[galaxy-dev] tool of installing tool shed repositories
Hi, there: I'm currently trying to migrate all repositories of main tool shed on http://toolshed.g2.bx.psu.edu/ to local, but got some problems. I'm wondering whether there is an existing tool can automatically do the job? thanks rgds, Ray ngsf...@hygenomics.com[5UQ[BL(6~BS2JV6(11-04-16-34-29).png___ 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 of installing tool shed repositories
Hi Ray, there is some work in that direction to easily import and export repositories. The export feature is already integrated and should help you. You will end up with a tarball with all informations about that repository and the import should be easier. If you want to work on the import part, I think your work is more than welcome! Cheers, Bjoern Hi, there: I'm currently trying to migrate all repositories of main tool shed on http://toolshed.g2.bx.psu.edu/ to local, but got some problems. I'm wondering whether there is an existing tool can automatically do the job? thanks rgds, Ray __ ngsf...@hygenomics.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/
[galaxy-dev] Fw: Re: tool of installing tool shed repositories
ngsf...@hygenomics.com From: ngsf...@hygenomics.com Date: 2013-11-04 17:53 To: Björn Grüning Subject: Re: Re: [galaxy-dev] tool of installing tool shed repositories hi Bjoern: I am trying to bulk import repositories, by developing some tools following the thought similar to those in toolshed tools test. I just want to make sure whether there are some tools already exist. rgds, Ray ngsf...@hygenomics.com From: Björn Grüning Date: 2013-11-04 16:46 To: ngsf...@hygenomics.com CC: galaxy-dev Subject: Re: [galaxy-dev] tool of installing tool shed repositories Hi Ray, there is some work in that direction to easily import and export repositories. The export feature is already integrated and should help you. You will end up with a tarball with all informations about that repository and the import should be easier. If you want to work on the import part, I think your work is more than welcome! Cheers, Bjoern Hi, there: I'm currently trying to migrate all repositories of main tool shed on http://toolshed.g2.bx.psu.edu/ to local, but got some problems. I'm wondering whether there is an existing tool can automatically do the job? thanks rgds, Ray __ ngsf...@hygenomics.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] Missing test results on (Test) Tool Shed
On Tue, Oct 22, 2013 at 10:43 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Oct 7, 2013 at 7:32 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, Thanks for the information, it uncovered a problem with the testing framework that has been resolved in 10817:6b0c3592dde1. The listed repositories should start showing useful results next time the nightly tests run. --Dave B. Hi Dave, I must sound like a scratched record (is there a replacement phrase now that LPs are a cultural artefact?): Currently listed under Latest revision: failing tool tests but missing any test results: http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls (I've got a lot of fresh failures pointing at a separate issue, email to follow with a new title). Peter More missing test results, yet listed under Latest revision: failing tool tests: http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id The common feature is they all depend on Biopython - perhaps that failed to install, and the tests were skipped? Over on the main tool shed, those three are all showing errors relating to a failed Biopython install. 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/
[galaxy-dev] Supporting file sets for running a tool with multiple input files
Hi, Is there any news regarding support for the following scenario in Galaxy: - User has N files which he would like to process with a Galaxy tool using the same parameters - User uploads a (.tar or .zip ?) file to Galaxy and selects this as the input file for the tool - Tool produces an output .zip file with the N result files I know Galaxy-P had a workaround for this some time ago. But has this been solved in the main Galaxy code base? Or are there any feasible workarounds that I can add to my Toolshed package to ensure my .zip file does not get unzipped at upload (default Galaxy behaviour)? Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://www.pri.wur.nl/ ___ 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] Supporting file sets for running a tool with multiple input files
Hi Pieter, We've worked out what we think is the right way to solve this for Galaxy and expect work to start soon. See the trello card ( https://trello.com/c/325AXIEr/613-tools-dataset-collections) for more details. For your particular tool, the first workaround that comes to mind would be adding a new datatype, say, ZippedInputFiles in your toolshed repository that gets included and used by users, though I haven't actually tried that. That said, I'd probably wait, this feature is high on our list of things to do next. -Dannon On Mon, Nov 4, 2013 at 5:44 AM, Lukasse, Pieter pieter.luka...@wur.nlwrote: Hi, Is there any news regarding support for the following scenario in Galaxy: - User has N files which he would like to process with a Galaxy tool using the same parameters - User uploads a (.tar or .zip ?) file to Galaxy and selects this as the input file for the tool - Tool produces an output .zip file with the N result files I know Galaxy-P had a workaround for this some time ago. But has this been solved in the main Galaxy code base? Or are there any feasible workarounds that I can add to my Toolshed package to ensure my .zip file does not get unzipped at upload (default Galaxy behaviour)? Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nl ___ 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] Errors running DRMAA and PBS on remote server running Torque 4
Hi Carrie, It is a bug in Torque/4.x series. It can be fixed for a time by restarting the Torque pbs_server process, but it’s going to come back. It’s not galaxy-specific as any python-drmaa request will fail once Torque starts experiencing the issue. Regards, Alex From: Ganote, Carrie L cgan...@iu.edumailto:cgan...@iu.edu Date: Tuesday, October 15, 2013 at 4:58 PM To: 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: [galaxy-dev] Errors running DRMAA and PBS on remote server running Torque 4 Hi List, I've sprouted some grays in the last week after my Galaxy instances all simultaneously ceased to submit jobs to our main cluster. Some Galaxy instances are running the PBS job runner, and others use DRMAA. For the DRMAA runner I was getting: galaxy.jobs.runners ERROR 2013-10-15 08:40:14,942 (1024) Unhandled exception calling queue_job Traceback (most recent call last): File galaxy-dist/lib/galaxy/jobs/runners/__init__.py, line 60, in run_next method(arg) File galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 188, in queue_job external_job_id = self.ds.runJob(jt) File build/bdist.linux-x86_64/egg/drmaa/__init__.py, line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File build/bdist.linux-x86_64/egg/drmaa/helpers.py, line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer File build/bdist.linux-x86_64/egg/drmaa/errors.py, line 90, in error_check raise _ERRORS[code-1](code %s: %s % (code, error_buffer.value)) InternalException: code 1: (qsub) cannot access script file: Unauthorized Request MSG=can not authorize request (0-Success) And in my PBS runner: galaxy.jobs.runners.pbs WARNING 2013-10-14 17:13:07,319 (550) pbs_submit failed (try 1/5), PBS error 15044: Resources temporarily unavailable To give some background, I had recently requested a new virtual machine to put my test/dev Galaxy on. I copied our production Galaxy to this new VM. I secured a new domain name for it and set it running. Everything was going well until I tried to hook it up to the cluster; at first I got an error saying that I didn't have permission to submit jobs. Makes sense, the new VM was not a qualified submit host for the cluster. I asked the sysadmins to add the VM as a submit host to the cluster using qmgr. As soon as this was done, not only could I still not submit jobs from the test Galaxy, but no Galaxy was able to submit jobs to the cluster. The issue isn't with Galaxy here but the underlying calls that it makes - for drmaa, I tracked it back to pbs-drmaa/bin/drmaa-run. For PBS, I'm sure it's somewhere in with libtorque. In every case, I could call qsub from the command line and it would correctly submit jobs, which was more perplexing. I re-installed python, drmaa.egg, pbs-drmaa, and rebooted the VM. I of course restarted Galaxy with each step, to no avail. I worked with the admins to see what was happening in the server logs, but the same cryptic error showed up - cannot authorize request. I've had this issue before in the past, more or less, but usually just gave up on it. It seemed to come and go sporadically, but rebooting the clusters seemed to help. This time, with our production server no longer functioning, I begged for help and the admins looked through the pbs_server config but couldn't find any mistypes or problems. Reloading the config by sending hangup signals to pbs_server didn't help. Then we tried pausing the scheduler and restarting pbs_server completely - and eureka, all problems went away. PBS and DRMAA runners are back up and working fine. This really seems to be a bug in Torque 4.1.5.1. I hope this saves someone a lot of headache! Newer versions of Torque may be the answer. I would also advise against making changes to the pbs_server configuration while in production - we have monthly maintenance, and I don't think I'll ever request changes when there won't be an immediate reboot to flush the server! Cheers, Carrie ___ 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 of installing tool shed repositories
Hello Ray and Björn, I'm currently working on the feature for importing a repository capsule into a Tool Shed. It's been on my plate for a while, but other priorities have side-tracked this work. Based on your exchange, I'm now working to finish up this feature, so it should be available in the next few days. Thanks, Greg Von Kuster On Nov 4, 2013, at 3:46 AM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de wrote: Hi Ray, there is some work in that direction to easily import and export repositories. The export feature is already integrated and should help you. You will end up with a tarball with all informations about that repository and the import should be easier. If you want to work on the import part, I think your work is more than welcome! Cheers, Bjoern Hi, there: I'm currently trying to migrate all repositories of main tool shed on http://toolshed.g2.bx.psu.edu/ to local, but got some problems. I'm wondering whether there is an existing tool can automatically do the job? thanks rgds, Ray __ ngsf...@hygenomics.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/ ___ 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] latest galaxy-central version
It keeps doing posts, and I'm not seeing any new errors. POST http://su2c-dev.ucsc.edu:8383/library_common/library_item_updates 200 OK 121ms When I did a browser refresh, I got the following javascript error: (I am logged in) Galaxy.currUser is undefined on Line 631 in history-panel.js When I opened the data library where the bam file was copying, everything is rendered ok. It seems the browser refresh fixed things. -Robert On Nov 4, 2013, at 11:14 AM, James Taylor ja...@jamestaylor.org wrote: Robert, I'm not sure what is going on here, other than that the javascript that converts buttons into dropdown menus has not fired. Are there any javascript errors? Marten is working on rewriting libraries, and we will be eliminating the progressive loading popupmenus for something much more efficient, but this also might indicate a bug so let us know if there is anything odd in the console. -- James Taylor, Associate Professor, Biology/CS, Emory University On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch baert...@soe.ucsc.edu wrote: HI James, I just pulled in the latest code to see how you changed from iframe to divs. Very exciting update. I tried importing a bam file into the library using the admin tool that reads the file directly from a path on the server. During the copy operation, the screen gets into a weird state. ps -ef shows these two processes running: python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpywxnFE /data/galaxy-central/database/tmp/tmpXkEvSY 8876:/data/galaxy-central/database/job_working_directory/004/4547/dataset_8876_files:/data/galaxy-central/database/files/008/dataset_8876.dat samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat /tmp/tmpNbcggh/sorted Do you finish rendering the screen after the copy operation is complete? -Robert Screen Shot 2013-11-04 at 10.53.02 AM.png ___ 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] latest galaxy-central version
Hello, I have also seen some of these errors while developing libraries. The library code is not in central however it might be related to recent changes to the history panel. Carl Eberhard might now more, adding him to the conversation. --Marten On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch baert...@soe.ucsc.eduwrote: It keeps doing posts, and I'm not seeing any new errors. POST http://su2c-dev.ucsc.edu:8383/library_common/library_item_updates 200 OK 121ms When I did a browser refresh, I got the following javascript error: (I am logged in) Galaxy.currUser is undefined on Line 631 in history-panel.js When I opened the data library where the bam file was copying, everything is rendered ok. It seems the browser refresh fixed things. -Robert On Nov 4, 2013, at 11:14 AM, James Taylor ja...@jamestaylor.org wrote: Robert, I'm not sure what is going on here, other than that the javascript that converts buttons into dropdown menus has not fired. Are there any javascript errors? Marten is working on rewriting libraries, and we will be eliminating the progressive loading popupmenus for something much more efficient, but this also might indicate a bug so let us know if there is anything odd in the console. -- James Taylor, Associate Professor, Biology/CS, Emory University On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch baert...@soe.ucsc.eduwrote: HI James, I just pulled in the latest code to see how you changed from iframe to divs. Very exciting update. I tried importing a bam file into the library using the admin tool that reads the file directly from a path on the server. During the copy operation, the screen gets into a weird state. ps -ef shows these two processes running: python /data/galaxy-central/tools/data_source/upload.py /data/galaxy-central /data/galaxy-central/database/tmp/tmpywxnFE /data/galaxy-central/database/tmp/tmpXkEvSY 8876:/data/galaxy-central/database/job_working_directory/004/4547/dataset_8876_files:/data/galaxy-central/database/files/008/dataset_8876.dat samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat /tmp/tmpNbcggh/sorted Do you finish rendering the screen after the copy operation is complete? -Robert Screen Shot 2013-11-04 at 10.53.02 AM.png ___ 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] Security vulnerability in Galaxy filtering tools
A security vulnerability was recently discovered by John Chilton with Galaxy's Filter data on any column using simple expressions and Filter on ambiguities in polymorphism datasets tools that can allow for arbitrary execution of code on the command line. The fix for these tools has been committed to the Galaxy source. The timing of this commit coincides with the next Galaxy stable release (which has also been pushed out today). To apply the fix and simultaneously update to the new Galaxy stable release, ensure you are on the stable branch and upgrade to the latest changeset: % hg branch stable % hg pull -u For Galaxy installations that administrators are not yet ready to upgrade to the latest release, there are three workarounds. First, for Galaxy installations running on a relatively new version of the stable release (e.g. release_2013.08.12), Galaxy can be updated to the specific changeset that that contains the fix. This will include all of the stable (non-feature) commits that have been accumulated since the 8/12 release plus any new features included with (and prior to) the 8/12 release, but without all of the new features included in the 11/4 release. Ensure you are on the stable branch and then upgrade to the specific changeset: % hg pull -u -r e094c73fed4d Second, the patch can be downloaded and applied manually: % wget -o security.patch https://bitbucket.org/galaxy/galaxy-central/commits/e094c73fed4dc66b589932edb83412cb8b827cd3raw/ and then: % hg patch security.patch or: % patch -p1 security.patch Third, the tools can be completely disabled by removing them from the tool configuration file (by default, tool_conf.xml) and restarting all Galaxy server processes. The relevant lines in tool_conf.xml are: tool file=stats/dna_filtering.xml / tool file=stats/filtering.xml / The full 11/4 Galaxy Distribution News Brief will be available later today and will contain details of changes since the last release. --nate Galaxy Team ___ 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] Nov 04, 2013 Galaxy Distribution
Nov 04, 2013 Galaxy Distribution http://wiki.galaxyproject.org/News/2013_11_04_Galaxy_Distribution *usegalaxy.org* *CompleteNews Brief http://wiki.galaxyproject.org/DevNewsBriefs/2013_11_04* *Highlights:* * A/*security vulnerability*/with filter tools trapped and fixed:*Upgrade or Patch NOW http://wiki.galaxyproject.org/DevNewsBriefs/2013_11_04#Security_Fix_NOW* * Galaxy Tool Migration:48 tools migrated to Tool Shed http://wiki.galaxyproject.org/DevNewsBriefs/2013_11_04#New_Tool_Migrationsfor a leaner distribution. * Improvedtools for administrators http://wiki.galaxyproject.org/DevNewsBriefs/2013_11_04#Admin(email verification, reports). * The framework forTools http://wiki.galaxyproject.org/DevNewsBriefs/2013_11_04#Tools,Visualizations http://wiki.galaxyproject.org/DevNewsBriefs/2013_11_04#Visualizations, and theCore http://wiki.galaxyproject.org/DevNewsBriefs/2013_11_04#Corehave been upgraded for performance and scalability. * Come see! A whopping26 pull requests incorporated http://wiki.galaxyproject.org/DevNewsBriefs/2013_11_04#Pull_Requests_Merged!. Many thanks to our open source community! * NumerousTool Shed enhancements and upgrades http://wiki.galaxyproject.org/DevNewsBriefs/2013_11_04#Tool_Shed: Api,READMEs, Functional Tests, easier installs, and much much more. * Plus enhancements toWorkflows http://wiki.galaxyproject.org/DevNewsBriefs/2013_11_04#Workflows,API http://wiki.galaxyproject.org/DevNewsBriefs/2013_11_04#API,CloudLaunch http://wiki.galaxyproject.org/DevNewsBriefs/2013_11_04#CloudLaunch,UI http://wiki.galaxyproject.org/DevNewsBriefs/2013_11_04#UI, andBug Fixes http://wiki.galaxyproject.org/DevNewsBriefs/2013_11_04#Bug_Fixes. http://getgalaxy.org http://getgalaxy.org/ http://bitbucket.org/galaxy/galaxy-dist http://galaxy-dist.readthedocs.org http://galaxy-dist.readthedocs.org/ new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable upgrade: $ hg pull $ hg update release_2013.11.04 /Thanks for using Galaxy!/ The Galaxy Team http://wiki.galaxyproject.org/Galaxy%20Team Posted to theGalaxy News http://wiki.galaxyproject.org/Newson 2013-11-04 ___ 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] Configurable toolshed package installation to support tool-dependency-resolver-plugins
Simon, As you have probably noticed a new stable galaxy was released. It includes 95% of what we discussed including this implicit check to see if tool shed packages are enabled. Your help implementing, testing, and driving these changes was greatly appreciated! I couldn't however pull the trigger and mark packages resolved via modules as Installed - so they will still appear to be in an error state (though your check is in there and they won't attempt to be installed, they will be just marked as errors). The upshot is you can change this one line of code in your Galaxy instance to get the behavior you desire (patch attached). The reason I don't want to mark these packages as Installed is that I am worried about Galaxy deployments that maybe want to use modules are first but transition to tool shed packages down the road. I am unsure what will happen if things are marked as Installed even if no files corresponding to the installation exist. I think the state NEVER_INSTALLED may be preferable - but I need to understand more about what that means. For your own instance, if you are certainly committed to using modules and not using the tool shed - it should be easy to apply the above patch. Is this a fair compromise for the time being? Until I can resolve this last issue, the Trello card remains open, but it should now be quite trivial to modify Galaxy to get the behavior you desire and hopefully this can serve as a model for how others can hook in other dependency resolution mechanisms. I would be eager to hear how this experiment progresses and how you feel about the implementation. Thanks for your contributions, -John On Mon, Oct 14, 2013 at 8:33 PM, Guest, Simon simon.gu...@agresearch.co.nz wrote: At Mon, 14 Oct 2013 20:22:06 -0500, John Chilton wrote: Simon, Very cool! I have two concerns. Rather than adding a new configuration option I think I would prefer to just check the configured dependency resolvers and then infer from them if the tool shed will be used. The configuration option strikes me as having to configure the same thing twice, and this change would make your setup slightly easier. Do you have any objection to me reworking your patch to do this? On the other hand, perhaps it is made more clear to the deployer that they are definitely disabling tool dependency installations if they have to add the explicit option this way. Hi John, I have no problem with you reworking it in that way. There are two reasons I didn't do that myself: 1. I would have had to change the interface to the dependency resolvers somehow to support this query, and I wasn't sure that was a good thing. 2. I wanted to make it explicit that toolshed package installation was disabled in this case, as I thought that would make it more likely this change gets accepted into the mainline. Whichever way you Greg and Dave are happy with is OK by me. Actually, I like your implicit approach better, so hope that's the one that gets agreed. cheers, Simon # HG changeset patch # User John Chilton jmchil...@gmail.com # Date 1383627567 21600 # Mon Nov 04 22:59:27 2013 -0600 # Branch stable # Node ID a278fe29f7217feb3145e785de92287f76455636 # Parent 5c789ab4144ac9db6c91b5646032894cae016309 Patch latest galaxy stable to mark packages resolved via modules when tool shed resolution disabled to be marked as INSTALLED in admin interface instead of ERROR. diff -r 5c789ab4144a -r a278fe29f721 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py Mon Nov 04 15:04:42 2013 -0500 +++ b/lib/tool_shed/util/common_install_util.py Mon Nov 04 22:59:27 2013 -0600 @@ -467,7 +467,7 @@ if app.toolbox.dependency_manager.find_dep( package_name, package_version, type='package') != INDETERMINATE_DEPENDENCY: ## TODO: Do something here such as marking it installed or ## configured externally. -pass +status = app.model.ToolDependency.installation_status.INSTALLED tool_dependency.status = status else: tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies ) ___ 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] Retrieve list of published workflows from API
Hey Phillip, I have looked through the API closely and I don't see a way to do this. I have created a Trello card for this. https://trello.com/c/LDm3dQvB Contributions welcome :). -John On Fri, Nov 1, 2013 at 12:24 PM, Philip Mabon philipma...@gmail.com wrote: Is there a way to interact with the published workflows section of Galaxy using only the API? Only workflows that I imported or constructed myself show up using the get_workflows from bioblend. 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/ 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/
