[galaxy-dev] API extension
Hi All, We have just released the first beta version of a Galaxy API extension, that greatly simplifies some of the typical jobs that are performed by external jobs, that uses the Galaxy API. Please note that this API extension project is *NOT a part of the Galaxy project*. The Galaxy developer team can not in any way be expected to support this Python module. Please also note that this project is still in beta. The extended API consists of a single Python source file. The download includes a Python script for easy installation. If you want to try it out, please visit our project wiki page for examples of usage and more info about download, installation and setup. http://moma.ki.au.dk/mediawiki/index.php/Galaxy_extended_API We hope you find this useful. Kind regards - Frank -- Frank Sørensen, B.Sc., Programmer Molecular Diagnostic Laboratory (MDL) Molekylær Medicinsk Afdeling (MOMA) Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N Tlf. +45 7845 5363 ___ 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] About the Galaxy Data Library
Hi all, I was checking out how to upload large files into Galaxy and I stumbled upon using Data Libraries. In the tutorial, I saw that the 'Create new data library sets' link has a dropdown next to it. When I ran our Galaxy instance, I found out that ours has none. Is that feature available only in the updated version of Galaxy, or could it be activated by changing something in the universe_wsgi.ini? Thanks in advance for any help, CL ___ 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] Adding mm10 to available genomes
Hi Larry Have you added mm10 Mouse Dec. 2011 (GRCm38/mm10) (mm10) to ~/galaxy_dist/tool-data/shared/ucsc/builds.txt and restarted the server? Regards, Hans On 06/08/2012 06:19 PM, Larry Helseth wrote: I'm trying to add mm10 to a Galaxy instance built using Mercurial on May 31st (using Postgres). I've added the .fa file, prepared bwa, bowtie, samtool indexes, etc., edited all of the .loc files for individual tools and restarted the server daemon. mm10 appears in the list of genomes available for these tools but doesn't appear in the list of all genomes when I try uploading a file (Get Data/Upload File from your computer) OR when I try adding the file through the admin library interface (Administration/Data/Manage libraries/Add datasets). I tried editing ~/galaxy-dist/scripts/loc_files/create_all_fasta_loc.py to add a line for mm10. restarting Galaxy but that genome still doesn't appear in the list. Do I need to edit an entry in Postgres? When I restart Galaxy without the daemon mode (or tail the paster.log) I see that clicking on Get Data/Upload File is calling GET /tool_runner?tool_id=upload1 for the my URL/root/tool_menu. Am I supposed to upload new genomes through the Library? screencast.g2.bx.psu.edu http://screencast.g2.bx.psu.edu is still down so I can't watch the video tutorials about configuring custom genomes. I'd appreciate any suggestions. Thanks in advance! Adios, Larry Larry Helseth, Ph.D. Center for Molecular Medicine NorthShore University HealthSystem Evanston, IL ___ 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/
Re: [galaxy-dev] About the Galaxy Data Library
Hello Ciara, See the following Galaxy wiki page for details about configuring this option. http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Greg Von Kuster On Jun 11, 2012, at 2:54 AM, Ciara Ledero wrote: Hi all, I was checking out how to upload large files into Galaxy and I stumbled upon using Data Libraries. In the tutorial, I saw that the 'Create new data library sets' link has a dropdown next to it. When I ran our Galaxy instance, I found out that ours has none. Is that feature available only in the updated version of Galaxy, or could it be activated by changing something in the universe_wsgi.ini? Thanks in advance for any help, CL ___ 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/
Re: [galaxy-dev] Adding mm10 to available genomes
Thanks! That worked. On Mon, Jun 11, 2012 at 2:41 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Larry Have you added mm10Mouse Dec. 2011 (GRCm38/mm10) (mm10) to ~/galaxy_dist/tool-data/**shared/ucsc/builds.txt and restarted the server? Regards, Hans On 06/08/2012 06:19 PM, Larry Helseth wrote: I'm trying to add mm10 to a Galaxy instance built using Mercurial on May 31st (using Postgres). I've added the .fa file, prepared bwa, bowtie, samtool indexes, etc., edited all of the .loc files for individual tools and restarted the server daemon. mm10 appears in the list of genomes available for these tools but doesn't appear in the list of all genomes when I try uploading a file (Get Data/Upload File from your computer) OR when I try adding the file through the admin library interface (Administration/Data/Manage libraries/Add datasets). I tried editing ~/galaxy-dist/scripts/loc_**files/create_all_fasta_loc.py to add a line for mm10. restarting Galaxy but that genome still doesn't appear in the list. Do I need to edit an entry in Postgres? When I restart Galaxy without the daemon mode (or tail the paster.log) I see that clicking on Get Data/Upload File is calling GET /tool_runner?tool_id=upload1 for the my URL/root/tool_menu. Am I supposed to upload new genomes through the Library? screencast.g2.bx.psu.edu http://screencast.g2.bx.psu.**eduhttp://screencast.g2.bx.psu.edu is still down so I can't watch the video tutorials about configuring custom genomes. I'd appreciate any suggestions. Thanks in advance! Adios, Larry Larry Helseth, Ph.D. Center for Molecular Medicine NorthShore University HealthSystem Evanston, IL __**_ 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/
Re: [galaxy-dev] About FTP Upload
On Jun 10, 2012, at 10:36 PM, Ciara Ledero wrote: Hi all, I checked basics.py after reading a similar post and saw this: self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None ) self.ftp_upload_site = kwargs.get( 'ftp_upload_site', None ) Can you guys tell me what the None part means? Hi Ciara, It means, effectively, that these options are disabled by default. None is a built-in constant in Python: http://docs.python.org/library/constants.html --nate Cheers, CL ___ 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/
Re: [galaxy-dev] Task Manager: This Galaxy instance is not the job manager.
Hi, I think this bug is already fixed in the latest galaxy-central. I upgraded to the latest version last week or so and now it works fine again. Best, Sarah - Original Message - From: Rémy Dernat remy...@gmail.com To: Edward Kirton eskir...@lbl.gov Cc: galaxy-dev@lists.bx.psu.edu Sent: Friday, June 8, 2012 9:14:14 AM Subject: Re: [galaxy-dev] Task Manager: This Galaxy instance is not the job manager. Hi, Same issue here with multi servers. When I connect to the job manager instance, I have This Galaxy instance is not the job manager. If using multiple servers, please directly access the job manager instance to manage jobs. On the web server instance : Server Error URL: http://162.38.181.30:8000/galaxy/admin/jobs Module paste.exceptions.errormiddleware : 143 in __call__ app_iter = self . application ( environ , start_response ) Module paste.debug.prints : 98 in __call__ environ , self . app ) Module paste.wsgilib : 539 in intercept_output app_iter = application ( environ , replacement_start_response ) Module paste.recursive : 80 in __call__ return self . application ( environ , start_response ) Module paste.httpexceptions : 632 in __call__ return self . application ( environ , start_response ) Module galaxy.web.framework.base : 160 in __call__ body = method ( trans , ** kwargs ) Module galaxy.web.framework : 184 in decorator return func ( self , trans , * args , ** kwargs ) Module galaxy.web.base.controller : 2428 in jobs job_lock = trans . app . job_manager . job_queue . job_lock ) AttributeError: 'NoopQueue' object has no attribute 'job_lock' extra data full traceback URL: http://162.38.181.30:8000/galaxy/admin/jobs Module paste.exceptions.errormiddleware : 143 in __call__ app_iter = self . application ( environ , start_response ) Module paste.debug.prints : 98 in __call__ environ , self . app ) Module paste.wsgilib : 539 in intercept_output app_iter = application ( environ , replacement_start_response ) Module paste.recursive : 80 in __call__ return self . application ( environ , start_response ) Module paste.httpexceptions : 632 in __call__ return self . application ( environ , start_response ) Module galaxy.web.framework.base : 160 in __call__ body = method ( trans , ** kwargs ) Module galaxy.web.framework : 184 in decorator return func ( self , trans , * args , ** kwargs ) Module galaxy.web.base.controller : 2428 in jobs job_lock = trans . app . job_manager . job_queue . job_lock ) AttributeError: 'NoopQueue' object has no attribute 'job_lock' Regards, Rem 2012/6/7 Edward Kirton eskir...@lbl.gov yes, i've had the same error ever since the last galaxy-dist release. i previously had multiple servers and switched to the one manager, two handlers. rewrite rules didn't need to be changed. On Thu, May 24, 2012 at 8:14 AM, Sarah Diehl di...@immunbio.mpg.de wrote: Hi all, I have a similar, maybe related problem. I'm running a configuration as described at http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling . I have three webservers, one manager and two handlers. Everything is behind an Apache and the rewrite rules are set accordingly. When I try to access Manage Jobs, I also get the error This Galaxy instance is not the job manager. If using multiple servers, please directly access the job manager instance to manage jobs.. I have set the rewrite rule for admin/jobs to point to the manager server. When I access the manager directly from localhost I get the same error, while all other servers (web and handler) throw a server error: 127.0.0.1 - - [24/May/2012:15:37:50 +0200] GET /admin/jobs HTTP/1.1 500 - - Mozilla/5.0 (X11; Linux x86_64; rv:10.0.4) Gecko/20120424 Firefox/10.0.4 Error - type 'exceptions.AttributeError': 'NoopQueue' object has no attribute 'job_lock' URL: http://localhost:8080/admin/jobs File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/base/controller.py', line 2428 in jobs job_lock = trans.app.job_manager.job_queue.job_lock ) AttributeError: 'NoopQueue' object has no attribute 'job_lock' Before the update everything worked fine (I also ran multiple servers then). Best regards, Sarah On 05/16/2012 10:27 PM, Dave Lin
Re: [galaxy-dev] Configuring Galaxy for FTP upload
On Jun 11, 2012, at 9:10 AM, Nate Coraor wrote: On Jun 10, 2012, at 8:56 PM, Ciara Ledero wrote: Hi all, So I was not able to configure Galaxy immediately after this post of mine due to the tasks that I first needed to do. Looking back, I forgot to ask this question: Do I need to perform the things stated in http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP? I just have set ftp_upload_dir to a created folder and ftp_upload_site to something other than None. Hi Ciara, You only need to do this if you plan to allow users to upload files to their histories via FTP (or another file transfer mechanism). If you don't need this functionality, you don't need to configure it. --nate Nate, Were there plans to remove the 'FTP'-ness from this to indicate that any method for data transferal (sftp, scp, etc) works? chris ___ 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] Configuring Galaxy for FTP upload
On Jun 11, 2012, at 3:45 PM, Fields, Christopher J wrote: On Jun 11, 2012, at 9:10 AM, Nate Coraor wrote: On Jun 10, 2012, at 8:56 PM, Ciara Ledero wrote: Hi all, So I was not able to configure Galaxy immediately after this post of mine due to the tasks that I first needed to do. Looking back, I forgot to ask this question: Do I need to perform the things stated in http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP? I just have set ftp_upload_dir to a created folder and ftp_upload_site to something other than None. Hi Ciara, You only need to do this if you plan to allow users to upload files to their histories via FTP (or another file transfer mechanism). If you don't need this functionality, you don't need to configure it. --nate Nate, Were there plans to remove the 'FTP'-ness from this to indicate that any method for data transferal (sftp, scp, etc) works? chris Yes, that's the plan. --nate ___ 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/
