Re: [galaxy-dev] Error with tool migration
Kerry, Greg's fix in 11800:a53f2f700699 has been applied to the stable branch as 11804:a9a0ac9c1afa, and the galaxy-dist repository has been updated to that changeset. --Dave B. On 12/18/2013 07:14 PM, Kerry Deutsch wrote: No, we're pulling galaxy-dist. Thanks for the quick reply, Kerry On Wed, Dec 18, 2013 at 4:07 PM, Greg Von Kuster g...@bx.psu.edu mailto:g...@bx.psu.edu wrote: Hello Kerry, I've committed a fix for this in 11800:a53f2f700699 to the galaxy-central branch. Is that the branch you're pulling? Thanks for reporting this. Greg Von Kuster On Dec 18, 2013, at 5:48 PM, Kerry Deutsch kerry.deut...@systemsbiology.org mailto:kerry.deut...@systemsbiology.org wrote: Hello - I pulled down the latest changes today (it was long overdue), and am running into the following error when I run the tool migration: sh ./scripts/migrate_tools/0008_tools.sh install_dependencies No handlers could be found for logger galaxy.tools.data Repositories will be installed into configured tool_path location ../shed_tools [localhost] local: rm -rf ./database/tmp/tmp-toolshed-mtdWuQjBx Skipping installation of tool dependency samtools version 0.1.18 since it is installed in /users/galaxy/galaxy_deps/bin/samtools/0.1.18/devteam/package_samtools_0_1_18/171cd8bc208d Traceback (most recent call last): File ./scripts/migrate_tools/migrate_tools.py, line 21, in module app = MigrateToolsApplication( sys.argv[ 1 ] ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py, line 83, in __init__ install_dependencies=install_dependencies ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 121, in __init__ is_repository_dependency=is_repository_dependency ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 509, in install_repository is_repository_dependency=is_repository_dependency ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 351, in handle_repository_contents guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) File /users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 259, in get_guid full_path = str( os.path.abspath( os.path.join( root, name ) ) ) UnboundLocalError: local variable 'name' referenced before assignment Ideas? Thanks much! Kerry ___ 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] Consultez mon profil LinkedIn
LinkedIn J'aimerais vous inviter à rejoindre mon réseau professionnel en ligne, sur le site LinkedIn. Rémy Rémy Dernat System and Web programmer IT. Engineer chez CNRS Région de Montpellier , France Veuillez confirmer que vous connaissez Rémy Dernat : https://www.linkedin.com/e/1kvf56-hpe8ktzg-6h/isd/18792641650/8XO3w_SR/?hs=falsetok=0uQnxIC24FSC01 -- Vous recevez des invitations à vous connecter par e-mail. Cliquez ici si vous ne souhaitez plus recevoir ces e-mails : http://www.linkedin.com/e/1kvf56-hpe8ktzg-6h/qaQIbd-APagZF22GBAQuFmcZcI_00a44mJ/goo/galaxy-dev%40bx%2Epsu%2Eedu/20061/I6122389523_1/?hs=falsetok=1GA9M3SyMFSC01 (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. ___ 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] Sysadmin Question
Hi, I'm at the Florida State University HPC and setting up an a Galaxy server that will be used to submit jobs to our HPC cluster. I'm using apache as a proxy for the Galaxy server and I'm in the process of setting up ldap authentication. I had planned to mount our HPC file system (with user home directories) on the Galaxy server so that users would have access to their data but I'm wondering if I have the wrong idea about how Galaxy works and if there is a way to map users to their home directories in Galaxy easily. Thanks for any pointers. Donny Shrum ___ 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] Sysadmin Question
Hi Donny, Galaxy expects data to be copied in to its data store (by default, galaxy-dist/database/files/), and it's not designed to access data in the way you're suggesting. However, there are some workarounds. First, if the data is added to a Data Library (an admin feature, although once a library is created, non-admin users can be given write access to specific libraries), data can be uploaded to libraries without copying it in to Galaxy. This is documented here: https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles The Galaxy user must have read access to the data in question to be imported. Datasets in Galaxy can also have their path set explicitly, a feature which some Galaxy admins have used to create a Galaxy tool that allows users to browse their local filesystem space and import datasets without copying them. Hope this helps, --nate On Thu, Dec 19, 2013 at 3:23 PM, Shrum, Donald C dcsh...@admin.fsu.edu wrote: Hi, I'm at the Florida State University HPC and setting up an a Galaxy server that will be used to submit jobs to our HPC cluster. I'm using apache as a proxy for the Galaxy server and I'm in the process of setting up ldap authentication. I had planned to mount our HPC file system (with user home directories) on the Galaxy server so that users would have access to their data but I'm wondering if I have the wrong idea about how Galaxy works and if there is a way to map users to their home directories in Galaxy easily. Thanks for any pointers. Donny Shrum ___ 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] Request: Option to reduce server data transfer for big workflow in cluster
You've been extremely helpful, I appreciate it. So we went ahead and decided that we need this feature. We're planning to have a lot of people running huge pipelines, ones that work best on one node, and there's no reason to do all this writing to any shared file system when it works best on one node using /tmp/ for intermediate step data. So I've been working on that. So far I've made the checkbox for using one node (in run.mako). In workflow.py I catch this and set a new variable in each step of the workflow called use_one_node, if checkbox is checked. Now I'm trying to find where jobs are run, so that I can put the logic in for getting a node to run on, and setting that as a variable on each step. Could you point me in the direction of the files/classes associated with running the history's jobs, and getting nodes (or sending jobs to condor?)? Thanks, and I'll be sure to push this upstream after it's done if you'd like it. Maybe as something you can turn on from the universal_wsgi. ___ 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/
