datasets unattended and accumulating disk space. I found the following Galaxy thread: http://dev.list.galaxyproject.org/Re-Improving-Administrative-Data-Clean-Up-pgcleanup-py-vs-cleanup-datasets-py-td4659330.html And am trying to use the script it mentions: python ./scripts/cleanup_datasets/admin_cleanup_datasets.py universe_wsgi.ini -d 30 --smtp smtp server --fromaddr rsa...@jcvi.org I chose –d 30 to remove all datasets older than 30 days, which currently only targets one dataset. The resulting stdout indicates success: # 2014-03-25 16:27:47 - Handling stuff older than 30 days Marked HistoryDatasetAssociation id 301 as deleted From: rsa...@jcvi.org To: isi...@jcvi.org Subject: Galaxy Server Cleanup - 1 datasets DELETED -- Galaxy Server Cleanup - The following datasets you own on Galaxy are older than 30 days and have been DELETED: Small.fastq in history Unnamed history You may be able to undelete them by logging into Galaxy, navigating to the appropriate history, selecting Include Deleted Datasets from the history options menu, and clicking on the link to undelete each dataset that you want to keep. You can then download the datasets. Thank you for your understanding and cooporation in this necessary cleanup in order to keep the Galaxy resource available. Please don't hesitate to contact us if you have any questions. -- Galaxy Administrators Marked 1 dataset instances as deleted But when I check the database, the status of dataset 301 is unchanged (ok-false-false-true). I then run the same cleanup_datasets.py routine from above (but with –d 30), but dataset 301 is still present. I tried a second time, this time using –d 0, but still no deletion (which is not surprising since the dataset's deleted status is still false). If I run admin_cleanup_datasets.py again with the same parameters, the stdout says no datasets matched the criteria, so it seems to remember it's previous execution, but it's NOT actually updating the database. What am I doing wrong? -- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 -- From: Carl Eberhard carlfeberh...@gmail.commailto:carlfeberh...@gmail.com Date: Tuesday, March 18, 2014 2:09 PM To: Peter Cock p.j.a.c...@googlemail.commailto:p.j.a.c...@googlemail.com Cc: Ravi Sanka rsa...@jcvi.orgmailto:rsa...@jcvi.org, galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: [CONTENT] Re: [galaxy-dev] Re: Unable to remove old datasets The cleanup scripts enforce a sort of lifetime for the datasets. The first time they're run, they may mark a dataset as deleted and also reset the update time and you'll have to wait N days for the next stage of the lifetime. The next time they're run, or if a dataset has already been marked as deleted, the actual file removal happens and purged is set to true (if it wasn't already). You can manually pass in '-d 0' to force removal of datasets recently marked as deleted. The purge scripts do not check 'allow_user_dataset_purge', of course. On Tue, Mar 18, 2014 at 11:50 AM, Carl Eberhard carlfeberh...@gmail.commailto:carlfeberh...@gmail.com wrote: I believe it's a (BAD) silent failure mode in the server code. If I understand correctly, the purge request isn't coughing an error when it gets to the 'allow_user_dataset_purge' check and instead is silently marking (or re-marking) the datasets as deleted. I would rather it fail with a 403 error if purge is explicitly requested. That said, it of course would
