[galaxy-dev] [Solved] Galaxy and Cluster options
Hello! Sorry but I'm not able to answer the e-mail in the thread as I wasn't subscribed to the mailing list! But I now am. Thanks to L-A, Carlos and Chris for their answers! I can live with the config based tool configuration... but a dynamic one would be nice to have! Cheers, Tanguy signature.asc Description: This is a digitally signed message part ___ 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] Problem using Galaxy on the cloud
Jan; I appreciate the help, I am in no way a competent UNIX/Linux user. I just have 2 shuffled fastq files in an S3 bucket-I pasted the URL for these into Galaxy's upload file URL/Text box and that seems to be where the trouble started. On my first try loading the data files, I got a message saying there was no disk space. I'm trying to reproduce here but can't seem to figure out how the disk is filling up. A new filesystem should look like: $ df -h FilesystemSize Used Avail Use% Mounted on /dev/xvda1 20G 13G 6.1G 68% / udev 3.7G 4.0K 3.7G 1% /dev tmpfs 1.5G 660K 1.5G 1% /run none 5.0M 0 5.0M 0% /run/lock none 3.7G 0 3.7G 0% /run/shm /dev/xvdb 414G 201M 393G 1% /mnt /dev/xvdg1700G 654G 47G 94% /mnt/galaxyIndices /dev/xvdg2 10G 1.7G 8.4G 17% /mnt/galaxyTools /dev/xvdg35.0G 81M 5.0G 2% /mnt/galaxyData with 6Gb of free space on '/'. If you pasted a file, like: https://s3.amazonaws.com/chapmanb/example.fastq into the text box, it should show up as: /mnt/galaxyData/files/000/dataset_1.dat in the /mnt/galaxyData mount, which has all of the space for storing files. So I'm not sure exactly what is filling up your root partition. Could you try checking a couple of places and see if any of the filesystem usage is different from what we expect: $ du -sh /home/ubuntu/ 361M /home/ubuntu/ $ sudo du -sh /var/log/ 3.1M /var/log/ I'm cc'ing Enis in case he has any other ideas where we might be accidentally filling up the root filesystem. Thanks again for the feedback and sorry about the problems, Brad I tried again, and it worked. Then, when I tried to run velveth, it got hung up again with the no disk space issue. I browsed around in the /dev/xvda1 file system and there were quite a few files (I pasted them below). I assumed they were files relating to BloudBioLinux and I was not sure if I could get rid of any of the files. It was nothing I put there. I started the instance using BioCloudCentral. Maybe it would be better to just start Galaxy the long way (choosing a public AMI under launch instance...)? ubuntu@ip-10-44-117-85:/$ ls bin etc initrd.img lib64 mnt proc sbin sys var boot export lib lost+found opt root selinux tmp vmlinuz dev homelib32 media pkg run srv usr Thanks again, Jan On Mar 6, 2012, at 8:47 PM, Brad Chapman wrote: Jan; Glad to hear you got Galaxy running successfully. It sounds like everything is good to go once we sort out the disk space issue. However, when I try to use NX to get the virtual desktop going I get the message usr/bin/nxserver: line 381: echo: write error: No space left on device. Using the df -h command, I get: FilesystemSize Used Avail Use% Mounted on /dev/xvda1 20G 19G 0 100% / udev 8.4G 4.0K 8.4G 1% /dev tmpfs 3.4G 660K 3.4G 1% /run none 5.0M 0 5.0M 0% /run/lock none 8.4G 0 8.4G 0% /run/shm /dev/xvdb 404G 202M 383G 1% /mnt /dev/xvdg1700G 654G 47G 94% /mnt/galaxyIndices /dev/xvdg2 10G 1.7G 8.4G 17% /mnt/galaxyTools /dev/xvdg3200G 11G 190G 6% /mnt/galaxyData So, I guess my question as a new user is: How do I point Galaxy and CloudBioLinux to all of this unused space? By default CloudMan will put files into /mnt/galaxyData. However, as you noticed the main filesystem got filled up at some point. Could this have happened while transferring files over from S3? Are there files in your home directory that you could delete or move to /mnt/galaxyData to free up space? CloudBioLinux and CloudMan shouldn't put a large number of files in the root directory, but when the root filesystem is full it's going to be very unhappy. Once you manually clear up some room there hopefully things will run smoother. If that doesn't help let us know and we can dig into it further. Thanks, Brad ___ 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] Problem with filter tool accepting all rows
Hi all, I just debugged a problem one of our users was having filtering BLAST tabular output using the Filter tool (version 1.1.0), where it was accepting 100% of the data. He had entered the filter condition as: 'c8-c7=0.8*c23' If you know how the tool works internally (essentially evaluating the string as a Python expression where c1 etc are variables), you can guess what happened. This evaluates as a non-empty string, which Python regards as True. Therefore every row in the file was accepted. What he should have used was 'c8-c7=0.8*c23' without the quotes. I think this is an easy mistake to make, especially if copy pasting an example from documentation. Can Galaxy do anything about this? Note that a simple hack to remove leading and closing quote characters would break some valid use cases, e.g. 'gi:' + c1 == c2 + '|D1', where there happens to be a quote character at the start and end. 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/
[galaxy-dev] Welcome.html page
Hi Nate, I got a silly question for you. My galaxy is running now but I'd like to customize it. I've changed the welcome.html page but the galaxy mirror site is showing the old one. Do I need to change some other files or other configurations? Also, I add lable in tool_conf.xml file but it does not show up either. Is there another file I need to change too? Best, Huayan ___ 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] toolsectionlabel error (problem configuring toolshed hotplug?)
Greg Von Kuster greg@... writes: Hi Alex, The ToolSectionLabel element is causing the problem as it is not currently supported in the new tool shed repository installation implementation. I'll try to get a fix for this today. In the meantime, eliminating the section label from your tool config should work as a temporary workaround. I'll send you a note when I have the fix - sorry for the inconvenience. FYI - I have a fairly complex change set coming today that will introduce tool versioning for Galaxy tools, whether they are installed from a tool shed, or are available with the distribution. This will affect the tool shed as well as repositories installed from tool sheds that contain tools. This versioning feature will provide a chain of ancestor tool versions and descendant tool versions for any tool instance. It would be great if you and others that have set up local Galaxy tool sheds can test this out. I will get fixes for issues (if any exist) as fast as possible. My hope is that this will be the last major feature introduced until we get everything stabilized a bit more between the tool shed and Galaxy. Thanks! Greg Von Kuster On Feb 3, 2012, at 10:20 AM, Bossers, Alex wrote: Somehow I seem to miss something when configuring our latest up-to-date galaxy_central version to use the galaxy toolshed. When as admin I want to install a tool I can browse the given 2 repositories and select view tools. When I select install to local galaxy it drops an error on 2 tools I tested thus far: --- Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'ToolSectionLabel' object has no attribute 'name' URL: http://galaxy02:8080/galaxy/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edurepo_info_dict=293ac398f098023d041933b74935d0b4771444a6:7b22636f646f6e6c6f676f223a205b22436f646f6e2062617365642073657175656e6365206c6f676f2067656e657261746f722e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f64617669646d75727068792f636f646f6e6c6f676f222c2022323037313634353062653837225d7dincludes_tools=True Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view environ, self.app) Module paste.wsgilib:539 in intercept_output view app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view body = method( trans, **kwargs ) Module galaxy.web.framework:173 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.admin_toolshed:322 in install_repository view tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) Module galaxy.web.controllers.admin_toolshed:804 in build_tool_panel_section_select_field view options.append( ( tool_section.name, tool_section.id ) ) AttributeError: 'ToolSectionLabel' object has no attribute 'name' --- The steps I took: Updated the universe to load the extra shed_tool_conf.xml file. Set the toolpath to ../toolshedtools in shed_tool_conf.xml Gave the directory read write permissions for galaxy user:dev_group Restarted galaxy. Any additional configs to make somewhere? In the original tool_conf.xml file? Alex ___Please keep all replies on the list by using reply allin your mail client. To manage your subscriptions to thisand other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu Hi Greg, I got the exactly same error today. I can install tools from main tool shed before without any problem. I tried hg incoming and hg pull -u to update my local instance. Here is the result for hg summary (galaxy_env)galaxy@osbc-147:~/galaxy-dist$ hg summary parent: 6621:26920e20157f tip Improve language in 'Import workflow' dialog. branch: default commit: 34 modified, 93 unknown update: (current) It looks like we are using diff branch (?) How could I apply your modification? Also I am not using local tool shed either. Thanks Lisa ___ 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] toolsectionlabel error (problem configuring toolshed hotplug?)
Hi Lisa, It looks like you are current with the tip from the galaxy-dist repository. What are you attempting to do, what exactly is the error you are seeing, and what is shown in your paster log? Thanks, Greg Von Kuster On Mar 6, 2012, at 9:08 PM, Lisa wrote: Hi Greg, I got the exactly same error today. I can install tools from main tool shed before without any problem. I tried hg incoming and hg pull -u to update my local instance. Here is the result for hg summary (galaxy_env)galaxy@osbc-147:~/galaxy-dist$ hg summary parent: 6621:26920e20157f tip Improve language in 'Import workflow' dialog. branch: default commit: 34 modified, 93 unknown update: (current) It looks like we are using diff branch (?) How could I apply your modification? Also I am not using local tool shed either. Thanks Lisa ___ 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] uploads stuck in history
Hi Nate, I wasn't before, but I switched to nginx now. Non-uploading is still happening in firefox (10.0.2 on ubuntu 11.10). I can't be 100% sure that my nginx install was correct, but it's definitely serving galaxy and not complaining. Is there any way to verify uploads are processed through nginx? jorrit On 03/05/2012 08:37 PM, Nate Coraor wrote: By any chance, do you all happen to be using the nginx upload module? I am guessing not. --nate On Feb 23, 2012, at 3:16 AM, Bossers, Alex wrote: I confirm the same strange behaviour since some of the last updates on the central version. We are at the latest now. It is also with medium (10Mb+ tarballs) AND large files! Furthermore its seems to be in FireFox only They upload fine using IE8 or 9. Didn't test other browsers though. Annoying it is indeed. Alex -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Jorrit Boekel Verzonden: woensdag 22 februari 2012 10:15 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] uploads stuck in history Dear list, I have stumbled on some strange behaviour when uploading files to galaxy via the upload.py tool. At times, the upload seems to be stalled in history and is never actually performed, followed by a seemingly infinite history update (see log below). My system is Ubuntu 11.10 and runs Python 2.7.2. I find the behaviour in both my own modified galaxy install (based on galaxy-dist), and in a fresh clone from galaxy-central. I have tried to upload different files, and all seem to sometimes trigger the behaviour, but not all the time. A restart of galaxy sometimes sorts things out. Common for the debug messages is that it seems there is never a job id generated as in galaxy.tools.actions.upload_common INFO 2012-02-22 10:06:36,186 tool upload1 created job id 2. Has anyone seen similar things or can it be a problem with my system? cheers, jorrit --Debug messa: galaxy.web.framework DEBUG 2012-02-22 09:47:43,730 Error: this request returned None from get_history(): http://localhost:8080/ 127.0.0.1 - - [22/Feb/2012:09:47:43 +0200] GET / HTTP/1.1 200 - - Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] GET /root/tool_menu HTTP/1.1 200 - http://localhost:8080/; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] GET /history HTTP/1.1 200 - http://localhost:8080/; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] POST /root/user_get_usage HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 127.0.0.1 - - [22/Feb/2012:09:47:50 +0200] GET /tool_runner?tool_id=upload1 HTTP/1.1 200 - http://localhost:8080/root/tool_menu; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] POST /tool_runner/upload_async_create HTTP/1.1 200 - http://localhost:8080/; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] GET /tool_runner/upload_async_message HTTP/1.1 200 - http://localhost:8080/; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] GET /history HTTP/1.1 200 - http://localhost:8080/tool_runner/upload_async_message; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] POST /root/user_get_usage HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 127.0.0.1 - - [22/Feb/2012:09:48:13 +0200] GET /tool_runner?tool_id=upload1 HTTP/1.1 200 - http://localhost:8080/root/tool_menu; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 127.0.0.1 - - [22/Feb/2012:09:48:15 +0200] POST /root/history_item_updates HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 127.0.0.1 - - [22/Feb/2012:09:48:19 +0200] POST /root/history_item_updates HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 127.0.0.1 - - [22/Feb/2012:09:48:23 +0200] POST /root/history_item_updates HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 127.0.0.1 - - [22/Feb/2012:09:48:27 +0200] POST /root/history_item_updates HTTP/1.1 200 - http://localhost:8080/history; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 127.0.0.1 - - [22/Feb/2012:09:48:31 +0200] POST /root/history_item_updates HTTP/1.1 200 -
[galaxy-dev] How to hide an output in the history depending on its size ?
Hello everybody, My question is included in the subject of this email: Is there a way to force Galaxy to hide a specific output (of a tool) if this output is empty (or if the file does not exist in the job_working_directory repository) ? Thank you in advance, Have a nice day A. Bernard -- Aurélien Bernard IE Bioprogrammeur - CNRS Université des sciences Montpellier II Institut des Sciences de l'Evolution France ___ 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] Gal-Cloudman AMI Fails
Awesome! Thanks On Tue, Mar 6, 2012 at 11:08 PM, Dannon Baker dannonba...@me.com wrote: John, I'm still working on figuring out who created the AMI you're running across (it isn't under the main Galaxy cloud account, see the '072133624695' in the name string), but for future reference we'll always keep the recommended AMI to use listed on usegalaxy.org/cloud. At this point, it's still ami-da58aab3 (861460482541/galaxy-cloudman-2011-03-22). -Dannon On Mar 6, 2012, at 10:47 PM, John Major wrote: Hello GalFolks- I saw a new galaxy-cloudman AMI appear ( 072133624695/galaxy-cloudman-2012-02-26 ) and was interested in giving it a whirl. But when I tried to launch it got the following error: The requested instance type's architecture (x86_64) does not match the architecture in the manifest for aki-407d9529 (i386) Is this a dev-AMI? Or should I be expecting this to run? Thanks- John ___ 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] toolsectionlabel error (problem configuring toolshed hotplug?)
Hi Greg, When as admin I want to install a tool from main tool shed to local galaxy,I got this error. URL: http://128.146.132.147:1234/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu/repo_info_dict=ae427cbeabf65b952fc515302aad902c2f9f0112:7b22686d6d6572223a205b22484d4d657220746f6f6c73222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6564776172642d6b6972746f6e2f686d6d657c2022363666383236326531363836225d7dincludes_tools=True File '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 173 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 322 in install_repository tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 804 in build_tool_panel_section_select_field options.append( ( tool_section.name, tool_section.id ) ) AttributeError: 'ToolSectionLabel' object has no attribute 'name' Your help are absolutely appreciated. Liusong On Wed, Mar 7, 2012 at 9:58 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Lisa, It looks like you are current with the tip from the galaxy-dist repository. What are you attempting to do, what exactly is the error you are seeing, and what is shown in your paster log? Thanks, Greg Von Kuster On Mar 6, 2012, at 9:08 PM, Lisa wrote: Hi Greg, I got the exactly same error today. I can install tools from main tool shed before without any problem. I tried hg incoming and hg pull -u to update my local instance. Here is the result for hg summary (galaxy_env)galaxy@osbc-147:~/galaxy-dist$ hg summary parent: 6621:26920e20157f tip Improve language in 'Import workflow' dialog. branch: default commit: 34 modified, 93 unknown update: (current) It looks like we are using diff branch (?) How could I apply your modification? Also I am not using local tool shed either. Thanks Lisa ___ 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] toolsectionlabel error (problem configuring toolshed hotplug?)
Liusong, This problem has been corrected in our galaxy-central repository, but the fix must not yet be available in our galaxy-dist repository (which you are using). I believe a new release to the galaxy-dist repository will be available in the next few days if you want to wait for it. If not, change your ~/.hg/hgrc file so that the default path pulls from our galaxy-central repository, something like this. [paths] default = https://your user@bitbucket.org/galaxy/galaxy-central Sorry for the inconvenience, Greg Von Kuster On Mar 7, 2012, at 1:13 PM, Liusong Yang wrote: Hi Greg, When as admin I want to install a tool from main tool shed to local galaxy,I got this error. URL: http://128.146.132.147:1234/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu/repo_info_dict=ae427cbeabf65b952fc515302aad902c2f9f0112:7b22686d6d6572223a205b22484d4d657220746f6f6c73222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6564776172642d6b6972746f6e2f686d6d657c2022363666383236326531363836225d7dincludes_tools=True File '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 173 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 322 in install_repository tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 804 in build_tool_panel_section_select_field options.append( ( tool_section.name, tool_section.id ) ) AttributeError: 'ToolSectionLabel' object has no attribute 'name' Your help are absolutely appreciated. Liusong On Wed, Mar 7, 2012 at 9:58 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Lisa, It looks like you are current with the tip from the galaxy-dist repository. What are you attempting to do, what exactly is the error you are seeing, and what is shown in your paster log? Thanks, Greg Von Kuster On Mar 6, 2012, at 9:08 PM, Lisa wrote: Hi Greg, I got the exactly same error today. I can install tools from main tool shed before without any problem. I tried hg incoming and hg pull -u to update my local instance. Here is the result for hg summary (galaxy_env)galaxy@osbc-147:~/galaxy-dist$ hg summary parent: 6621:26920e20157f tip Improve language in 'Import workflow' dialog. branch: default commit: 34 modified, 93 unknown update: (current) It looks like we are using diff branch (?) How could I apply your modification? Also I am not using local tool shed either. Thanks Lisa ___ 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] Running SICER
Hi Vidya, SICER is currently restricted to 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' dbkeys. The issue here is that SICER itself has the needed chromosome length information hard coded. I wrote to the authors last year suggesting a simple way to avoid having to modify the SICER code to add additional genome information, and while the response was positive, I do not know if it will be acted upon. The modifications needed to be made to the SICER code are relatively straightforward, so you can run your own instance and make them if you wish, but we try to avoid running modified code on our public servers. Thanks for using Galaxy, Dan On Feb 29, 2012, at 3:40 AM, Vidya .H.K wrote: Hi, I am trying to run SICER-peak calling tool in galaxy. I am not able run the analysis, as an error message SICER is not available for the genome is frequently flagged. Can any one suggest me a soultion for the same. Regards VIDYA ___ 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] HMMER wrappers
good tip On Tue, Mar 6, 2012 at 3:28 PM, Peter Cock p.j.a.c...@googlemail.comwrote: marked as hidden in the XML ___ 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] Problem using Galaxy on the cloud
Jan; Thanks for getting back with all the detailed information. I dug into this further and understand what is happening: - tools/data_source/upload.py calls lib/galaxy/datatypes/sniff.py:stream_to_file - stream_to_file uses pythons tempfile module - tempfile defaults to using /tmp - As large files stream in the temporary space fills up, causing the issue you are seeing. The best way to work around this is to have the galaxy user on Amazon export TMPDIR to point at a temporary directory on /mnt/galaxyData instead of the root filesystem. I'm hoping that Enis or Dannon might be able to help out with the best place to set this in CloudMan to avoid the issue, I've cc'ed them in. If you want to manually fix it to get some work done, you could create a directory /mnt/galaxyData/tmp and then symlink /tmp there: ln -s /mnt/galaxyData/tmp /tmp Hope this helps and we can come up with a more permanent fix. Thanks again, Brad Thanks Brad, Sorry it has taken me so long to respond. I had a meeting sort of day. I started another instance to recreate what is happening to me in more detail. I hope this helps. I tried to color code things so you could follow everything more easily. This is what I have when I start up Galaxy through BioCloudCentral before I import any files... Get cloud support with Ubuntu Advantage Cloud Guest http://www.ubuntu.com/business/services/cloud ubuntu@ip-10-44-78-218:~$ df -h FilesystemSize Used Avail Use% Mounted on /dev/xvda1 20G 13G 6.1G 68% / udev 8.4G 4.0K 8.4G 1% /dev tmpfs 3.4G 644K 3.4G 1% /run none 5.0M 0 5.0M 0% /run/lock none 8.4G 0 8.4G 0% /run/shm /dev/xvdb 404G 201M 383G 1% /mnt After starting to import data (pasted https://s3.amazonaws.com/thunnus/BluefinAQ30_shuffled.fastq), it starts filling up immediately FilesystemSize Used Avail Use% Mounted on /dev/xvda1 20G 19G 0 100% / udev 8.4G 4.0K 8.4G 1% /dev tmpfs 3.4G 660K 3.4G 1% /run none 5.0M 0 5.0M 0% /run/lock none 8.4G 0 8.4G 0% /run/shm /dev/xvdb 404G 201M 383G 1% /mnt /dev/xvdg1700G 654G 47G 94% /mnt/galaxyIndices /dev/xvdg2 10G 1.7G 8.4G 17% /mnt/galaxyTools /dev/xvdg3500G 81M 500G 1% /mnt/galaxyData ___ 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/
