[galaxy-dev] macs error
Hi, I also have problems with macs and macs2 after update. I got this error which seems a python version issue. But I can not find this file. File cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py, line 82, in respond ImportError: No module named simplejson Any suggestions? Thanks a lot. Changyu Traceback (most recent call last): File /ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jobs/runners/__init__.py, line 152, in prepare_job job_wrapper.prepare() File /ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jobs/__init__.py, line 697, in prepare config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) File /ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/tools/__init__.py, line 2757, in build_config_files f.write( fill_template( template_text, context=param_dict ) ) File /ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py, line 82, in respond ImportError: No module named simplejson ___ 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_dependency_dir (Installed, missing tool dependencies)
Hi Greg, I figured it out. I forgot to check the box Check to uninstall or leave blank to deactivate . I need to uninstall the tool shed but I leave the box blank firstly. So, it is not uninstalled but just deactivated. Thank you so much! From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, March 11, 2014 8:47 AM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool_dependency_dir (Installed, missing tool dependencies) Hello, It's difficult to determine the cause of the problem in your environment based on the details you've provided. If you have defined your tool_dependeny_dir configuration setting in your universe_wsgi.ini to be ../tool_dependencies, then the tool shed installation process will install tool dependencies there. If you see them installed elsewhere, then that setting must have been set differently at the time they were installed. You can try setting it to the location where your tool dependencies have been installed (i.e., the Galaxy installation directory), restat your server and uninstall them. Then you can reset it to the more appropriate location (e.g., ../tool_dependencies), restart yiour server and reinstall them. If you have tool dependencies installed in multiple locations, you'll have to be careful to use a process that will eventually result in all tool dependencies installed into a single location. Greg Von Kuster On Mar 6, 2014, at 5:41 PM, Wang, Xiaofei xfw...@ku.edumailto:xfw...@ku.edu wrote: Dear there, I am trying to install some tools from toolshed on my local galaxy instance, like bwa_wrappers, package_picard_1_56_0, package_samtools_0_1_18, and sam_to_bam. For the first time, I got a warning before installing, something like this set the value of your tool_dependency_dir setting in universe_wsgi_ini and restart before installing. Then, I followed the answer on this thread (Problem installing tool_ Galaxy local) as below. I edited the universe_wsgi_ini like this: #Path to the directory in which managed tool dependencies are placed. To use # the dependency system, see the documentation at: # http://wiki.g2.bx.psu.edu/Admin/Config/http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20DependenciesToolhttp://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies%20Dependencieshttp://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies #tool_dependency_dir = None tool_dependency_dir = ../tool_dependencies Then, I restarted and installed the tool again. Galaxy create a directory named tool_dependencies at the same level in local file system hierarchy as the galaxy installation directory (same level as galaxy-dist). Some softwares such as bwa and picard are installed automatically here. But, when I checked in the admin manage installed tool shed repositories, the installation status is Installed, missing tool dependencies for the four tools I mentioned above. I do not know why this happened in my case? I tried to figure it out follow this thread The migrated BWA installed but missing dependencies. But, I did not get the idea. Could you tell me why this happen and how to fix it up? Thank you so much! -- Your setting for tool_dependency_dir should not be as you've stated: tool_dependency_dir = tool_dependencies It should be an actual path on your local file system, something like: tool_dependency_dir = ../tool_dependencies If you use the above setting, then Galaxy should create a directory named tool_dependency_dir at the same level in your local file system hierarchy as your Galaxy installation directory. I cannot guarantee that this change will solve your problem, but it will be a step in the right direction. After making this change, let us know if you still see problems. Greg Von Kuster ___ 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] Unable to remove old datasets
Greetings, Despite being an admin, I am unable to remove old datasets from our Galaxy instance. I am following the procedure detailed in: https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets 1. delete_userless_histories.sh 2. purge_histories.sh 3. purge_libraries.sh 4. purge_folders.sh 5. delete_datasets.sh -- desired to remove datasets before their outer container had been deleted 6. purge_datasets.sh None of the scripts have been changed. They all call cleanup_datasets.py with –d at 10 and –r enabled. But it does not appear to have any effect. All datasets (both those older than 10 days and those more recent) in galaxy root/database/files are still present, despite the –r setting in each script. Is there some parameter or such that needs to be set in the universe config that will allow this process to work? -- Ravi Sanka ICS – Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 -- ___ 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] Unable to remove old datasets
Have the owners of the old datasets marked them as permanently deleted? Peter On Thu, Mar 13, 2014 at 5:35 PM, Sanka, Ravi rsa...@jcvi.org wrote: Greetings, Despite being an admin, I am unable to remove old datasets from our Galaxy instance. I am following the procedure detailed in: https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets delete_userless_histories.sh purge_histories.sh purge_libraries.sh purge_folders.sh delete_datasets.sh -- desired to remove datasets before their outer container had been deleted purge_datasets.sh None of the scripts have been changed. They all call cleanup_datasets.py with -d at 10 and -r enabled. But it does not appear to have any effect. All datasets (both those older than 10 days and those more recent) in galaxy root/database/files are still present, despite the -r setting in each script. Is there some parameter or such that needs to be set in the universe config that will allow this process to work? -- Ravi Sanka ICS - Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 -- ___ 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] Empty history pane
Hello, Our site maintains a local Galaxy installation (Nov.4th distributuion). One of our usrers has lost the ability to view anything in his history pane. He is able to run tools and view the list of 'Saved Histories' in the middle pane but the History pane itself stays empty. When I impersonate him I can see his history pane. Very weird. Any insight would be much appreciated. Thanks, Liisa___ 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] Write permission for database/files
Hi All, Galaxy opens a directory under database/files when the #of data files increased. So, it goes 1,2,3 … etc. I want to give a write permission for these specific directories when they are created without changing umask in the user profile. Is there anybody who can tell me where galaxy creates these directories. Thanks in advance. Best, Alper Kucukural, PhD Bioinformatics Core, University of Massachusetts Medical School 368 Plantation St.Room AS4.2067 Worcester, MA 01605-2324 Phone: 774-312-4493 E-mail: alper.kucuku...@umassmed.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] installed bwa but there are no bwa files produced in galaxy-dist folder
Hello guys, I've got a problem with the integration of the BWA Tool in Galaxy. I installed BWA and Galaxy in a virtual box and now I want integrate BWA as a tool. For this I have to do this steps: $ sudo cp /home/ubuntu/galaxy-dist/bwa-0.7.4/bwa /usr/local/bin now bwa can be run from the command line $ bwa The Galaxy tool also requires a loc file which contains the locations of indexes for locally stored genome builds. We don't have any so we can just use the empty sample: $ cp tool-data/bwa_index.loc.sample tool-data/bwa_index.loc $ sh run.sh --reload The problem is, that in my tool-data folder doesn't exist bwa files even if bwa is installed and aso linked in the bin folder! I hope you can help me, because I don't know what to do now! Thanks and greets, Anna ___ 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] Puppet Modules
Hi Eric and Sys Admin, It's a great news ! We have already published a puppet module for a basic galaxy install and update: http://forge.puppetlabs.com/urgi/galaxy We also plan to update it for configuration files management. Eric, it could be a great initiative to merge our efforts in a single module. Any ideas ? Cheers, Olivier. Olivier Inizan Unité de Recherches en Génomique-Info (UR INRA 1164), INRA, Centre de recherche de Versailles, bat.18 RD10, route de Saint Cyr 78026 Versailles Cedex, FRANCE olivier.ini...@versailles.inra.fr Tél: +33 1 30 83 38 25 Fax: +33 1 30 83 38 99 http://urgi.versailles.inra.fr [urgi.versailles.inra.fr] Twitter: @OlivierInizan On Wed, 12 Mar 2014, Eric Rasche wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Sys Admins, I'm working on some puppet modules for managing galaxy. I'm not sure how many of you use puppet, but I figured it would be useful to the community. I'll place them on puppet forge when I'm done. So far I'm doing the following: - - enabling initial deployment (updating?) with the vcsrepo module - - managing the following files: job_conf.xml, tool_conf.xml, tool_sheds_conf.xml, universe_wsgi.ini If there's anything that you find important to be managed, or features you'd like to see, please email me and let me know! Cheers, Eric - -- Eric Rasche Programmer II Center for Phage Technology Texas AM University College Station, TX 77843 404-692-2048 e...@tamu.edu rasche.e...@yandex.ru -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.17 (GNU/Linux) iQIcBAEBAgAGBQJTIH0RAAoJEMqDXdrsMcpV2g8P/08nTnb/RLdz6WGfDbryHtBB 6Q5yr4HV2IM/idgjpLQX93jRCyahVuS1E8Sgc1x9ViGml93/ssHJZ9GIsf1PJM5/ erygrVS6njhWgefMQpoEipfTOHqxCvHhJk5xnvRc/EeUj0Lkj6YKoVpzae/6XilH Tav9/ocTNrH40HBjuFGsK7Q/IP1C+vNr/q7GPXq6Ek6dWd23qxRCYszuGgS2t3s/ i/+YmZCwHH0I25ssujGsYzsrsTfOBVBNvAj9dUmvyE+9WSLZQVw4919VKXDKNuSs 7oFBPJD2hpqSKJxf7IFChFL9WhQ4e1gykx+Z+7MhBpekUeYvwIzABxFNmQLOdl+Q 4R+mEADyAopD2enl23XkePX/FRag839zYSeEOWjvEfC8qgUWFXEJyjJ9JLqXE+Bc QOAMpmC/BMI5qIxIvKJ2ASZuqBXFxdRcGs1xaqJ2bWN+vm1fD+jzpD33KjHcegQr gf0UvhJj3aoR0Pua3vuWkWP6wPBt08F6Qab/6tQGIeQUyzZRCGyVggd4SgN+Xml5 0OB5olauA+Nr0wD+tDiCQwE+iIL/U61nU5A0yCmEMVfBem8YyKPtjuNZ7E/OZ9fy gv4uVmGDIfM+IySnWlmxqX2nYb8AODrZiQifT3kG93jh4HtNaoc4yTNeRYcFwTNi r8tJpajbO8Q0MVVj+bWn =aFP5 -END PGP SIGNATURE- ___ 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] Purging datasets as part of workflow?
Hi, Is there an automatic way to permanently delete and purge datasets that are the result of intermittent tools in a workflow? That is, how can one automatically keep only the first and the last steps of an workflow without having to manually delete all the intermittent datasets and running the purge scripts? Thanks, Sveinung Gundersen -- Sveinung Gundersen, PhD. Head engineer, ELIXIR.NO / The Genomic HyperBrowser team Department of Informatics, University of Oslo, Boks 1072 Blindern, NO-0316 OSLO, Norway Email: sveinung.gunder...@medisin.uio.no. Phone: +47 93 00 94 54 ___ 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] Purging datasets as part of workflow?
On Thu, Mar 13, 2014 at 6:30 PM, Sveinung Gundersen sveinung.gunder...@medisin.uio.no wrote: Hi, Is there an automatic way to permanently delete and purge datasets that are the result of intermittent tools in a workflow? That is, how can one automatically keep only the first and the last steps of an workflow without having to manually delete all the intermittent datasets and running the purge scripts? Thanks, Sveinung Gundersen +1 In the workflows editor we can star particular outputs to be kept, and the rest are deleted. I'd much prefer they be more aggressively permanently deleted. Alternately, when editing a workflow there (used to be) a delete dataset action - how about a permanently delete action which would be great for some big-data workflows? 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/
Re: [galaxy-dev] [CONTENT] Re: Unable to remove old datasets
I do not think so. Several individual datasets have been deleted (clicked the upper-right X on the history item box) but no History has been permanently deleted. Is there any indication in the database if target dataset or datasets were marked for permanent deletion? In the dataset table, I see fields deleted, purged, and purgable, but nothing that says permanently deleted. -- Ravi Sanka ICS Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 -- On 3/13/14 1:45 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Have the owners of the old datasets marked them as permanently deleted? Peter On Thu, Mar 13, 2014 at 5:35 PM, Sanka, Ravi rsa...@jcvi.org wrote: Greetings, Despite being an admin, I am unable to remove old datasets from our Galaxy instance. I am following the procedure detailed in: https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories %20and%20Datasets delete_userless_histories.sh purge_histories.sh purge_libraries.sh purge_folders.sh delete_datasets.sh -- desired to remove datasets before their outer container had been deleted purge_datasets.sh None of the scripts have been changed. They all call cleanup_datasets.py with -d at 10 and -r enabled. But it does not appear to have any effect. All datasets (both those older than 10 days and those more recent) in galaxy root/database/files are still present, despite the -r setting in each script. Is there some parameter or such that needs to be set in the universe config that will allow this process to work? -- Ravi Sanka ICS - Sr. Bioinformatics Engineer J. Craig Venter Institute 301-795-7743 -- ___ 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] 回复： Re: Local Galaxy web layout
Hello Shenwiyn, the position of the menu items is defined by the order of these items in the galaxy.menu.js file. What do you mean by changing the galaxy interface? Martin On Mon, Mar 10, 2014 at 8:27 AM, Weiyan Shen shenw...@gmail.com wrote: Hi Sam, Using static/scripts/galaxy.menu.js,I can add/remove/change labels of my local Galaxy successfully,but I don't know how to change the positions ,as well as the Galaxy interface.So are there any details or guidances for this help?Thank youvery much. Regards, Shenwiyn -- 原始邮件 -- *发件人:* sam guerler;aysam.guer...@gmail.com; *发送时间:* 2014年2月19日(星期三) 晚上11:06 *收件人:* shenw...@gmail.comshenw...@gmail.com; *抄送:* hrhh...@fmi.ch; galaxy-devgalaxy-dev@lists.bx.psu.edu; *主题:* Re: Re: [galaxy-dev] Local Galaxy web layout Hi Shenwiyn, Can you specify what is not working? Did you find the file? Thanks, Sam On Wed, Feb 19, 2014 at 1:42 AM, shenw...@gmail.com shenw...@gmail.comwrote: Hi Sam and Hans-Rudolf， Thank you very much for your help.It seems that the static/scripts/galaxy.menu.js fail to work in my local Galaxy.As a result,would you please show me some more details about this? Regards, Shenwiyn *From:* sam guerler aysam.guer...@gmail.com *Date:* 2014-02-18 01:20 *To:* Hans-Rudolf Hotz h...@fmi.ch *CC:* shenw...@gmail.com; galaxy-dev galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] Local Galaxy web layout Hi Shenwiyn, This has changed recently. Please take a look at: static/scripts/galaxy.menu.js Using that file, you can add/remove/change labels and their position. It is recommended to run pack_scripts.py after changing the source file. Regards, Sam On Mon, Feb 17, 2014 at 11:33 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Shenwiyn Have a look at: ~/galaxy_dist/database/compiled_templates/base_panels.mako.py Regards, Hans-Rudolf On 02/17/2014 08:04 AM, shenw...@gmail.com wrote: Galaxy developers: I want to change my local Galaxy web layout,for example,delete the top button of Visualization and Cloud or change their positions.Could anyone show me some details about this? Thank you very much. shenw...@gmail.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/ ___ 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] tool_sheds_errors
Hi Folks, I figured out the problem of tool dependencies successfully. The installation status is installed for all tool sheds. The tools are also shown on left tool panel. But, I got problems when I used the tool sheds to analyze data. For example, When I used GFF-TO-BED (fml_gff3togtf), the error is: python: can't open file '~/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/ed53dca1c6ff/fml_gff3togtf/fml_gff_converter_programs /galaxy/bed_to_gff3_converter.py': [Errno 2] No such file or directory When I checked the ~/.../galaxy folder, there are four *.xml files. Then, I copied the four files from ~/.../script folder. Now, this tool works. But, I don't think this is a right way to figure out this because I also got similar problem (I think they are similar) when I used other tool sheds as below. So, I am guessing it might be a problem with my configure file (universe_wsgi.ini). Could anybody tell me why and how to figure it out? BWA wrapper error: when I used the BWA wrapper for Illunina, An error occurred with this dataset: Could not determine BWA version Error indexing reference sequence. /bin/sh: bwa: command not found I referred to this link to try to figure out the problem http://osdir.com/ml/galaxy-development-source-control/2011-10/msg00268.html. But, I think I need more details about the mentioned bwa binaries and path. When I used the snpEff, the error is: Unable to access jarfile /Users/pablocingolani/snpEff/snpEff.jar In fact, the snpEff.jar is located at ~/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a Could you give me some ideas? Thank you so much! From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, March 11, 2014 8:47 AM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] tool_dependency_dir (Installed, missing tool dependencies) Hello, It's difficult to determine the cause of the problem in your environment based on the details you've provided. If you have defined your tool_dependeny_dir configuration setting in your universe_wsgi.ini to be ../tool_dependencies, then the tool shed installation process will install tool dependencies there. If you see them installed elsewhere, then that setting must have been set differently at the time they were installed. You can try setting it to the location where your tool dependencies have been installed (i.e., the Galaxy installation directory), restat your server and uninstall them. Then you can reset it to the more appropriate location (e.g., ../tool_dependencies), restart yiour server and reinstall them. If you have tool dependencies installed in multiple locations, you'll have to be careful to use a process that will eventually result in all tool dependencies installed into a single location. Greg Von Kuster On Mar 6, 2014, at 5:41 PM, Wang, Xiaofei xfw...@ku.edumailto:xfw...@ku.edu wrote: Dear there, I am trying to install some tools from toolshed on my local galaxy instance, like bwa_wrappers, package_picard_1_56_0, package_samtools_0_1_18, and sam_to_bam. For the first time, I got a warning before installing, something like this set the value of your tool_dependency_dir setting in universe_wsgi_ini and restart before installing. Then, I followed the answer on this thread (Problem installing tool_ Galaxy local) as below. I edited the universe_wsgi_ini like this: #Path to the directory in which managed tool dependencies are placed. To use # the dependency system, see the documentation at: # http://wiki.g2.bx.psu.edu/Admin/Config/http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20DependenciesToolhttp://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies%20Dependencieshttp://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies #tool_dependency_dir = None tool_dependency_dir = ../tool_dependencies Then, I restarted and installed the tool again. Galaxy create a directory named tool_dependencies at the same level in local file system hierarchy as the galaxy installation directory (same level as galaxy-dist). Some softwares such as bwa and picard are installed automatically here. But, when I checked in the admin manage installed tool shed repositories, the installation status is Installed, missing tool dependencies for the four tools I mentioned above. I do not know why this happened in my case? I tried to figure it out follow this thread The migrated BWA installed but missing dependencies. But, I did not get the idea. Could you tell me why this happen and how to fix it up? Thank you so much! -- Your setting for tool_dependency_dir should not be as you've stated: tool_dependency_dir = tool_dependencies It should be an actual path on your local file system, something like: tool_dependency_dir = ../tool_dependencies If you use the above setting,
Re: [galaxy-dev] tool_sheds_errors
On Thu, Mar 13, 2014 at 5:32 PM, Wang, Xiaofei xfw...@ku.edu wrote: Hi Folks, I figured out the problem of tool dependencies successfully. The installation status is installed for all tool sheds. The tools are also shown on left tool panel. But, I got problems when I used the tool sheds to analyze data. For example, When I used GFF-TO-BED (fml_gff3togtf), the error is: python: can't open file '~/softwares/shed_tools/ toolshed.g2.bx.psu.edu/repos/vipints/fml_gff3togtf/ed53dca1c6ff/fml_gff3togtf/fml_gff_converter_programs /galaxy/bed_to_gff3_converter.py': [Errno 2] No such file or directory When I checked the ~/.../galaxy folder, there are four *.xml files. Then, I copied the four files from ~/.../script folder. Now, this tool works. But, I don't think this is a right way to figure out this because I also got similar problem (I think they are similar) when I used other tool sheds as below. So, I am guessing it might be a problem with my configure file (universe_wsgi.ini). Could anybody tell me why and how to figure it out? Hello, I am responsible for answering the first part of your error message, It is my mistake that I have to place the right path in the tool configuration file (xml). This will be fixed soon and update the repository to a new version. regards, Vipin | Rätsch Lab BWA wrapper error: when I used the BWA wrapper for Illunina, An error occurred with this dataset: Could not determine BWA version Error indexing reference sequence. /bin/sh: bwa: command not found I referred to this link to try to figure out the problem http://osdir.com/ml/galaxy-development-source-control/2011-10/msg00268.html. But, I think I need more details about the mentioned bwa binaries and path. When I used the snpEff, the error is: Unable to access jarfile /Users/pablocingolani/snpEff/snpEff.jar In fact, the snpEff.jar is located at ~/softwares/shed_tools/ toolshed.g2.bx.psu.edu/repos/pcingola/snpeff/c052639fa666/snpeff/snpEff_2_1a/snpEff_2_1a Could you give me some ideas? Thank you so much! ___ 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] Empty history pane
If it's possible, can you check (or ask the user to check) if there are any javascript errors if you open the browser console when experiencing this failure? On Thu, Mar 13, 2014 at 2:07 PM, Liisa Koski liisa.ko...@basf.com wrote: Hello, Our site maintains a local Galaxy installation (Nov.4th distributuion). One of our usrers has lost the ability to view anything in his history pane. He is able to run tools and view the list of 'Saved Histories' in the middle pane but the History pane itself stays empty. When I impersonate him I can see his history pane. Very weird. Any insight would be much appreciated. Thanks, Liisa ___ 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/
