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symlink to june_2007_style
by Robert Baertsch 17 Apr '13

17 Apr '13

When merging in the latest galaxy-central, I'm getting this error: merging lib/galaxy/webapps/galaxy/controllers/library_common.py merging lib/galaxy/webapps/galaxy/controllers/page.py merging lib/galaxy/webapps/galaxy/controllers/user.py merging run.sh merging scripts/manage_db.py abort: could not symlink to 'style': File exists: /Users/robertbaertsch/src/medbook-merge/medbook-galaxy-central/static/june_2007_style Should I do the following: $ mv june_2007_style style $ ln -s style june_2007_style and then $ hg merge

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snpEff on Galaxy
by Rob Leclerc 17 Apr '13

17 Apr '13

Does anyone have any experience running snpEff on Galaxy? We installed snpEff from the toolshed and now have the latest changeset (c052639fa666). We modified the config files to correct the pathnames but now we're running into a series of errors when we try to run '*Compute SNP effect*' with a file using the hg19 dataset *The first error was:* java.lang.RuntimeException: Property: 'hg37.genome' not found at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:78) at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:334) at ca.mcgill.mcb.pcingola.snpEffect.Config.read(Config.java:301) at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:67) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:582) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:261) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:77 This first error was confusing because the input file was for hg19, so it's not clear why there was a reference to hg37. Next, we then edited snpEff.config and added the line *hg37.genome : Homo_sapiens* * * with the other hg37.XX : Homo_sapiens keypairs. *This led to the second error:* ERROR: Cannot read file '/home/galaxy//snpEff/data//hg37/snpEffectPredictor.bin'. You can try to download the database by running the following command: java -jar snpEff.jar download hg37 java.lang.RuntimeException: java.io.FileNotFoundException: /home/galaxy/snpEff/data/hg37/snpEffectPredictor.bin (No such file or directory) at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:58) at ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:240) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:595) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:261) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:77) Caused by: java.io.FileNotFoundException: /home/galaxy/snpEff/data/hg37/snpEffectPredictor.bin (No such file or directory) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.<init>(FileInputStream.java:137) at java.io.FileInputStream.<init>(FileInputStream.java:96) at ca.mcgill.mcb.pcingola.util.Gpr.readFileSerializedGzThrow(Gpr.java:468) at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:55) ... 4 more The problem now is that is is looking for the hg37 directory, which doesn't exist but GRCh37.65 does exist. So we then change the directory name to hg37 and reran, resulting in the third error: VcfFileIterator.parseVcfLine(276): Fatal error reading file '/mnt/galaxyData/files/000/dataset_432.dat' (line: 1): 1 2338204 2338204 G/T + java.lang.RuntimeException: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '+' at ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:277) at ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:331) at ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.readNext(VcfFileIterator.java:1) at ca.mcgill.mcb.pcingola.fileIterator.FileIterator.hasNext(FileIterator.java:69) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.iterateVcf(SnpEffCmdEff.java:215) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.runAnalysis(SnpEffCmdEff.java:698) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:648) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:261) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:77) Caused by: java.lang.RuntimeException: WARNING: Unkown IUB code for SNP '+' at ca.mcgill.mcb.pcingola.vcf.VcfEntry.parseAlts(VcfEntry.java:530) at ca.mcgill.mcb.pcingola.vcf.VcfEntry.parse(VcfEntry.java:445) at ca.mcgill.mcb.pcingola.vcf.VcfEntry.<init>(VcfEntry.java:66) at ca.mcgill.mcb.pcingola.fileIterator.VcfFileIterator.parseVcfLine(VcfFileIterator.java:274) ... 8 more I'm going to assume that this is all related to the first issue, but I'm not sure how to fix the issue. Cheers! Rob Rob Leclerc, PhD <http://www.linkedin.com/in/robleclerc> <https://twitter.com/#!/robleclerc> P: (US) +1-(917)-873-3037 P: (Shanghai) +86-1-(861)-612-5469 Personal Email: rob.leclerc(a)aya.yale.edu

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Re: [galaxy-dev] Improving Administrative Data Clean Up (pgcleanup.py vs cleanup_datasets.py)
by Lance Parsons 17 Apr '13

17 Apr '13

I have implemented a basic script to perform administrative dataset deletion and email notification. Right now it's limited to the history_dataset_assocation update_time and an optional tool_id string. I have pushed it to a galaxy-central fork and will issue a pull request once I've tested it a bit more. I'm open to comments or suggestions, it could certainly be extended. Hopefully people find this useful. See https://bitbucket.org/lance_parsons/galaxy-central-dataset-cleanup/commits/… admin_dataset_cleanup.py Documentation --------------------------------------------------------- Mark datasets as deleted that are older than specified cutoff and (optionaly) with a tool_id that matches the specified search string. This script is useful for administrators to cleanup after users who leave many old datasets around. It was modeled after the cleanup_datasets.py script originally distributed with Galaxy. Basic Usage: admin_cleanup_datasets.py universe_wsgi.ini -d 60 \ --template=email_template.txt Required Arguments: config_file - the Galaxy configuration file (universe_wsgi.ini) Optional Arguments: -d --days - number of days old the dataset must be (default: 60) --tool_id - string to search for in dataset tool_id --template - Mako template file to use for email notification -i --info_only - Print results, but don't email or delete anything -e --email_only - Email notifications, but don't delete anything Useful for notifying users of pending deletion --smtp - Specify smtp server If not specified, use smtp settings specified in config file --fromaddr - Specify from address If not specified, use error_email_to specified in config file Email Template Variables: cutoff - the cutoff in days email - the users email address datasets - a list of tuples containing 'dataset' and 'history' names xiandongmeng(a)lbl.gov wrote: > Hi Lance, > > I have same questions as yours about cleanup data in Galaxy. > > We maintain a local instance of the Galaxy system. I am thinking a way to delete datasets which are not accessed/updated for a certain period of time, no matter if users deleted them. In addition, sending an email to users before deleting their dataset. It looks like the current scripts for clean up only purges deleted histories/datasets. I was trying to find a way to use API functions to delete old files which are not deleted, but am not successful. I found the update_time is not access time in the dataset table. A reference file may be used frequently but the update_time is pretty old. This would be a problem if deleting file by the update_time. I think files should be deleted by the access time. Is it enough to resolve this problem by checking the update_time of the HistoryDatasetAssociation table? > > Thanks for your help, > > X. Meng > Joint Genome Institute, LBNL > > <quote author='Lance Parsons'> > Nate Coraor wrote: >> On Mar 22, 2013, at 11:56 AM, Lance Parsons wrote: >> >>> I have been running a Galaxy server for our sequencing researchers for a >>> while now and it's become increasingly successful. The biggest resource >>> challenge for us has been, and continues to be disk space. As such, I'd >>> like to implement some additional cleanup scripts. I thought I run a few >>> questions by this list before I got too far into things. >>> >>> In general, I'm wondering how to implement updates/additions to the >>> cleanup system that will be in line with the direction that the Galaxy >>> project is headed. The pgcleanup.py script is the newest piece of code >>> in this area (and even adds cleanup of exported histories, which are >>> absent from the older cleanup scripts). Also, the pgcleanup.py script >>> uses a "cleanup_event" table that I don't believe is used by the older >>> cleanup_datasets.py script. However, the new pgcleanup.py script only >>> works for Postgres, and worse, only for version 9.1+. I run my system on >>> RedHat (CentOS) and thus we use version 8.4 of Postgres. Are there plans >>> to support other databases or older versions of Postgres? >> Hi Lance, >> >> pgcleanup.py makes extensive use of Writable CTEs, so there is not really >> a way to port it to older versions. For 8.4 or MySQL, you can still use >> the older cleanup_datasets.py. > After looking at it a bit more, I see what you mean. Are there plans to > implement and additional cleanup scripts for non-postgres 9.1 users? > Just curious so I don't reinvent the wheel, I'd be happy to help with > existing efforts. >>> I'd like to implement a script to delete (set the deleted flag) for >>> certain datasets (e.g. raw data imported from our archive, for old, >>> inactive users, etc.). I'm wondering if it would make sense to try and >>> extend pgcleanup.py or cleanup_datasets.py. Or perhaps it would be best >>> to just implement a separate script, though that seems like I'd have to >>> re-implement a lot of boilerplate code for configuration reading, >>> connections, logging, etc. Any tips on generally acceptable (supported) >>> procedures for marking a dataset as deleted? >> You could probably reuse a lot of the code from either of the cleanup >> scripts for this. > Right. It seems to make sense to me to focus on the cleanup_datasets.py > since that will work for everyone. I would like to essentially mimic > the user deleting a dataset. I'd then email them to let them know that > some old data had been marked for deletion and let the rest of the > scripts proceed as normal, cleaning that up if they don't undelete it. > > It looks like I would want to mark the HistoryDatasetAssociations as > deleted? Is that correct? Would I need to do anything else to simulate > the user deleting the dataset? > > Thanks for the help, > Lance >> Thanks, >> --nate >> > -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Fwd: [Gmod-announce] 2013 GMOD Summer School: Apply now!
by Dave Clements 17 Apr '13

17 Apr '13

Hello all, The 2013 GMOD Summer School is now accepting applications. Galaxy will again be included in the topics covered. And Amelia says: Applications are competitive, so we encourage you to apply well before the > deadline, June 10th. So, if you are interested, act soon. Dave C ---------- Forwarded message ---------- From: Amelia Ireland <amelia.ireland(a)gmod.org> Date: Wed, Apr 17, 2013 at 11:15 AM Subject: [Gmod-announce] 2013 GMOD Summer School: Apply now! To: gmod-announce <gmod-announce(a)lists.sourceforge.net>, gmod-devel(a)lists.sourceforge.net We are now accepting applications for the 2013 GMOD Summer School, to be held NESCent, Durham, North Carolina from July 19th to 23rd. The GMOD Summer School is the best way to learn how to install, configure, and use popular GMOD tools, including GBrowse, JBrowse, Galaxy, MAKER, Tripal, WebApollo, and Chado; courses are taught by the tool developers, and there will be evening sessions for those who want to work on their own data or troubleshoot issues with the developers. More information and online application form: http://gmod.org/wiki/2013_GMOD_Summer_School Applications are competitive, so we encourage you to apply well before the deadline, June 10th. If you have any questions, please contact help(a)gmod.org and we will be happy to answer them. -- Amelia Ireland GMOD Community Support http://gmod.org || @gmodproject ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ Gmod-announce mailing list Gmod-announce(a)lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/gmod-announce -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Reports Web Application fails to start (unable to import TracksterConfig)
by Lance Parsons 17 Apr '13

17 Apr '13

After upgrading to the latest distribution release (4.1.2013) I can no longer start the reports web application. The reports-webapp.log shows the following exception. I've created a bug report on Trello for reference: https://trello.com/c/o0S3klAF Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/lib/galaxy/util/pastescript/serve.py", line 1056, in run invoke(command, command_name, options, args[1:]) File "/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/lib/galaxy/util/pastescript/serve.py", line 1062, in invoke exit_code = runner.run(args) File "/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/lib/galaxy/util/pastescript/serve.py", line 227, in run result = self.command() File "/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/lib/galaxy/util/pastescript/serve.py", line 650, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/lib/galaxy/util/pastescript/loadwsgi.py", line 375, in loadobj return context.create() File "/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/lib/galaxy/util/pastescript/loadwsgi.py", line 813, in create return self.object_type.invoke(self) File "/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/lib/galaxy/util/pastescript/loadwsgi.py", line 249, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call val = callable(*args, **kw) File "/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/lib/galaxy/webapps/reports/buildapp.py", line 61, in app_factory add_ui_controllers( webapp, app ) File "/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/lib/galaxy/webapps/reports/buildapp.py", line 33, in add_ui_controllers from galaxy.web.base.controller import BaseUIController File "/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/lib/galaxy/web/base/controller.py", line 23, in <module> from galaxy.visualization.genome.visual_analytics import get_tool_def File "/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/lib/galaxy/visualization/genome/visual_analytics.py", line 3, in <module> from galaxy.tools.parameters.basic import IntegerToolParameter, FloatToolParameter, SelectToolParameter File "/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/lib/galaxy/tools/__init__.py", line 57, in <module> from galaxy.visualization.genome.visual_analytics import TracksterConfig ImportError: cannot import name TracksterConfig Removing PID file reports_webapp.pid -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Bug report and patch for <version_command> whitespace
by Peter Cock 17 Apr '13

17 Apr '13

Hello all, I recently tried adding a <version_command> tag as follows, <version_command interpreter="python"> blastxml_to_top_descr.py --version </version_command> This kind of white space is tolerated in the <version> tag, so should work here too I think. However, it resulting the Galaxy attempting to run 'python' (which stalled as there was no user input), and then 'blastxml_to_top_descr.py --version'. The following simple change fixes this bug. In the meantime, I have used the workaround to removing the white space in the XML file: <version_command interpreter="python">blastxml_to_top_descr.py --version</version_command> Could someone please test this and commit it to the trunk, Regards, Peter -- $ hg diff diff -r 94e890fea3a4 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed Apr 17 15:03:12 2013 +0100 +++ b/lib/galaxy/tools/__init__.py Wed Apr 17 15:45:53 2013 +0100 @@ -1094,7 +1094,7 @@ self.version_string_cmd = None version_cmd = root.find("version_command") if version_cmd is not None: - self.version_string_cmd = version_cmd.text + self.version_string_cmd = version_cmd.text.strip() version_cmd_interpreter = version_cmd.get( "interpreter", None ) if version_cmd_interpreter: executable = self.version_string_cmd.split()[0]

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Unable to finish job
by Ramon Tiburski 17 Apr '13

17 Apr '13

I,m getting this error when I try to convert some data, can someone help me? Traceback (most recent call last): File "/home/ramao/galaxy/lib/galaxy/jobs/runners/local.py", line 156, in run_job job_wrapper.finish( stdout, stderr, exit_code ) File "/home/ramao/galaxy/lib/galaxy/jobs/__init__.py", line 412, in finish dataset.datatype.set_meta( dataset, overwrite = False ) #call datatype.set_meta directly for the initial set_meta call during dataset creation File "/home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/earthsystem.py", line 318, in set_meta NetCDF.set_meta(self,dataset) File "/home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/earthsystem.py", line 261, in set_meta ncml= execAndGetStdout("ncdump -x "+dataset.file_name) File "/home/ramao/shed_tools/web.uniparthenope.it/repos/montella/galaxy_es_core/a8f8a904173c/galaxy_es_core/earthsystem.py", line 48, in execAndGetStdout output=local(cmd, capture=True) File "/home/ramao/galaxy/eggs/Fabric-1.4.2-py2.7.egg/fabric/operations.py", line 1012, in local error(message=msg, stdout=out, stderr=err) File "/home/ramao/galaxy/eggs/Fabric-1.4.2-py2.7.egg/fabric/utils.py", line 305, in error return func(message) File "/home/ramao/galaxy/eggs/Fabric-1.4.2-py2.7.egg/fabric/utils.py", line 26, in abort sys.exit(1) SystemExit: 1

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Re: [galaxy-dev] [galaxy-user] Put an apache password on galaxy?
by Nate Coraor 17 Apr '13

17 Apr '13

On Apr 16, 2013, at 4:30 PM, Lee Katz wrote: > Thanks Jen. I tried a few more things before posting to galaxy-dev, and it turns out that I had the default virtual host still running, while I tried to have a galaxy virtualhost running alongside it. I think it should be possible to do that still, but it simplified and corrected it when I removed the default virtual host from apache/sites-enabled > > I have a second question now. Where would I put the .htaccess file for it to be read correctly? I tried this line in my new virtualhost file, but no password prompt appears > > AccessFileName /home/galaxy/bin/galaxy-dist/static/.htaccess > > More info: > All directories are chmod 775 for user galaxy starting with /home/galaxy/ > > $ cat static/.htaccess > AuthType Basic > AuthName "Yay Bioinformatics" > AuthUserFile /home/galaxy/bin/galaxy-dist/htpasswd > require valid-user > $ cat htpasswd > EDLB:xxxxxxxxxxxxx > $ ll static/.htaccess > -rw-r--r-- 1 galaxy galaxy 117 Apr 8 17:16 static/.htaccess > ll htpasswd > -rw-r--r-- 1 root root 19 Apr 8 17:32 htpasswd Hi Lee, It's best to simply put the authentication configuration directly in the Apache config file where you're defining the VirtualHost. Note that Galaxy also has functionality to restrict access itself, if you prefer. The relevant configuration option is 'require_login'. --nate > > > > > > On Mon, Apr 15, 2013 at 4:28 PM, Jennifer Jackson <jen(a)bx.psu.edu> wrote: > Hello Lee, > > Please see the section " External user authentication" on this wiki: > http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy > > If you still need help, posting this question over on the galaxy-dev(a)bx.psu.edu mailing list (but not cross-posting) with more details about what you have tried (how this solution was not a fit, etc.) will give you question the best exposure to the development community. > http://wiki.galaxyproject.org/MailingLists > > Best, > > Jen > Galaxy team > > > On 4/15/13 1:06 PM, Lee Katz wrote: >> Hi, I am relatively new to Galaxy. I would like to set it up as an apache password protected site. I have tried to do it, but I realize now that it has its own server built-in and that it is ineffective to set up .htaccess because it isn't reading .htaccess (or so I think). >> >> More information: Apache works (test page loads, and I can change it), and Galaxy works (I even made a new tool that is working). I have Ubuntu 12. >> >> My basic, basic need is to set up a server-level password like what .htaccess would provide. Could anyone help? Thank you. >> >> -- >> Lee Katz, Ph.D. >> >> >> ___________________________________________________________ >> 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/ > > -- > Jennifer Hillman-Jackson > Galaxy Support and Training > > http://galaxyproject.org > > > > -- > Lee Katz, Ph.D. > ___________________________________________________________ > 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/

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Local Galaxy Install - Multiple Job Handlers - Uploads waiting to run endlessly
by Adam Brenner 17 Apr '13

17 Apr '13

Howdy Galaxy Admins, I am installing Galaxy on our HPC cluster and running into a strange issue that I can no longer debug further. I am running the latest galaxy build as of Tuesday April 9th. hg clone https://bitbucket.org/galaxy/galaxy-dist/ hg update stable When a user tries to upload a file via the web interface, nginx reverse proxy setup as described here http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy, the upload stays in a state of "Job is waiting to run." The job stays like this for both FTP uploads, and uploads via browser. The dataset is a 319 bytes (both FTP and upload via browser) My universe_wsgi.ini variables are like so: .. under [app:main] .... new_file_path = /som/galaxy/tmp file_path = /som/galaxy/datasets/files track_jobs_in_database = True job_manager = manager job_handlers = handler0,handler1 ... before [app:main] in [server:main] .... [server:main] use = egg:Paste#http port = 8080 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:manager] use = egg:Paste#http port = 8079 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler0] use = egg:Paste#http port = 8090 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 [server:handler1] use = egg:Paste#http port = 8091 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5 Galaxy, for now, is running under the root user and is installed in /data/apps/galaxy (NFS mount) and the tmp files are stored on a GlusterFS system under /som/galaxy/. I have tried removing the extra job managers and handlers so I just have server:main and this still continues to happen. The paster.log files (with DEBUG = True) does not show any errors from python or issues writing to file. All POST and GET responses are recorded and nothing else. What I find strange is that if I look in new_file_path I do see my dataset as upload_file_data_Zx_1rK and cat'ing the file shows the correct contents. The items listed in my file_path (the dataset_*.dat) files are empty/blank..but are created. Any ideas as to why its failing? Is it nginx? I only have it redirect 8080, and none of the other job managers / handlers...is that an issue? Do you think its permissions on the my file_path or new_file_path directories? A very stumped Adam..... -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne(a)uci.edu

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Re: [galaxy-dev] (no subject)
by Dave Bouvier 16 Apr '13

16 Apr '13

David, The reason shed_tools should be outside the Galaxy path is that tool shed mercurial repositories can interfere with the Galaxy mercurial repository, since mercurial will find more than one .hg directory. As long as the data you want to store is not a mercurial repository, you should be safe, but my advice would still be to locate it outside the Galaxy path to avoid any possibility of conflicts. --Dave B. On 4/16/13 16:28:01.000, David Bonsall wrote: > Thanks Dave > > A quick update from /galaxy-dist .... > > % hg update stable > > > .....did the trick! > > > Btw, I have another question I have since added sub-directories to /galaxy-dist to store blast databases etc. Is this bad? Will mercurial be able to update. I remember a warning to not install shed-tools directory in the main galaxy stem for this reason. Does this rule apply to all directories? > > > Best Wishes > > David > > > > On Tue, Apr 16, 2013 at 9:16 PM, Dave Bouvier <dave(a)bx.psu.edu > <mailto:dave@bx.psu.edu>> wrote: > > David, > > Thank you for reporting this error, which was due to a new tool shed > feature being introduced in -central, which had not yet been wrapped > in a backwards compatibility layer for -dist. As of > 9440:bbb229927c68, the issue should be resolved. > > --Dave B. > > On 4/11/13 12:51:03.000, David Bonsall wrote: > > Dear Galaxy team, > > I'm trying to install NCBI + tools on a local instance of galaxy > (rep: > 8.1546099212f), but I get the following error, which I do not > get when > trying to install other tools. > > Thank you for all your hard work. It's all much appreciated > > David > > > > Error Traceback: > View as: Interactive | Text | XML (full) > ⇝ HTTPError: HTTP Error 500: Internal Server Error > URL: > http://127.0.0.1:8080/admin___toolshed/prepare_for_install?__tool_shed_url=… > <http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http…> > Module weberror.evalexception.__middleware:364 in respond > view > >> app_iter = self.application(environ, detect_start_response) > Module paste.recursive:84 in __call__ view > >> return self.application(environ, start_response) > Module paste.httpexceptions:633 in __call__ view > >> return self.application(environ, start_response) > Module galaxy.web.framework.base:125 in __call__ view > >> return self.handle_request( environ, start_response ) > Module galaxy.web.framework.base:182 in handle_request view > >> body = method( trans, **kwargs ) > Module galaxy.web.framework:228 in decorator view > >> return func( self, trans, *args, **kwargs ) > Module galaxy.webapps.galaxy.__controllers.admin_toolshed:894 in > prepare_for_install view > >> common_install_util.get___dependencies_for_repository( trans, > tool_shed_url, repo_info_dict, includes_tool_dependencies ) > Module tool_shed.util.common_install___util:90 in > get_dependencies_for___repository view > >> required_repo_info_dicts = get_required_repo_info_dicts( > tool_shed_url, util.listify( repo_info_dict ) ) > Module tool_shed.util.common_install___util:283 in > get_required_repo_info_dicts view > >> response = urllib2.urlopen( url ) > Module urllib2:126 in urlopen view > >> return _opener.open(url, data, timeout) > Module urllib2:400 in open view > >> response = meth(req, response) > Module urllib2:513 in http_response view > >> 'http', request, response, code, msg, hdrs) > Module urllib2:438 in error view > >> return self._call_chain(*args) > Module urllib2:372 in _call_chain view > >> result = func(*args) > Module urllib2:521 in http_error_default view > >> raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) > HTTPError: HTTP Error 500: Internal Server Error > > > _____________________________________________________________ > 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/ > <http://galaxyproject.org/search/mailinglists/> > >

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