Re: [galaxy-dev] Toolshed error when browsing own repo's
Hi, I stopped toolshed, dropped the database, and recreated it. Relaunched toolshed without errors. I have create a login again, created a category (no problems), and tried to create a repo, which upon saving gives me the error again. Is it a problem that I use the same user for access to both the galaxy db and the toolshed db? My versions (excuse me for not posting this earlier): -- Python 2.6.6 -- Postgres version 8.4.9: bash-4.1$ psql -c select version(); template1 version - PostgreSQL 8.4.9 on x86_64-redhat-linux-gnu, compiled by GCC gcc (GCC) 4.4.5 20110214 (Red Hat 4.4.5-6), 64-bit (1 row) -- Galaxy version: it is the latest update [galaxy@galaxy galaxy-dist]$ hg head changeset: 6799:40f1816d6857 tag: tip user:Greg Von Kuster g...@bx.psu.edu date:Wed Mar 07 13:35:34 2012 -0500 summary: Fix for populating the tool panel and generating the integrated_tool_panel.xml file. Joachim On 04/02/2012 05:16 PM, Greg Von Kuster wrote: Try completely dropping and recreating your tool shed database. Also, what version of Galaxy are you running and what version of Python are you running? What database / version are you using? On Apr 2, 2012, at 11:13 AM, Joachim Jacob wrote: Thanks for the suggestions, but no joy. 1. I have created hgweb.config like this in the main install dir [galaxy@galaxy galaxy-dist]$ pwd /home/galaxy/galaxy-dist [galaxy@galaxy galaxy-dist]$ cat hgweb.config [paths] 2. I have removed all repo directories from the toolshed database [galaxy@galaxy 000]$ pwd /home/galaxy/toolshed/database/community_files/000 3. I restart the toolshed with my modified init script (centos6.2) 4. I try to create a new repo (page loads) 5. I get to 'browse my repositories': again the page won't load, showing the error from below. Did I do something wrong, or are my steps from above not correct? Thanks for the help! Kind regards, Joachim On 04/02/2012 05:00 PM, Greg Von Kuster wrote: This is the problem - it's unclear how your local tool shed environment is missing this file as it must have been generated the first time your started your tool shed application ( via sh run_community.sh ). Since this file does not exist, you must not yet have created any repositories, so manually create the file with contents like this, and you should be able to create a repository. [paths] If you have created repositories in the past, then this file must have been inadvertently removed from disk, so you'll have to add entries for each repository you have on disk, something like this. [paths] repos/test/filter = database/community_files/000/repo_1 ... where test is replaced with your reppository owner, filter is replaced with your repository name, and the path is replaced with your repository path. If you don't care about keeping your repositories on disk (if you in fact have any), you can delete them, and create the hgeweb.config file with just the [paths] setting and no entries. This will result in a new, pristine tool shed environment. Greg Von Kuster On Apr 2, 2012, at 10:38 AM, Joachim Jacob wrote: I am sorry, but I do not have a hgweb.config file in the install dir. On 04/02/2012 04:23 PM, Greg Von Kuster wrote: It should be in your Galaxy installation directory, and your on-disk repositories will be in a directory under the setting you've defined for the file_path configuration in your community_wsgi.ini file. On Apr 2, 2012, at 10:17 AM, Joachim Jacob wrote: Hi Greg, If it is most likely a configuration error, I will check my settings, and let you know my progress. But one note: I do not have a hgweb.config file. Where is it supposed to reside? I cannot find this info on the toolshed wiki. Joachim On 04/02/2012 03:30 PM, Greg Von Kuster wrote: Hi Joachim, I've not seen this in any of my tool shed development environments, nor using the test or main Galaxy tool sheds, so it is unlikely that this is a bug. It looks more likely to be a configuration problem in your local tool shed environment. Do the repositories defined in your hgweb.config match those you have on disk? Greg Von Kuster On Apr 2, 2012, at 8:38 AM, Joachim Jacob wrote: Hi all, On a local Toolshed freshly installed, I got these errors when browsing my repository. Perhaps a bug? Cheers, Joachim Server Error URL: http://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositorieshttp://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositorieshttp://192.168.10.26:9009/repository/browse_repositories?webapp=communityoperation=my_repositories
Re: [galaxy-dev] Fastq Groomer
On Tue, Apr 3, 2012 at 1:57 AM, Xu, Jianpeng jianpeng...@emory.edu wrote: Hi, I have installed our local galaxy. I have a question for Fastq Groomer: Is it an interior tool within Galaxy ? I mean you already incorporate it into Galaxy? Or, you incorporate an external tool into Galaxy ? Do you know some programs that can be used to do the quality score conversion ? Thanks a lot. It is a Python script the Galaxy team wrote specifically for Galaxy, which uses the Galaxy FASTQ handling code. The source is here: https://bitbucket.org/galaxy/galaxy-central/src/default/tools/fastq/fastq_groomer.py https://bitbucket.org/galaxy/galaxy-central/src/default/tools/fastq/fastq_groomer.xml 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/
Re: [galaxy-dev] [galaxy-user] Blast2GO local instance Re: Table with gene count reads
On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster g...@bx.psu.edu wrote: On Mar 24, 2012, at 7:30 AM, Peter Cock wrote: Have you seen the README file that comes with the Blast2GO wrapper? Perhaps the 'install from toolshed' could be tweaked to make this kind of documentation more visible... If you are installing a single repository that contains a file named one of (case is ignored) readme, readme.txt, read_me, read_me.txt, the contents of the file will be displayed on the tool panel section selection page. An example using the antismash repository on the main tool shed is below. This new feature is available in change set revision 6945:5ea04ccb61e8, which is currently running on the Galaxy tool shed and our central development repository. It will be available in the next Galaxy distribution. Great. In this case I've actually called the file blast2go.txt (to match the use of blast2go.xml and blast2go.py). I didn't want to use a generic name like README since there could be other tools installed in the same folder (this predates the auto-install system). Is this naming pattern common used enough to justify including in the Galaxy Tool Shed code for spotting a README file? Care must be taken when following instructions in README files since some of the information may be outdated. For example, the Galaxy functional test framework was recently enhanced to support testing tools included in installed repositories, but I've seen some README files currently in repositories that instruct installers to move test data to the Galaxy installation environment, which is no longer necessary. Some of my tools' README files will need a little clarification following those changes to Galaxy. Thanks, 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/
Re: [galaxy-dev] [galaxy-user] Blast2GO local instance Re: Table with gene count reads
On Apr 3, 2012, at 6:07 AM, Peter Cock wrote: On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster g...@bx.psu.edu wrote: On Mar 24, 2012, at 7:30 AM, Peter Cock wrote: Have you seen the README file that comes with the Blast2GO wrapper? Perhaps the 'install from toolshed' could be tweaked to make this kind of documentation more visible... If you are installing a single repository that contains a file named one of (case is ignored) readme, readme.txt, read_me, read_me.txt, the contents of the file will be displayed on the tool panel section selection page. An example using the antismash repository on the main tool shed is below. This new feature is available in change set revision 6945:5ea04ccb61e8, which is currently running on the Galaxy tool shed and our central development repository. It will be available in the next Galaxy distribution. Great. In this case I've actually called the file blast2go.txt (to match the use of blast2go.xml and blast2go.py). I didn't want to use a generic name like README since there could be other tools installed in the same folder (this predates the auto-install system). Is this naming pattern common used enough to justify including in the Galaxy Tool Shed code for spotting a README file? Since the read me file contains instructions for installing the tools in the repository, would it be better to assume only 1 installation file that includes different instructions per contained tool if necessary? If multiple read me files are allowed per repository, they would all have to be merged together with the entire content displayed on the tool panel section selection screen anyway, so allowing only a single file would be better. The read me in your blast2go repository is named blast2go.txt, so I suppose we could expand the read me file name list to include repository name.txt. I'll do this. Care must be taken when following instructions in README files since some of the information may be outdated. For example, the Galaxy functional test framework was recently enhanced to support testing tools included in installed repositories, but I've seen some README files currently in repositories that instruct installers to move test data to the Galaxy installation environment, which is no longer necessary. Some of my tools' README files will need a little clarification following those changes to Galaxy. My next big feature will be supporting installation of tool dependencies automatically with the repository contents, so keep that in mind if you're making changes to install instructions. This enhancement will take a bit of time. Thanks, 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/
Re: [galaxy-dev] Proteomics category on main toolshed?
Hi Greg, I'm afraid to say I might have been a bit ahead of myself in asking you to create that Proteomics category. We're almost ready to upload our tools, but at the last minute we've discovered a bunch of issues we need to sort out. I'm going away for Easter and won't be back until the 16th ... so I guess the earliest our tools would be up is after the 16th. Sorry about that. I hope you're OK with a 0 beside the Proteomics category for now. Ira On 30/03/2012, at 10:03 AM, Ira Cooke wrote: Thanks ... that would definitely be a good idea. Well try to implement proper tests for all the tools. Ira On 30/03/2012, at 10:01 AM, Greg Von Kuster wrote: Thanks Ira, Just so you know, the Galaxy functional test framework now supports testing installed tools if the repository tools include tests and test datasets are included in the repository in a test-data subdirectory. Here is the relevant section of the tool shed wiki describing this: http://wiki.g2.bx.psu.edu/Tool%20Shed#Using_Galaxy.27s_functional_test_framework_to_test_tools_installed_into_your_local_Galaxy_instance Greg On Mar 29, 2012, at 6:53 PM, Ira Cooke wrote: Dear Greg, Thanks very much for that. I'll do a last proof-read of the tools and upload later on today. We're working on some better documentation ... to get it all working takes some extra setup steps on the part of the user. Ira On 30/03/2012, at 9:49 AM, Greg Von Kuster wrote: Hello Ira, I've added the category to the main tool shed. Thanks for the request and your upcoming contributions! Greg Von Kuster On Mar 29, 2012, at 5:33 PM, Ira Cooke wrote: Dear list, I would like to add a suite of proteomics tools to the toolshed but there is currently no suitable category. Would it be possible to add a category called Proteomics? Thanks Ira ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Proteomics category on main toolshed?
No worries, Ira - have a great Easter vacation! On Apr 3, 2012, at 7:20 AM, Ira Cooke wrote: Hi Greg, I'm afraid to say I might have been a bit ahead of myself in asking you to create that Proteomics category. We're almost ready to upload our tools, but at the last minute we've discovered a bunch of issues we need to sort out. I'm going away for Easter and won't be back until the 16th ... so I guess the earliest our tools would be up is after the 16th. Sorry about that. I hope you're OK with a 0 beside the Proteomics category for now. Ira On 30/03/2012, at 10:03 AM, Ira Cooke wrote: Thanks ... that would definitely be a good idea. Well try to implement proper tests for all the tools. Ira On 30/03/2012, at 10:01 AM, Greg Von Kuster wrote: Thanks Ira, Just so you know, the Galaxy functional test framework now supports testing installed tools if the repository tools include tests and test datasets are included in the repository in a test-data subdirectory. Here is the relevant section of the tool shed wiki describing this: http://wiki.g2.bx.psu.edu/Tool%20Shed#Using_Galaxy.27s_functional_test_framework_to_test_tools_installed_into_your_local_Galaxy_instance Greg On Mar 29, 2012, at 6:53 PM, Ira Cooke wrote: Dear Greg, Thanks very much for that. I'll do a last proof-read of the tools and upload later on today. We're working on some better documentation ... to get it all working takes some extra setup steps on the part of the user. Ira On 30/03/2012, at 9:49 AM, Greg Von Kuster wrote: Hello Ira, I've added the category to the main tool shed. Thanks for the request and your upcoming contributions! Greg Von Kuster On Mar 29, 2012, at 5:33 PM, Ira Cooke wrote: Dear list, I would like to add a suite of proteomics tools to the toolshed but there is currently no suitable category. Would it be possible to add a category called Proteomics? Thanks Ira ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Output files from Galaxy
Hi, I have installed the local galaxy. I am trying to run some programs. I have a question now: If I run a program and the output file will be in the history. If I want to do something with the output file, it looks like I have to download it at first. Is there a way to do something with the output file without downloading it ? Where does the output file store ? Is there a way to configure to put the output file under a specific directory ? Thanks a lot. Jianpeng This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] incorrect tmp dir handling in picard AddOrReplaceReadGroups
Every time I run Picard's AddOrReplaceReadGroups, my system tmp directory fills, and the tool stops. I'm left scratching my head, because it seems that the JVM sets the system /tmp directory on my local galaxy-central branch, instead of the new_file_path I have defined in universe_wsgi.ini. This issue seems to have been fixed in commit 07560293b167https://bitbucket.org/galaxy/galaxy-central/changeset/07560293b167, and I can confirm that my picard_wrapper.py includes the amended line. I am using OpenJDK: java version 1.6.0_20 OpenJDK Runtime Environment (IcedTea6 1.9.10) (rhel-1.40.1.9.10.el6_1-x86_64) OpenJDK 64-Bit Server VM (build 19.0-b09, mixed mode) Since my config is pointing to /scratch/tmp, but the JVM is using /tmp, and other tools in galaxy are respecting the config, what could be the disconnect? Thank you, Matt -- Matt Shirley Ph.D Candidate - BCMB Pevsner Lab http://pevsnerlab.kennedykrieger.org/ Johns Hopkins Medicine ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Missing tool previews in tool shed, e.g. hmmer.xml
On Tue, Apr 3, 2012 at 7:25 PM, Greg Von Kuster g...@bx.psu.edu wrote: Invalid tools are now displayed in the Preview tools and inspect metadata by tool version section - here is the list for the hmmer repository. Lovely - that will help with the existing tools which are not all fully compliant with these new requirements :) 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/
Re: [galaxy-dev] incorrect tmp dir handling in picard AddOrReplaceReadGroups
Hi, Matt.
Thanks for reporting this - it's definitely a misfeature...
The tool wrapper tools/picard/picard_AddOrReplaceReadGroups.xml does
not explicitly set the tmpdir parameter, so I've added --tmpdir
${__new_file_path__} to the command line generated. That will
over-ride the default value /tmp for opts.tmpdir in
picard_wrapper.py to use the new_file_path.
It is now in galaxy-central - please update your local copy and test
it to confirm this solves your problem?
On Tue, Apr 3, 2012 at 2:55 PM, Matt Shirley matt.shir...@jhmi.edu wrote:
Every time I run Picard's AddOrReplaceReadGroups, my system tmp directory
fills, and the tool stops. I'm left scratching my head, because it seems
that the JVM sets the system /tmp directory on my local galaxy-central
branch, instead of the new_file_path I have defined in universe_wsgi.ini.
This issue seems to have been fixed in commit 07560293b167, and I can
confirm that my picard_wrapper.py includes the amended line. I am using
OpenJDK:
java version 1.6.0_20
OpenJDK Runtime Environment (IcedTea6 1.9.10)
(rhel-1.40.1.9.10.el6_1-x86_64)
OpenJDK 64-Bit Server VM (build 19.0-b09, mixed mode)
Since my config is pointing to /scratch/tmp, but the JVM is using /tmp, and
other tools in galaxy are respecting the config, what could be the
disconnect? Thank you,
Matt
--
Matt Shirley
Ph.D Candidate - BCMB
Pevsner Lab
Johns Hopkins Medicine
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--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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Re: [galaxy-dev] Production environment and Apache's sendfile
On Mar 9, 2012, at 4:12 AM, Yuri D'Elia wrote: Hi everyone. I've set up a galaxy production environment and it seems to be working. I've identified a couple of issues though: If I enable apache_xsendfile, the little eye icon (Display data in browser) on each dataset stops working. I get the following instead: The requested URL /datasets/7e93e3cf926fb2b3/display/ was not found on this server My document root is not the same as the galaxy root (as suggested). Everything else seems to work. Is this a bug? Hi Yuri, Could you check your Apache error log to see if there's anything relevant there? Second question: I want to rotate the galaxy log file (as specified with paster.py serve --log-file. I can't find a way to reopen the logfile in galaxy without taking down the whole service, or a way to redirect the log to a pipe together while using --daemon. I cannot let the file grow forever. Any suggestions? Unfortunately, there's no way to reopen the log without restarting the process. This is the way we handle our servers. Thanks, --nate Right now I've setup logrotate to copytruncate the log (the log is opened in append anyway), but it's not a very nice solution. Does paster support some standard signal such as SIGUSR1 to re-open log files? Thanks. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
