Re: [galaxy-dev] DESeq for Galaxy
Hi All, I installed the toolshed htseq_bams_to_count_matrix repository , i gave the gene model gtf file(ex: tss.gtf file) Gene model (GFF) file to count reads over from your current history: in this section and all bam files. it gives error as empty format: tabular, database: hg19 Traceback (most recent call last): File /data/galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix/htseq_bams_to_count_matrix/htseqsams2mx.py, line 45, in module import HTSeq.scripts.count as htcount Thanks On Wed, Aug 21, 2013 at 10:44 AM, Mahtab Mirmomeni m.mirmom...@student.unimelb.edu.au wrote: You can use htseq_bams_to_count_matrix repository by fubar in the test toolshed. On Wed, Aug 21, 2013 at 2:37 PM, Sridhar Srinivasan sridhar2bioi...@gmail.com wrote: Hi All, Thanks for the suggestions. I installed the Toolshed ( Differential_Count (version 0.21) ). It asks for the input matrix - rows are contigs, columns are counts for each sample. Any idea on how to generate this matrix file?? Thanks On Tue, Aug 20, 2013 at 12:53 PM, Mahtab Mirmomeni m.mirmom...@student.unimelb.edu.au wrote: Hi Sridhar, I'm using differential_count_model repository by fubar in the test toolshed which has both EdgeR and Deseq2 and it's working for me. Thanks Mahtab On Tue, Aug 20, 2013 at 5:03 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Sridhar, we are developing a DESeq2 tool at the moment, if you want to join get in touch with me. Its developed here: https://github.com/bgruening/galaxytools/tree/master/deseq2 I will upload our latest progress during the day. Cheers, Bjoern Dear users, Could anybody suggest the valid DESeq toolshed for RNA sequencing??? Thanks Sridhar ___ 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] DESeq for Galaxy
Sridhar, The error message you provide suggests that the HTSeq python module is not available when Galaxy tries to run the tool. Please confirm that you installed that tool through the admin interface from the test toolshed and that the admin interface for toolshed installed tools shows the installed repository in your Galaxy instance has the htseq dependency successfully installed like the end of the page below : - Repository Actions Installed tool shed repository 'htseq_bams_to_count_matrix' Tool shed:testtoolshed.g2.bx.psu.edu Name:htseq_bams_to_count_matrix Description: Revision:f69b55c71ae5 Owner:fubar Location:/mnt/galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix Deleted:False Dependencies of this repository Installed repository dependencies NameRevisionOwnerInstallation statuspackage_numpy_1_7http://115.146.84.239/admin_toolshed/manage_repository?id=148934b1ed5706b5 af9633757cf0blankenbergInstalledpackage_pysam_0_7_5http://115.146.84.239/admin_toolshed/manage_repository?id=96c0d701aac155a0 a4e35f23093ffubarInstalledpackage_freetype_2_4http://115.146.84.239/admin_toolshed/manage_repository?id=dee0124e4d3ab063 4e54e357ac25bgrueningInstalledpackage_matplotlib_litehttp://115.146.84.239/admin_toolshed/manage_repository?id=c32939704028ccc3 8df6bbf48c3afubarInstalled Installed tool dependencies* - click the name to browse the dependency installation directory* NameVersionTypeInstallation statusfreetypehttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=148934b1ed5706b5 2.4.11packagematplotliblitehttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=dee0124e4d3ab063 1.2.1packagenumpyhttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=94e61e06dbd29e52 1.7.1packagepysamhttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=c32939704028ccc3 0.7.5packagehtseqhttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=96c0d701aac155a0 0.5.4p3package On Wed, Aug 21, 2013 at 4:05 PM, Sridhar Srinivasan sridhar2bioi...@gmail.com wrote: Hi All, I installed the toolshed htseq_bams_to_count_matrix repository , i gave the gene model gtf file(ex: tss.gtf file) Gene model (GFF) file to count reads over from your current history: in this section and all bam files. it gives error as empty format: tabular, database: hg19 Traceback (most recent call last): File /data/galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix/htseq_bams_to_count_matrix/htseqsams2mx.py, line 45, in module import HTSeq.scripts.count as htcount Thanks On Wed, Aug 21, 2013 at 10:44 AM, Mahtab Mirmomeni m.mirmom...@student.unimelb.edu.au wrote: You can use htseq_bams_to_count_matrix repository by fubar in the test toolshed. On Wed, Aug 21, 2013 at 2:37 PM, Sridhar Srinivasan sridhar2bioi...@gmail.com wrote: Hi All, Thanks for the suggestions. I installed the Toolshed ( Differential_Count (version 0.21) ). It asks for the input matrix - rows are contigs, columns are counts for each sample. Any idea on how to generate this matrix file?? Thanks On Tue, Aug 20, 2013 at 12:53 PM, Mahtab Mirmomeni m.mirmom...@student.unimelb.edu.au wrote: Hi Sridhar, I'm using differential_count_model repository by fubar in the test toolshed which has both EdgeR and Deseq2 and it's working for me. Thanks Mahtab On Tue, Aug 20, 2013 at 5:03 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Sridhar, we are developing a DESeq2 tool at the moment, if you want to join get in touch with me. Its developed here: https://github.com/bgruening/galaxytools/tree/master/deseq2 I will upload our latest progress during the day. Cheers, Bjoern Dear users, Could anybody suggest the valid DESeq toolshed for RNA sequencing??? Thanks Sridhar ___ 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
Re: [galaxy-dev] Biopython dependency on matplotlib
Hi Greg, that bug was fixed I think! Thanks, Bjoern Hello Peter and Bjoern, Can you clarify the tool shed bug to which you are referring with the statement: Still that TS bug needs to be fixed I think before the next stable release. I'll take a look as soon as I get clarification. Thanks! On Aug 12, 2013, at 11:31 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 16:26 +0100, Peter Cock wrote: On Mon, Aug 12, 2013 at 4:19 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Peter, Hi Bjoern ( Greg), RE: http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61 I'm wondering why in the Biopython package dependencies matplotlib is currently marked as prior installation required? i.e. package name=numpy version=1.7.1 repository changeset_revision=c75482be1d3a name=package_numpy_1_7 owner=iuc prior_installation_required=True toolshed=http://toolshed.g2.bx.psu.edu; / /package package name=matplotlib version=1.2.1 repository changeset_revision=9d164359606b name=package_matplotlib_1_2 owner=iuc prior_installation_required=True toolshed=http://toolshed.g2.bx.psu.edu; / /package Biopython needs NumPy pre-installed because Biopython has some C code which must be compiled against the NumPy headers. However, all the other Biopython Python dependencies are soft in the sense that the 3rd Python libraries just need to be available at run time (e.g. via $PYTHONPATH). Have I misunderstood the function of the Galaxy Tool Shed term prior_installation_required, or can we omit this and have it default to prior_installation_required=False for matplotlib (and other similar cases)? No that is correct, in that case we can omit the prior_installation_required=True flag for matplotlib. OK, good. Thanks for clarifying that. -- More generally, if that is the case, I would probably opt to make the Biopython package only depend on numpy, and leave declaring soft dependencies (or recommended packages in the terminology of some Linux distributions) down to the package/tool calling Biopython. For instance, my sequence manipulation tools which use just core Biopython can depend on just the main Biopython package. Another tool which uses Biopython and matplotlib to produce a graph would depend on both Biopython and the matplotlib packages. Another tool which uses Biopython's GenomeDiagram to produce a figure would depend on both Biopython and the (not yet written) ReportLab packages. I though a full fledged biopython would be better than a trimmed version. But your are the biopython expert. If you think the developer should take care of it, than I will eliminate the dependencies. My concern was, that if you use biopython and plot your genome you normally do not know that you need reportlab (because it come with biopython on most of the distributions). Actually in my github account I have the reportlab dependency included (but commented out). I think its up to you. I do not mind. It rather depends on how the Biopython you are using was installed, and if the installation route took care of these soft/recommended dependencies or not. My inclination is to leave this to the Galaxy tool author to make explicit when packaging their tool. If they forget, then the script calling Biopython should fail with an indicative ImportError or in some cases are more precise error about what exactly is missing. i.e. Lets have NumPy as the only dependency in the Galaxy package for Biopython. This has practical advantages like right now were a problem with the 'soft' dependency on matplotlib is blocking me from installing the Biopython package. Ok, I removed the soft dependencies and uploaded it again. Still that TS bug needs to be fixed I think before the next stable release. Regards, 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/ ___ 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] Action type 'template_command' on galaxy-dist?
Hi, also fixed, yes! Good start in a day, to write positive mails :) Bjoern Hello Bjoern, I believe this issue was corrected in changeset 10412:29ab5a6d75a7, which was committed to the stable branch and is running on both tool sheds. At least I am unable to reproduce the behavior you describe using 3 similar repositories in my local tool shed. Please let me know if you still encounter this issue. Thanks, Greg Von Kuster On Aug 13, 2013, at 12:49 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Dave, for us I think everything is fixed. But we had a bad bug in the 'single revision' implementation of the new 'Tool dependency definition' type. We had something like that: A (tool dependency definition) - B (tool) - C (workflow) We changed A (that was numpy) and thought it would be ok to install the workflow afterwards. Because, if A has only one revision associated than it should be working. But B had a reference to the old revision of A (in the XML file) which causes an error. Or the TS wanted to install two different versions of A. Our fix was to upload B again and than C, to renew the revision tags. That was more a hack than a solution :) I do not know if that still occurs with the latest version of galaxy, we tested it with the old stable version. Thanks, Bjoern Peter, Björn, The August Galaxy release is out, and the template_command is now in the stable repository and branch. Regarding matplotlib and numpy, I currently only see matplotlib depending on the 74c21f9bdc39 revision of numpy. Is this still an issue, or has it been resolved? --Dave B. On 8/12/13 11:36:00.000, Bjoern Gruening wrote: On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote: On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote: Maybe I should retitle this thread... On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Thank you - installing the NumPy package now works for me, http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 I'm moving on to something odd with matplotlib instead... Peter There are currently two revisions to the main Tool Shed package for numpy, http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 Rev 0: c75482be1d3a - needs not-yet-released features Rev 1: 74c21f9bdc39 - simplified I'm trying to install a package dependent on this via matplotlib - but installing the matplotlib package fails: http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_2 This is something odd, why does it think it needs to install the rev 0 c75482be1d3a version of package_numpy_1_7? See screenshot, except here: Repository dependencies - installation of these additional repositories is required Name RevisionOwner Installation status package_freetype_2_4 8761091302c4iuc Installed package_numpy_1_7 74c21f9bdc39iuc Installed package_numpy_1_7 c75482be1d3aiuc Uninstalled Yes, the matplotlib tool_dependencies.xml does list the original revision: package name=numpy version=1.7.1 repository changeset_revision=c75482be1d3a name=package_numpy_1_7 owner=iuc prior_installation_required=True toolshed=http://toolshed.g2.bx.psu.edu; / /package package name=freetype version=2.4.11 repository changeset_revision=8761091302c4 name=package_freetype_2_4 owner=iuc prior_installation_required=True toolshed=http://toolshed.g2.bx.psu.edu; / /package But I thought as a Tool dependency definition only the tip revision is ever used? That is also what I understood, regardless of the revision there is only one install able revision. But I guess the TS is generating the path to numpy from the package tag and that points to an old non existing version. Hmm. Something for Greg to look at then. After attempting to install this, the status is Installed, missing repository dependencies and this oddity about wanting two revisions of NumPy persists. The actual failure appears to be in compiling matplotlib itself... I don't think it is finding the NumPy installation. Is it possible to view the INSTALLATION.log from within the Galaxy Admin web interface? Yes you should see all installed files/folder and the INSTALLATION.log in your web browser. Can you give me a little more information on how to see this from within Galaxy? 1. Open my Galaxy instance and log in, 2. Click on Admin from top menu 3. Click on Manage installed tool shed repositories on left 4. Select repository of interest 5. Click, Manage tool dependencies 6. Choose one of the dependencies There should be a tree like structure to navigate to your INSTALLATION.log file besides your env.sh file. At this
Re: [galaxy-dev] DESeq for Galaxy
Hi Ross, i Installed through admin interface . for pysam and freetype it showed new... and rest installed.. Thanks On Wed, Aug 21, 2013 at 11:47 AM, Ross ross.laza...@gmail.com wrote: Sridhar, The error message you provide suggests that the HTSeq python module is not available when Galaxy tries to run the tool. Please confirm that you installed that tool through the admin interface from the test toolshed and that the admin interface for toolshed installed tools shows the installed repository in your Galaxy instance has the htseq dependency successfully installed like the end of the page below : - Repository Actions Installed tool shed repository 'htseq_bams_to_count_matrix' Tool shed:testtoolshed.g2.bx.psu.edu Name:htseq_bams_to_count_matrix Description: Revision:f69b55c71ae5 Owner:fubar Location:/mnt/galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix Deleted:False Dependencies of this repository Installed repository dependencies NameRevisionOwner Installation statuspackage_numpy_1_7http://115.146.84.239/admin_toolshed/manage_repository?id=148934b1ed5706b5 af9633757cf0blankenbergInstalledpackage_pysam_0_7_5http://115.146.84.239/admin_toolshed/manage_repository?id=96c0d701aac155a0 a4e35f23093ffubarInstalledpackage_freetype_2_4http://115.146.84.239/admin_toolshed/manage_repository?id=dee0124e4d3ab063 4e54e357ac25bgrueningInstalledpackage_matplotlib_litehttp://115.146.84.239/admin_toolshed/manage_repository?id=c32939704028ccc3 8df6bbf48c3afubarInstalled Installed tool dependencies* - click the name to browse the dependency installation directory* NameVersionTypeInstallation statusfreetypehttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=148934b1ed5706b5 2.4.11packagematplotliblitehttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=dee0124e4d3ab063 1.2.1packagenumpyhttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=94e61e06dbd29e52 1.7.1packagepysamhttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=c32939704028ccc3 0.7.5packagehtseqhttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=96c0d701aac155a0 0.5.4p3package On Wed, Aug 21, 2013 at 4:05 PM, Sridhar Srinivasan sridhar2bioi...@gmail.com wrote: Hi All, I installed the toolshed htseq_bams_to_count_matrix repository , i gave the gene model gtf file(ex: tss.gtf file) Gene model (GFF) file to count reads over from your current history: in this section and all bam files. it gives error as empty format: tabular, database: hg19 Traceback (most recent call last): File /data/galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix/htseq_bams_to_count_matrix/htseqsams2mx.py, line 45, in module import HTSeq.scripts.count as htcount Thanks On Wed, Aug 21, 2013 at 10:44 AM, Mahtab Mirmomeni m.mirmom...@student.unimelb.edu.au wrote: You can use htseq_bams_to_count_matrix repository by fubar in the test toolshed. On Wed, Aug 21, 2013 at 2:37 PM, Sridhar Srinivasan sridhar2bioi...@gmail.com wrote: Hi All, Thanks for the suggestions. I installed the Toolshed ( Differential_Count (version 0.21) ). It asks for the input matrix - rows are contigs, columns are counts for each sample. Any idea on how to generate this matrix file?? Thanks On Tue, Aug 20, 2013 at 12:53 PM, Mahtab Mirmomeni m.mirmom...@student.unimelb.edu.au wrote: Hi Sridhar, I'm using differential_count_model repository by fubar in the test toolshed which has both EdgeR and Deseq2 and it's working for me. Thanks Mahtab On Tue, Aug 20, 2013 at 5:03 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Sridhar, we are developing a DESeq2 tool at the moment, if you want to join get in touch with me. Its developed here: https://github.com/bgruening/galaxytools/tree/master/deseq2 I will upload our latest progress during the day. Cheers, Bjoern Dear users, Could anybody suggest the valid DESeq toolshed for RNA sequencing??? Thanks Sridhar ___ 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
Re: [galaxy-dev] Tool Shed upload/migration revision checking bug?
Morning Greg, seems to be also fixed in latest release. Will reopen the thread if I encounter it again. Thanks a lot, Bjoern Hello Peter and Bjoern, I believe this issue was handled in the August Galaxy release, but the main tool shed had not yet been upgraded to that release when you were seeing this behavior. Unless I misunderstand the steps necessary to reproduce the behavior, I am not able to do so. Here is what I've tried in my local tool shed: 1) Create a repopsitory named package_atlas_3_10 owned by username test with repository type tool_dependency_definition. 2 Populate the package_atlas_3_10 repository with a tool_dependencies.xml file that looks like this: tool_dependency package name=atlas version=3.10.1 install version=1.0 actions !-- first action is always downloading -- action type=download_by_urlfile:///var/chemicaltoolbox/atlas.tar/action action type=move_directory_files source_directory./source_directory destination_directory$INSTALL_DIR/destination_directory /action action type=set_environment environment_variable name=ATLAS_LIB_DIR action=set_to$INSTALL_DIR/lib/environment_variable environment_variable name=ATLAS_INCLUDE_DIR action=set_to$INSTALL_DIR/include/environment_variable /action /actions /install readmeATLAS_LIB_DIR and ATLAS_INCLUDE_DIR will be set (including libatlas.a). During ATLAS library compilation, ATLAS performs code efficiency checks. These checks can only provide optimal results, if frequency scaling is disabled on the CPU, and no other load-intense processes are running. Ideally, you should compile on an empty cluster node with CPU frequency scaling disabled (see cpufreq-selector or cpufreq-set). /readme /package /tool_dependency 3) Create a repository named package_confab_1_0_1owned by test with repository type tool_dependency_definition. 4) Attempt to upload a tool_dependencies.xml file to package_confab_1_0_1that looks like this - notice that the owner hello is invalid since the required package_atlas_3_10 repository is actually owned by test. tool_dependency package name=atlas version=3.10.1 repository name=package_atlas_3_10 owner=hello prior_installation_required=True / /package package name=confab version=1.0.1 install version=1.0 actions action type=download_by_urlhttp://confab.googlecode.com/files/Confab-1.0.1.tar.gz/action !-- populate the environment variables from the dependent repos -- action type=set_environment_for_install repository name=package_atlas_3_10 owner=hello package name=atlas version=3.10.1 / /repository /action action type=shell_commandcmake . -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DEIGEN2_INCLUDE_DIR= $EIGEN_SOURCE_PATH//action action type=shell_commandmake/action action type=shell_commandmake install/action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readmeCompiling Confab requires g++, CMake 2.4+ and Eigen version 2 (libeigen2-dev). Optional but required for a few features is libxml2 and zlib./readme /package /tool_dependency The above upload raises a server error, and the following stack trace is displayed in the borwser. Internal Server Error Galaxy was unable to sucessfully complete your request URL: http://localhost:9009/upload/upload?repository_id=cd0d8ada19d98f27 Module galaxy.web.framework.middleware.error:149 in __call__ app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ environ, self.app) Module paste.wsgilib:543 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request body = method( trans, **kwargs ) Module galaxy.web.framework:98 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.webapps.tool_shed.controllers.upload:147 in upload altered, root_elem = commit_util.handle_tool_dependencies_definition( trans, uploaded_file_name ) Module tool_shed.util.commit_util:321 in
Re: [galaxy-dev] DESeq for Galaxy
Sridhar, Kindly try rerunning the failed job to confirm that it still fails now that the tool installation should have well and truly finished - it does take a while. If it still fails the same way, please send me a copy of the installation log for the htseq dependency found in: [your tool_dependency_directory]/htseq/0.5.4p3/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/INSTALLATION.log On Wed, Aug 21, 2013 at 4:38 PM, Sridhar Srinivasan sridhar2bioi...@gmail.com wrote: Hi Ross, i Installed through admin interface . for pysam and freetype it showed new... and rest installed.. Thanks On Wed, Aug 21, 2013 at 11:47 AM, Ross ross.laza...@gmail.com wrote: Sridhar, The error message you provide suggests that the HTSeq python module is not available when Galaxy tries to run the tool. Please confirm that you installed that tool through the admin interface from the test toolshed and that the admin interface for toolshed installed tools shows the installed repository in your Galaxy instance has the htseq dependency successfully installed like the end of the page below : - Repository Actions Installed tool shed repository 'htseq_bams_to_count_matrix' Tool shed:testtoolshed.g2.bx.psu.edu Name:htseq_bams_to_count_matrix Description: Revision:f69b55c71ae5 Owner:fubar Location:/mnt/galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix Deleted:False Dependencies of this repository Installed repository dependencies NameRevisionOwner Installation statuspackage_numpy_1_7http://115.146.84.239/admin_toolshed/manage_repository?id=148934b1ed5706b5 af9633757cf0blankenbergInstalledpackage_pysam_0_7_5http://115.146.84.239/admin_toolshed/manage_repository?id=96c0d701aac155a0 a4e35f23093ffubarInstalledpackage_freetype_2_4http://115.146.84.239/admin_toolshed/manage_repository?id=dee0124e4d3ab063 4e54e357ac25bgrueningInstalledpackage_matplotlib_litehttp://115.146.84.239/admin_toolshed/manage_repository?id=c32939704028ccc3 8df6bbf48c3afubarInstalled Installed tool dependencies* - click the name to browse the dependency installation directory* NameVersionTypeInstallation statusfreetypehttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=148934b1ed5706b5 2.4.11packagematplotliblitehttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=dee0124e4d3ab063 1.2.1packagenumpyhttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=94e61e06dbd29e52 1.7.1packagepysamhttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=c32939704028ccc3 0.7.5packagehtseqhttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=96c0d701aac155a0 0.5.4p3package On Wed, Aug 21, 2013 at 4:05 PM, Sridhar Srinivasan sridhar2bioi...@gmail.com wrote: Hi All, I installed the toolshed htseq_bams_to_count_matrix repository , i gave the gene model gtf file(ex: tss.gtf file) Gene model (GFF) file to count reads over from your current history: in this section and all bam files. it gives error as empty format: tabular, database: hg19 Traceback (most recent call last): File /data/galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix/htseq_bams_to_count_matrix/htseqsams2mx.py, line 45, in module import HTSeq.scripts.count as htcount Thanks On Wed, Aug 21, 2013 at 10:44 AM, Mahtab Mirmomeni m.mirmom...@student.unimelb.edu.au wrote: You can use htseq_bams_to_count_matrix repository by fubar in the test toolshed. On Wed, Aug 21, 2013 at 2:37 PM, Sridhar Srinivasan sridhar2bioi...@gmail.com wrote: Hi All, Thanks for the suggestions. I installed the Toolshed ( Differential_Count (version 0.21) ). It asks for the input matrix - rows are contigs, columns are counts for each sample. Any idea on how to generate this matrix file?? Thanks On Tue, Aug 20, 2013 at 12:53 PM, Mahtab Mirmomeni m.mirmom...@student.unimelb.edu.au wrote: Hi Sridhar, I'm using differential_count_model repository by fubar in the test toolshed which has both EdgeR and Deseq2 and it's working for me. Thanks Mahtab On Tue, Aug 20, 2013 at 5:03 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Sridhar, we are developing a DESeq2 tool at the moment, if you want to join get in touch with me. Its developed here: https://github.com/bgruening/galaxytools/tree/master/deseq2 I will upload our latest progress during the day. Cheers, Bjoern Dear users, Could anybody suggest the valid DESeq toolshed for RNA sequencing??? Thanks Sridhar ___ Please keep all replies on the list by using reply all in your mail client. To manage your
Re: [galaxy-dev] One installable revision is not working for orphan-tool-dependencies - Was: Action type 'template_command' on galaxy-dist?
Hi Greg, a first test seems to work as expected for me, will test again with the whole CTB. If I understood your commit you are searching now for the next valid 'installable' revision, aka a revision with metadata. Does it make sense to have revisions for Tool dependency definition. Only one valid revision should be possible, per definition or? So we could skip that revision the system entirely for Tool dependency definition, or? Thanks for the fast fix! Bjoern Hello Bjoern, This issue should be resolved in change set 10412:29ab5a6d75a7, whcih is currently running on both tool sheds. No changes should be necessary to any of your current dependency definition files. This changeset was committed to the stable branch, so production Galaxy environments can be safely updated as well. Of course, tracking central in Galaxy environments will get the fix as usual. Thanks very much for reporting this! Greg Von Kuster On Aug 15, 2013, at 9:01 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Dave, the bug is unfortunately still present in the latest Galaxy version. If you try to install http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 you will end up with an error, because numpy is not found. That error appears because scipy was uploaded and afterwards numpy was changed. The consequence is that scipy references on old (not installable) version of numpy and crashes. I would expect that scipy is always looking for the latest version of numpy regardless of what is specified in the numpy XML file. Is that assumption wrong? That would raise the question if revisions are still needed for orphan-tool-dependencies or 'Tool dependency definition'. Is that bug easy to fix? Or do I need to upload all my repositories in the right order again? That would be the consequence, because otherwise I do not get the revision tag updated. Thanks! Bjoern Peter, Björn, The August Galaxy release is out, and the template_command is now in the stable repository and branch. Regarding matplotlib and numpy, I currently only see matplotlib depending on the 74c21f9bdc39 revision of numpy. Is this still an issue, or has it been resolved? --Dave B. On 8/12/13 11:36:00.000, Bjoern Gruening wrote: On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote: On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote: Maybe I should retitle this thread... On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Thank you - installing the NumPy package now works for me, http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 I'm moving on to something odd with matplotlib instead... Peter There are currently two revisions to the main Tool Shed package for numpy, http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 Rev 0: c75482be1d3a - needs not-yet-released features Rev 1: 74c21f9bdc39 - simplified I'm trying to install a package dependent on this via matplotlib - but installing the matplotlib package fails: http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_2 This is something odd, why does it think it needs to install the rev 0 c75482be1d3a version of package_numpy_1_7? See screenshot, except here: Repository dependencies - installation of these additional repositories is required Name RevisionOwner Installation status package_freetype_2_4 8761091302c4iuc Installed package_numpy_1_7 74c21f9bdc39iuc Installed package_numpy_1_7 c75482be1d3aiuc Uninstalled Yes, the matplotlib tool_dependencies.xml does list the original revision: package name=numpy version=1.7.1 repository changeset_revision=c75482be1d3a name=package_numpy_1_7 owner=iuc prior_installation_required=True toolshed=http://toolshed.g2.bx.psu.edu; / /package package name=freetype version=2.4.11 repository changeset_revision=8761091302c4 name=package_freetype_2_4 owner=iuc prior_installation_required=True toolshed=http://toolshed.g2.bx.psu.edu; / /package But I thought as a Tool dependency definition only the tip revision is ever used? That is also what I understood, regardless of the revision there is only one install able revision. But I guess the TS is generating the path to numpy from the package tag and that points to an old non existing version. Hmm. Something for Greg to look at then. After attempting to install this, the status is Installed, missing repository dependencies and this oddity about wanting two revisions of NumPy persists. The actual failure appears to be in compiling matplotlib itself... I don't think it is finding the NumPy installation. Is it possible to view the INSTALLATION.log from within the Galaxy Admin
Re: [galaxy-dev] Passing user_email to a data source
Hi Anthony I doubt it will solve your problem, but just as a general hint: you can use the email address for filtering. In our case, the user gets a different list of groups he/she can select from, eg: param name=group type=select label=Select your group options from_file=access_to_miseq column name=email index=0/ column name=value index=1/ filter type=static_value name=external_source_filter value=$__user_email__ column=0/ /options /param and our file '~/tool-data/access_to_miseq' looks like: 1...@fmi.ch gbioinfo 1...@fmi.ch gfungen 1...@fmi.ch gmeier # # a...@fmi.ch gfungen # # 1...@fmi.ch gfungen 1...@fmi.ch gmeier Regards, Hans-Rudolf On 08/20/2013 05:51 PM, Anthony Bretaudeau wrote: Hello, I'm trying to add a new data source to my Galaxy instance, using synchronous data depositing. The data source needs to know the email address of the user who tries to import data to the Galaxy server. I would have like to write something like that: inputs action=https://example.com/my/data/source; check_values=false method=get displayBrowse the XX data source $GALAXY_URL/display param name=user_email type=hidden value=$__user_email__ / /inputs Then Galaxy would have generated this url: https://example.com/my/data/source?GALAXY_URL=httpuser_email=t...@example.com But this doesn't work, because the $__user_email__ seems to be available only in command tag. I end up with this url which is useless: https://example.com/my/data/source?GALAXY_URL=httpuser_email=$__user_email__ Is there any way to do what I need to do? It would be great if variables were available in param tags too. Otherwise, maybe I could write a custom tool type to do this. Is there any guideline for this? I have seen someone talking about that a few months ago, but with no answer: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-September/011258.html Thanks for your help Regards Anthony Bretaudeau ___ 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] Galaxy Release Cycle Length
Hi Dave two months is a good time between releases. Much more important than the release cycle length is fixing identified bugs on the release branch as well. Regards, Hans-Rudolf On 08/20/2013 08:36 PM, Dave Clements wrote: Hello all, At one of the GCC2013 Birds of a Feather sessions http://wiki.galaxyproject.org/Events/GCC2013/BoF/PublicGalaxyServers the group was very clear that they would like to see less frequent releases of Galaxy. We're currently aiming to do a release every 2 months and have been pretty successful at making that target. In the past, we have tried doing releases more often and less often. Is there a sweet spot for the time between releases? Please reply to the group. We are interested in a discussion. Thanks, Dave C -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] DESeq for Galaxy
Hi Ross, I tried installing again it shows no item.. Also i couldn't find any .log file or the ( /htseq/0.5.4p3/fubar/htseq_bams_to_count_matrix) in the tool dependency directory. Thanks On Wed, Aug 21, 2013 at 12:13 PM, Ross ross.laza...@gmail.com wrote: Sridhar, Kindly try rerunning the failed job to confirm that it still fails now that the tool installation should have well and truly finished - it does take a while. If it still fails the same way, please send me a copy of the installation log for the htseq dependency found in: [your tool_dependency_directory]/htseq/0.5.4p3/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/INSTALLATION.log On Wed, Aug 21, 2013 at 4:38 PM, Sridhar Srinivasan sridhar2bioi...@gmail.com wrote: Hi Ross, i Installed through admin interface . for pysam and freetype it showed new... and rest installed.. Thanks On Wed, Aug 21, 2013 at 11:47 AM, Ross ross.laza...@gmail.com wrote: Sridhar, The error message you provide suggests that the HTSeq python module is not available when Galaxy tries to run the tool. Please confirm that you installed that tool through the admin interface from the test toolshed and that the admin interface for toolshed installed tools shows the installed repository in your Galaxy instance has the htseq dependency successfully installed like the end of the page below : - Repository Actions Installed tool shed repository 'htseq_bams_to_count_matrix' Tool shed:testtoolshed.g2.bx.psu.edu Name:htseq_bams_to_count_matrix Description: Revision:f69b55c71ae5 Owner:fubar Location:/mnt/galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix Deleted:False Dependencies of this repository Installed repository dependencies NameRevisionOwner Installation statuspackage_numpy_1_7http://115.146.84.239/admin_toolshed/manage_repository?id=148934b1ed5706b5 af9633757cf0blankenbergInstalledpackage_pysam_0_7_5http://115.146.84.239/admin_toolshed/manage_repository?id=96c0d701aac155a0 a4e35f23093ffubarInstalledpackage_freetype_2_4http://115.146.84.239/admin_toolshed/manage_repository?id=dee0124e4d3ab063 4e54e357ac25bgrueningInstalledpackage_matplotlib_litehttp://115.146.84.239/admin_toolshed/manage_repository?id=c32939704028ccc3 8df6bbf48c3afubarInstalled Installed tool dependencies* - click the name to browse the dependency installation directory* NameVersionTypeInstallation statusfreetypehttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=148934b1ed5706b5 2.4.11packagematplotliblitehttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=dee0124e4d3ab063 1.2.1packagenumpyhttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=94e61e06dbd29e52 1.7.1packagepysamhttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=c32939704028ccc3 0.7.5packagehtseqhttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=96c0d701aac155a0 0.5.4p3package On Wed, Aug 21, 2013 at 4:05 PM, Sridhar Srinivasan sridhar2bioi...@gmail.com wrote: Hi All, I installed the toolshed htseq_bams_to_count_matrix repository , i gave the gene model gtf file(ex: tss.gtf file) Gene model (GFF) file to count reads over from your current history: in this section and all bam files. it gives error as empty format: tabular, database: hg19 Traceback (most recent call last): File /data/galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix/htseq_bams_to_count_matrix/htseqsams2mx.py, line 45, in module import HTSeq.scripts.count as htcount Thanks On Wed, Aug 21, 2013 at 10:44 AM, Mahtab Mirmomeni m.mirmom...@student.unimelb.edu.au wrote: You can use htseq_bams_to_count_matrix repository by fubar in the test toolshed. On Wed, Aug 21, 2013 at 2:37 PM, Sridhar Srinivasan sridhar2bioi...@gmail.com wrote: Hi All, Thanks for the suggestions. I installed the Toolshed ( Differential_Count (version 0.21) ). It asks for the input matrix - rows are contigs, columns are counts for each sample. Any idea on how to generate this matrix file?? Thanks On Tue, Aug 20, 2013 at 12:53 PM, Mahtab Mirmomeni m.mirmom...@student.unimelb.edu.au wrote: Hi Sridhar, I'm using differential_count_model repository by fubar in the test toolshed which has both EdgeR and Deseq2 and it's working for me. Thanks Mahtab On Tue, Aug 20, 2013 at 5:03 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Sridhar, we are developing a DESeq2 tool at the moment, if you want to join get in touch with me. Its developed here: https://github.com/bgruening/galaxytools/tree/master/deseq2 I will upload our latest progress during the day. Cheers, Bjoern Dear users, Could anybody suggest the
[galaxy-dev] Troubleshooting file uploads (to Data Library)
Hi, I am having trouble uploading files to a Data Library, and I'm not sure where to begin troubleshooting. I'm uploading from a URL (but I had a similar issue from the desktop). The symptom is that the datasets in the library have the message This job is queued and never seem to progress. I am one of very few users of this instance (quite likely the only user right this moment). I don't think the server is busy, so I'm not sure why the files uploads don't seem to be proceeding. How can I investigate further? Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___ 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] Troubleshooting file uploads (to Data Library)
Sorry, missed some information: there are a handful of files, 35MB (gzipped) each. The issue occurs even if I only try to upload one of them though. The server is a 16-core machine. On 21 August 2013 17:08, Clare Sloggett s...@unimelb.edu.au wrote: Hi, I am having trouble uploading files to a Data Library, and I'm not sure where to begin troubleshooting. I'm uploading from a URL (but I had a similar issue from the desktop). The symptom is that the datasets in the library have the message This job is queued and never seem to progress. I am one of very few users of this instance (quite likely the only user right this moment). I don't think the server is busy, so I'm not sure why the files uploads don't seem to be proceeding. How can I investigate further? Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___ 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] DESeq for Galaxy
Sridhar, Tool shed installations always create those log files, even when they fail. I am unable to offer any further assistance without seeing the installation log for the dependency. What does: find [your tool dependency directory] -name INSTALLATION.log show? If necessary, try navigating through the tool page in your admin interface. The htseq dependency will contain the installation log I need to see. On Wed, Aug 21, 2013 at 5:06 PM, Sridhar Srinivasan sridhar2bioi...@gmail.com wrote: Hi Ross, I tried installing again it shows no item.. Also i couldn't find any .log file or the ( /htseq/0.5.4p3/fubar/htseq_bams_to_count_matrix) in the tool dependency directory. Thanks On Wed, Aug 21, 2013 at 12:13 PM, Ross ross.laza...@gmail.com wrote: Sridhar, Kindly try rerunning the failed job to confirm that it still fails now that the tool installation should have well and truly finished - it does take a while. If it still fails the same way, please send me a copy of the installation log for the htseq dependency found in: [your tool_dependency_directory]/htseq/0.5.4p3/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/INSTALLATION.log On Wed, Aug 21, 2013 at 4:38 PM, Sridhar Srinivasan sridhar2bioi...@gmail.com wrote: Hi Ross, i Installed through admin interface . for pysam and freetype it showed new... and rest installed.. Thanks On Wed, Aug 21, 2013 at 11:47 AM, Ross ross.laza...@gmail.com wrote: Sridhar, The error message you provide suggests that the HTSeq python module is not available when Galaxy tries to run the tool. Please confirm that you installed that tool through the admin interface from the test toolshed and that the admin interface for toolshed installed tools shows the installed repository in your Galaxy instance has the htseq dependency successfully installed like the end of the page below : - Repository Actions Installed tool shed repository 'htseq_bams_to_count_matrix' Tool shed:testtoolshed.g2.bx.psu.edu Name:htseq_bams_to_count_matrix Description: Revision:f69b55c71ae5 Owner:fubar Location:/mnt/galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix Deleted:False Dependencies of this repository Installed repository dependencies NameRevisionOwner Installation statuspackage_numpy_1_7http://115.146.84.239/admin_toolshed/manage_repository?id=148934b1ed5706b5 af9633757cf0blankenbergInstalledpackage_pysam_0_7_5http://115.146.84.239/admin_toolshed/manage_repository?id=96c0d701aac155a0 a4e35f23093ffubarInstalledpackage_freetype_2_4http://115.146.84.239/admin_toolshed/manage_repository?id=dee0124e4d3ab063 4e54e357ac25bgrueningInstalledpackage_matplotlib_litehttp://115.146.84.239/admin_toolshed/manage_repository?id=c32939704028ccc3 8df6bbf48c3afubarInstalled Installed tool dependencies* - click the name to browse the dependency installation directory* NameVersionTypeInstallation statusfreetypehttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=148934b1ed5706b5 2.4.11packagematplotliblitehttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=dee0124e4d3ab063 1.2.1packagenumpyhttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=94e61e06dbd29e52 1.7.1packagepysamhttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=c32939704028ccc3 0.7.5packagehtseqhttp://115.146.84.239/admin_toolshed/browse_tool_dependency?repository_id=94e61e06dbd29e52id=96c0d701aac155a0 0.5.4p3package On Wed, Aug 21, 2013 at 4:05 PM, Sridhar Srinivasan sridhar2bioi...@gmail.com wrote: Hi All, I installed the toolshed htseq_bams_to_count_matrix repository , i gave the gene model gtf file(ex: tss.gtf file) Gene model (GFF) file to count reads over from your current history: in this section and all bam files. it gives error as empty format: tabular, database: hg19 Traceback (most recent call last): File /data/galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/fubar/htseq_bams_to_count_matrix/f69b55c71ae5/htseq_bams_to_count_matrix/htseq_bams_to_count_matrix/htseqsams2mx.py, line 45, in module import HTSeq.scripts.count as htcount Thanks On Wed, Aug 21, 2013 at 10:44 AM, Mahtab Mirmomeni m.mirmom...@student.unimelb.edu.au wrote: You can use htseq_bams_to_count_matrix repository by fubar in the test toolshed. On Wed, Aug 21, 2013 at 2:37 PM, Sridhar Srinivasan sridhar2bioi...@gmail.com wrote: Hi All, Thanks for the suggestions. I installed the Toolshed ( Differential_Count (version 0.21) ). It asks for the input matrix - rows are contigs, columns are counts for each sample. Any idea on how to generate this matrix file?? Thanks On Tue, Aug 20, 2013 at 12:53 PM, Mahtab Mirmomeni m.mirmom...@student.unimelb.edu.au wrote: Hi Sridhar, I'm using differential_count_model
Re: [galaxy-dev] Troubleshooting file uploads (to Data Library)
Hi Clare a few points to start: - do you define the 'File Format'? (don't use 'Auto-detect' for big files) - and similar to a recent question on the list: check your proxy settings Regards, Hans-Rudof On 08/21/2013 09:09 AM, Clare Sloggett wrote: Sorry, missed some information: there are a handful of files, 35MB (gzipped) each. The issue occurs even if I only try to upload one of them though. The server is a 16-core machine. On 21 August 2013 17:08, Clare Sloggett s...@unimelb.edu.au mailto:s...@unimelb.edu.au wrote: Hi, I am having trouble uploading files to a Data Library, and I'm not sure where to begin troubleshooting. I'm uploading from a URL (but I had a similar issue from the desktop). The symptom is that the datasets in the library have the message This job is queued and never seem to progress. I am one of very few users of this instance (quite likely the only user right this moment). I don't think the server is busy, so I'm not sure why the files uploads don't seem to be proceeding. How can I investigate further? Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___ 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] Galaxy Release Cycle Length
Why the dislike for quick turnover? Could somebody present the arguments for people not having been at the BOF? People don't have to upgrade - unless its breaking changes that e.g. disable the possibility to download from the public toolshed which forced me to upgrade. The alternative to frequent releases are not better tested and documented releases. I think its impossible for the galaxy team to test on all the diverse configurations galaxy is deployed on. Then you really have accumulated many bugs, feedback from users comes in at once creating coordination need for developers going all at once into bugfixing mode for features they have worked on months ago etc… Then the fixes for these bugs also come only with the next release which is still many months away etc…. This makes it necessary to split development into major releases (say once a year) and minor, bugfix, releases (1-2 months after the major) - where is the gain for the users? I would not even split things between breaking changes and minor changes. I think this slows down development of the platform and what concerns people most, the tools, are developed independently of the platform and one can upgrade them any time. To give an example, the job_config is now much better than before and its good that I did not have to wait months from its development to deployment at our site. Now small additional features like setting the number of threads dynamically are suggested, and then I would have to wait again many,many months until the next release. Upgrading galaxy was o.k. and while its unfortunate to have to learn new settings and remember the old ones from sometimes not so good (but improving!) documentation, there is no way around it. I think I will now upgrade more often, because it went so well. I like release early, release often. best, ido On Aug 20, 2013, at 8:36 PM, Dave Clements cleme...@galaxyproject.org wrote: Hello all, At one of the GCC2013 Birds of a Feather sessions the group was very clear that they would like to see less frequent releases of Galaxy. We're currently aiming to do a release every 2 months and have been pretty successful at making that target. In the past, we have tried doing releases more often and less often. Is there a sweet spot for the time between releases? Please reply to the group. We are interested in a discussion. Thanks, Dave C -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] Galaxy Release Cycle Length
On Wednesday, August 21, 2013, Ido Tamir wrote: Why the dislike for quick turnover? Could somebody present the arguments for people not having been at the BOF? People don't have to upgrade - unless its breaking changes that e.g. disable the possibility to download from the public toolshed which forced me to upgrade. I personally don't immediately apply the updates to our (perhaps relatively small) Galaxy instance, unless it includes a bug fix I am particularly interested in, or I need it for a new tool I want to install. This is down to my time rather than anything else - as there is always the chance of things breaking, so needs planning accordingly. So monthly or two-monthly seems about right, but longer than that is frustrating if I am waiting for a fix. Sorter releases just means I will skip more of them, but there is still a time sink reviewing each set of release notes to make this judgement. ... I would not even split things between breaking changes and minor changes. I think this slows down development of the platform and what concerns people most, the tools, are developed independently of the platform and one can upgrade them any time. Actually as a Tool developer, things are often NOT independent of the Galaxy version - I have had to hold back releases to the Tool Shed because they won't work until a bug fix is released to the stable branch, and then allow some time before we can assume most potential users have the update installed. (This is another example where real version numbers like major.minor.revision for Galaxy releases would help - along with the related issue of tools being able to specify a minimum version of Galaxy they require) 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] Duplicated entries in Manage installed tool shed repositories table
On Tue, Aug 20, 2013 at 8:34 PM, Greg Von Kuster g...@bx.psu.edu wrote: Peter and Ross, I've not been able to reproduce this behavior, most likely because I am not following the precise steps you've used when you see it. Can you clarify what you do when you encounter it? Thanks! Greg Von Kuster If it happens to me again, I'll try to narrow down what triggered it. Meanwhile this sounds like another white ghost tool stuck in the new state: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016193.html 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] Tool Shed packages for BLAST+ binaries
On Tue, Aug 20, 2013 at 9:15 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I believe this was again due to the installation of an earlier repository hanging until the testing framework canceled the build. I've added the repository in question to the exclude list, and hopefully your blast repositories will be properly tested within the next few hours. --Dave B. Thanks Dave, Re: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/946749c8605f The output has changed, but we're back to missing any test results at all now, all I get is: ... Automated tool test results Tool test results Automated test environment Time tested: ~ 10 hours ago System: Linux 3.8.0-25-generic Architecture: x86_64 Python version: 2.7.4 Galaxy revision: 10419:4f4e01316260 Galaxy database version: 115 Tool shed revision: 10413:6e148e87d819 Tool shed database version: 21 Tool shed mercurial version: 2.2.3 Automated tool tests ... 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] Troubleshooting file uploads (to Data Library)
Hi Hans and all, The issue turned out to be a more general one with our job runners (it was also stopping non-data-transfer jobs running, if I'd noticed). Yep, I do specify file format when uploading. Thanks for your help! Clare On 21 August 2013 17:38, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Clare a few points to start: - do you define the 'File Format'? (don't use 'Auto-detect' for big files) - and similar to a recent question on the list: check your proxy settings Regards, Hans-Rudof On 08/21/2013 09:09 AM, Clare Sloggett wrote: Sorry, missed some information: there are a handful of files, 35MB (gzipped) each. The issue occurs even if I only try to upload one of them though. The server is a 16-core machine. On 21 August 2013 17:08, Clare Sloggett s...@unimelb.edu.au mailto:s...@unimelb.edu.au wrote: Hi, I am having trouble uploading files to a Data Library, and I'm not sure where to begin troubleshooting. I'm uploading from a URL (but I had a similar issue from the desktop). The symptom is that the datasets in the library have the message This job is queued and never seem to progress. I am one of very few users of this instance (quite likely the only user right this moment). I don't think the server is busy, so I'm not sure why the files uploads don't seem to be proceeding. How can I investigate further? Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 __**_ 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/http://galaxyproject.org/search/mailinglists/ -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___ 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] Workflow import is not working, KeyError: 'header_lines'
Hi Dannon, I'm seeing a problem which seems very similar to the one Bjoern had back in June with the same workflow (which appeared to have been fixed according to the old IUC thread Workflow import is not working). This server is running the current galaxy-dist release, $ sudo -u galaxy hg head changeset: 10411:c42567f43aa7 tag: tip user:greg date:Mon Aug 19 13:19:56 2013 -0400 summary: Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy. changeset: 10408:6822f41bc9bb branch: stable parent: 10393:d05bf67aefa6 user:Dave Bouvier d...@bx.psu.edu date:Mon Aug 19 13:06:17 2013 -0400 summary: Fix for case where running functional tests might overwrite certain files in database/files. I have just installed this workflow repository with its dependencies (some of where I had previously installed via the Tool Shed). Most of the tools were actually already manually installed but have been commented out in my tool_conf.xml file: http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow/606da4e1d925 Installation appeared to be successful, so I wanted to import the workflow into Galaxy. I clicked on the workflow and expected to see an SVG of the workflow and the import action to be available. In the browser I saw: quote Find secreted proteins with TMHMM and SignalP (this page displays SVG graphics) Internal Server Error Galaxy was unable to sucessfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. /quote On the terminal I have: 143.234.97.120 - - [21/Aug/2013:11:14:18 +0100] GET /galaxy/admin_toolshed/browse_repositories HTTP/1.1 200 - http://ppcollab/galaxy/admin; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] GET /galaxy/admin_toolshed/browse_repositories?async=falsesort=namepage=1show_item_checkboxes=falseoperation=manage_repositoryid=eede92f8a72bf85df-deleted=False HTTP/1.1 302 - http://ppcollab/galaxy/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] GET /galaxy/admin_toolshed/manage_repository?sort=namef-deleted=Falseasync=falseshow_item_checkboxes=falseid=eede92f8a72bf85dpage=1 HTTP/1.1 200 - http://ppcollab/galaxy/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:40 +0100] GET /galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 HTTP/1.1 200 - http://ppcollab/galaxy/admin_toolshed/manage_repository?sort=namef-deleted=Falseasync=falseshow_item_checkboxes=falseid=eede92f8a72bf85dpage=1; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:41 +0100] GET /galaxy/admin_toolshed/generate_workflow_image?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 HTTP/1.1 500 - http://ppcollab/galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 Error - type 'exceptions.KeyError': 'header_lines' URL: http://ppcollab/galaxy/admin_toolshed/generate_workflow_image?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/opt/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/opt/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 221 in decorator return func( self, trans, *args, **kwargs ) File
[galaxy-dev] Workflow action summary confusing, repeats Hide this dataset
Hi all,
I have found two potential bugs with how workflow actions are
described to the user when running a workflow.
I am looking over the run workflow dialogue for this workflow,
(I currently get a warning due to the filter tool having a new
Number of header lines to skip option)
http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
I manually imported the *.ga file due to issues with the Tool Shed
workflow import,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016209.html
I am running the latest galaxy-dist,
$ sudo -u galaxy hg head
changeset: 10411:c42567f43aa7
tag: tip
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.
changeset: 10408:6822f41bc9bb
branch: stable
parent: 10393:d05bf67aefa6
user:Dave Bouvier d...@bx.psu.edu
date:Mon Aug 19 13:06:17 2013 -0400
summary: Fix for case where running functional tests might
overwrite certain files in database/files.
--
For step 2, the details view says:
Actions:
Hide this dataset.
Hide this dataset.
I find that confusing, and initially thought there might be a
bug or duplicated action. Actually it is just a misleading
summary as this tool can produce TWO outputs:
post_job_actions: {
HideDatasetActionoutput_neg: {
action_arguments: {},
action_type: HideDatasetAction,
output_name: output_neg
},
HideDatasetActionoutput_pos: {
action_arguments: {},
action_type: HideDatasetAction,
output_name: output_pos
}
},
Perhaps the Hide this dataset message could be less
ambiguous by using the output variable names (as in
some of the other action descriptions)?
There are similar problems with the next steps too.
--
Steps 6 and 7 are also odd. For step 6 the details view says:
Actions:
Hide this dataset.
Rename output 'out_file1' to 'Filtered SignalP results'.
Hide this dataset.
Rename output 'out_file1' to 'Filtered SignalP results'.
Likewise for step 7,
Actions:
Hide this dataset.
Rename output 'output_pos' to 'Secreted proteins'.
Hide this dataset.
Rename output 'output_pos' to 'Secreted proteins'.
Again, there seems to be a duplication of the messages.
It should be hiding one output, and renaming the other, e.g.
post_job_actions: {
HideDatasetActionoutput_neg: {
action_arguments: {},
action_type: HideDatasetAction,
output_name: output_neg
},
RenameDatasetActionoutput_pos: {
action_arguments: {
newname: Secreted proteins
},
action_type: RenameDatasetAction,
output_name: output_pos
}
},
--
In some ways this is just a harmless cosmetic issue, but
it does seem confusing to me.
Thanks,
Peter
___
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Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries
On Wed, Aug 21, 2013 at 10:54 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Aug 20, 2013 at 9:15 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I believe this was again due to the installation of an earlier repository hanging until the testing framework canceled the build. I've added the repository in question to the exclude list, and hopefully your blast repositories will be properly tested within the next few hours. --Dave B. Thanks Dave, Re: http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/946749c8605f The output has changed, but we're back to missing any test results at all now, all I get is: ... Automated tool test results Tool test results Automated test environment Time tested: ~ 10 hours ago System: Linux 3.8.0-25-generic Architecture: x86_64 Python version: 2.7.4 Galaxy revision: 10419:4f4e01316260 Galaxy database version: 115 Tool shed revision: 10413:6e148e87d819 Tool shed database version: 21 Tool shed mercurial version: 2.2.3 Automated tool tests ... Test results now visible now (odd?), back to the install problem: Fatal error: Exit code 127 () /bin/sh: 1: blastn: not found /bin/sh: 1: blastn: not found Any clues from the Test Tool Shed log file would be helpful, Thanks, 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] Workflow action summary confusing, repeats Hide this dataset
Peter,
Thanks for noticing this -- the text in the UI should definitely reflect
which output it's referring to. Hide output_pos, etc.
https://trello.com/c/KAtwLSiV/1069-workflow-actions-cosmetic-issues
-Dannon
On Wed, Aug 21, 2013 at 7:16 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
Hi all,
I have found two potential bugs with how workflow actions are
described to the user when running a workflow.
I am looking over the run workflow dialogue for this workflow,
(I currently get a warning due to the filter tool having a new
Number of header lines to skip option)
http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow
I manually imported the *.ga file due to issues with the Tool Shed
workflow import,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016209.html
I am running the latest galaxy-dist,
$ sudo -u galaxy hg head
changeset: 10411:c42567f43aa7
tag: tip
user:greg
date:Mon Aug 19 13:19:56 2013 -0400
summary: Filter invalid objects when generating the list of
repository_dependencies objects that are associated with a tool shed
repository installed into Galaxy.
changeset: 10408:6822f41bc9bb
branch: stable
parent: 10393:d05bf67aefa6
user:Dave Bouvier d...@bx.psu.edu
date:Mon Aug 19 13:06:17 2013 -0400
summary: Fix for case where running functional tests might
overwrite certain files in database/files.
--
For step 2, the details view says:
Actions:
Hide this dataset.
Hide this dataset.
I find that confusing, and initially thought there might be a
bug or duplicated action. Actually it is just a misleading
summary as this tool can produce TWO outputs:
post_job_actions: {
HideDatasetActionoutput_neg: {
action_arguments: {},
action_type: HideDatasetAction,
output_name: output_neg
},
HideDatasetActionoutput_pos: {
action_arguments: {},
action_type: HideDatasetAction,
output_name: output_pos
}
},
Perhaps the Hide this dataset message could be less
ambiguous by using the output variable names (as in
some of the other action descriptions)?
There are similar problems with the next steps too.
--
Steps 6 and 7 are also odd. For step 6 the details view says:
Actions:
Hide this dataset.
Rename output 'out_file1' to 'Filtered SignalP results'.
Hide this dataset.
Rename output 'out_file1' to 'Filtered SignalP results'.
Likewise for step 7,
Actions:
Hide this dataset.
Rename output 'output_pos' to 'Secreted proteins'.
Hide this dataset.
Rename output 'output_pos' to 'Secreted proteins'.
Again, there seems to be a duplication of the messages.
It should be hiding one output, and renaming the other, e.g.
post_job_actions: {
HideDatasetActionoutput_neg: {
action_arguments: {},
action_type: HideDatasetAction,
output_name: output_neg
},
RenameDatasetActionoutput_pos: {
action_arguments: {
newname: Secreted proteins
},
action_type: RenameDatasetAction,
output_name: output_pos
}
},
--
In some ways this is just a harmless cosmetic issue, but
it does seem confusing to me.
Thanks,
Peter
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Re: [galaxy-dev] Workflow import is not working, KeyError: 'header_lines'
Hey Peter, I've reproduced this here, thanks. Unfortunately this got missed previously, once we had the import itself working. To be clear, though, the workflow itself is still completely functional, imports and runs, and the only issue is the inability to view the svg? I think what's causing this is that generate_workflow_image uses completely separate workflow modules which didn't have my previous fixes applied. This should be refactored so we don't have duplicated code sitting around, but I'll go ahead and patch it to get it working again shortly. On Wed, Aug 21, 2013 at 6:45 AM, Peter Cock p.j.a.c...@googlemail.comwrote: Hi Dannon, I'm seeing a problem which seems very similar to the one Bjoern had back in June with the same workflow (which appeared to have been fixed according to the old IUC thread Workflow import is not working). This server is running the current galaxy-dist release, $ sudo -u galaxy hg head changeset: 10411:c42567f43aa7 tag: tip user:greg date:Mon Aug 19 13:19:56 2013 -0400 summary: Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy. changeset: 10408:6822f41bc9bb branch: stable parent: 10393:d05bf67aefa6 user:Dave Bouvier d...@bx.psu.edu date:Mon Aug 19 13:06:17 2013 -0400 summary: Fix for case where running functional tests might overwrite certain files in database/files. I have just installed this workflow repository with its dependencies (some of where I had previously installed via the Tool Shed). Most of the tools were actually already manually installed but have been commented out in my tool_conf.xml file: http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow/606da4e1d925 Installation appeared to be successful, so I wanted to import the workflow into Galaxy. I clicked on the workflow and expected to see an SVG of the workflow and the import action to be available. In the browser I saw: quote Find secreted proteins with TMHMM and SignalP (this page displays SVG graphics) Internal Server Error Galaxy was unable to sucessfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. /quote On the terminal I have: 143.234.97.120 - - [21/Aug/2013:11:14:18 +0100] GET /galaxy/admin_toolshed/browse_repositories HTTP/1.1 200 - http://ppcollab/galaxy/admin; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] GET /galaxy/admin_toolshed/browse_repositories?async=falsesort=namepage=1show_item_checkboxes=falseoperation=manage_repositoryid=eede92f8a72bf85df-deleted=False HTTP/1.1 302 - http://ppcollab/galaxy/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] GET /galaxy/admin_toolshed/manage_repository?sort=namef-deleted=Falseasync=falseshow_item_checkboxes=falseid=eede92f8a72bf85dpage=1 HTTP/1.1 200 - http://ppcollab/galaxy/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:40 +0100] GET /galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 HTTP/1.1 200 - http://ppcollab/galaxy/admin_toolshed/manage_repository?sort=namef-deleted=Falseasync=falseshow_item_checkboxes=falseid=eede92f8a72bf85dpage=1 Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:41 +0100] GET /galaxy/admin_toolshed/generate_workflow_image?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 HTTP/1.1 500 - http://ppcollab/galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 Error - type 'exceptions.KeyError': 'header_lines' URL: http://ppcollab/galaxy/admin_toolshed/generate_workflow_image?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 File '/opt/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File
Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries
Peter, Here is the relevant log output for the installation of ncbi_blast_plus. A quick google informs me that exit code 64 means command line usage error, for what it's worth. install_and_test_repositories INFO 2013-08-20 23:34:43,270 Installing and testing revision 946749c8605f of repository ncbi_blast_plus owned by peterjc... install_repository_ncbi_blast_plus (install_and_test_tool_shed_repositories.functional.test_install_repositories.TestInstallRepository_ncbi_blast_plus) Install the repository ncbi_blast_plus from http://testtoolshed.g2.bx.psu.edu. ... tool_shed.util.shed_util_common DEBUG 2013-08-20 23:34:47,484 Adding new row (or updating an existing row) for repository 'ncbi_blast_plus' in the tool_shed_repository table, status set to 'New'. tool_shed.util.shed_util_common DEBUG 2013-08-20 23:34:47,674 Adding new row (or updating an existing row) for repository 'blast_datatypes' in the tool_shed_repository table, status set to 'New'. tool_shed.util.shed_util_common DEBUG 2013-08-20 23:34:47,886 Adding new row (or updating an existing row) for repository 'package_blast_plus_2_2_26' in the tool_shed_repository table, status set to 'New'. Warning: local() encountered an error (return code 64) while executing ' if [[ $(uname) == Linux ]]; then export FILENAME=ncbi-blast-2.2.26+-ia32-linux.tar.gz; fi if [[ $(arch) == x86_64 ]]; then export FILENAME=ncbi-blast-2.2.26+-x64-linux.tar.gz; fi if [[ $(uname) == Darwin ]]; then export FILENAME=ncbi-blast-2.2.26+-universal-macosx.tar.gz; fi echo Fetching $FILENAME if [[ $(uname) == Linux ]]; then wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi if [[ $(uname) == Darwin ]]; then curl -O ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi tar -zxvf $FILENAME echo Downloaded and decompressed ' galaxy.datatypes.registry DEBUG 2013-08-20 23:34:52,010 Loading datatypes from /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpskjEfq/tmp-toolshed-acalpdoM4u1f galaxy.datatypes.registry DEBUG 2013-08-20 23:34:52,022 Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml' tool_shed.util.tool_util DEBUG 2013-08-20 23:34:54,285 The '/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/tool-data/testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/946749c8605f/tool_data_table_conf.xml' data table file was not found, but was expected to be copied from 'tool_data_table_conf.xml.sample' during repository installation. galaxy.tools DEBUG 2013-08-20 23:34:55,359 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_blastx_wrapper/0.0.19, version: 0.0.19 into tool panel. galaxy.tools DEBUG 2013-08-20 23:34:55,435 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_tblastx_wrapper/0.0.20, version: 0.0.20 into tool panel. galaxy.tools DEBUG 2013-08-20 23:34:55,510 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_tblastn_wrapper/0.0.20, version: 0.0.20 into tool panel. galaxy.tools DEBUG 2013-08-20 23:34:55,541 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_blastdbcmd_info/0.0.6, version: 0.0.6 into tool panel. galaxy.tools DEBUG 2013-08-20 23:34:55,618 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_blastp_wrapper/0.0.20, version: 0.0.20 into tool panel. galaxy.tools DEBUG 2013-08-20 23:34:55,693 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_rpstblastn_wrapper/0.0.4, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-08-20 23:34:55,722 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_makeblastdb/0.0.5, version: 0.0.5 into tool panel. galaxy.tools DEBUG 2013-08-20 23:34:55,797 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_blastn_wrapper/0.0.20, version: 0.0.20 into tool panel. galaxy.tools DEBUG 2013-08-20 23:34:55,861 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/blastxml_to_tabular/0.0.11, version: 0.0.11 into tool panel. galaxy.tools DEBUG 2013-08-20 23:34:55,938 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_rpsblast_wrapper/0.0.4, version: 0.0.4 into tool panel. galaxy.tools DEBUG 2013-08-20 23:34:55,971 Loaded tool id: testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_blastdbcmd_wrapper/0.0.6, version: 0.0.6 into tool panel. --Dave B. On 8/21/13 08:08:49.000, Peter Cock wrote: On Wed, Aug 21, 2013 at 10:54 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Aug 20, 2013 at 9:15 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I believe this was again
Re: [galaxy-dev] Workflow import is not working, KeyError: 'header_lines'
Quick followup on this one -- had you manually tweaked this workflow prior to upload? I see all of the tool identifiers are the short form 'signalp3' and not the long-form toolshed included versions. On Wed, Aug 21, 2013 at 8:25 AM, Dannon Baker dannon.ba...@gmail.comwrote: Hey Peter, I've reproduced this here, thanks. Unfortunately this got missed previously, once we had the import itself working. To be clear, though, the workflow itself is still completely functional, imports and runs, and the only issue is the inability to view the svg? I think what's causing this is that generate_workflow_image uses completely separate workflow modules which didn't have my previous fixes applied. This should be refactored so we don't have duplicated code sitting around, but I'll go ahead and patch it to get it working again shortly. On Wed, Aug 21, 2013 at 6:45 AM, Peter Cock p.j.a.c...@googlemail.comwrote: Hi Dannon, I'm seeing a problem which seems very similar to the one Bjoern had back in June with the same workflow (which appeared to have been fixed according to the old IUC thread Workflow import is not working). This server is running the current galaxy-dist release, $ sudo -u galaxy hg head changeset: 10411:c42567f43aa7 tag: tip user:greg date:Mon Aug 19 13:19:56 2013 -0400 summary: Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy. changeset: 10408:6822f41bc9bb branch: stable parent: 10393:d05bf67aefa6 user:Dave Bouvier d...@bx.psu.edu date:Mon Aug 19 13:06:17 2013 -0400 summary: Fix for case where running functional tests might overwrite certain files in database/files. I have just installed this workflow repository with its dependencies (some of where I had previously installed via the Tool Shed). Most of the tools were actually already manually installed but have been commented out in my tool_conf.xml file: http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow/606da4e1d925 Installation appeared to be successful, so I wanted to import the workflow into Galaxy. I clicked on the workflow and expected to see an SVG of the workflow and the import action to be available. In the browser I saw: quote Find secreted proteins with TMHMM and SignalP (this page displays SVG graphics) Internal Server Error Galaxy was unable to sucessfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. /quote On the terminal I have: 143.234.97.120 - - [21/Aug/2013:11:14:18 +0100] GET /galaxy/admin_toolshed/browse_repositories HTTP/1.1 200 - http://ppcollab/galaxy/admin; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] GET /galaxy/admin_toolshed/browse_repositories?async=falsesort=namepage=1show_item_checkboxes=falseoperation=manage_repositoryid=eede92f8a72bf85df-deleted=False HTTP/1.1 302 - http://ppcollab/galaxy/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:26 +0100] GET /galaxy/admin_toolshed/manage_repository?sort=namef-deleted=Falseasync=falseshow_item_checkboxes=falseid=eede92f8a72bf85dpage=1 HTTP/1.1 200 - http://ppcollab/galaxy/admin_toolshed/browse_repositories; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:40 +0100] GET /galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 HTTP/1.1 200 - http://ppcollab/galaxy/admin_toolshed/manage_repository?sort=namef-deleted=Falseasync=falseshow_item_checkboxes=falseid=eede92f8a72bf85dpage=1 Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 143.234.97.120 - - [21/Aug/2013:11:14:41 +0100] GET /galaxy/admin_toolshed/generate_workflow_image?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 HTTP/1.1 500 - http://ppcollab/galaxy/admin_toolshed/view_workflow?repository_id=eede92f8a72bf85dworkflow_name=eef2c509eb9672ca81f4797561cfd5804652c810%3A46696e642073656372657465642070726f7465696e73207769746820544d484d4d20616e64205369676e616c50 Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:22.0) Gecko/20100101 Firefox/22.0 Error - type 'exceptions.KeyError': 'header_lines' URL:
Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries
On Wed, Aug 21, 2013 at 1:45 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, Here is the relevant log output for the installation of ncbi_blast_plus. A quick google informs me that exit code 64 means command line usage error, for what it's worth. install_and_test_repositories INFO 2013-08-20 23:34:43,270 Installing and testing revision 946749c8605f of repository ncbi_blast_plus owned by peterjc... install_repository_ncbi_blast_plus (install_and_test_tool_shed_repositories.functional.test_install_repositories.TestInstallRepository_ncbi_blast_plus) Install the repository ncbi_blast_plus from http://testtoolshed.g2.bx.psu.edu. ... tool_shed.util.shed_util_common DEBUG 2013-08-20 23:34:47,484 Adding new row (or updating an existing row) for repository 'ncbi_blast_plus' in the tool_shed_repository table, status set to 'New'. tool_shed.util.shed_util_common DEBUG 2013-08-20 23:34:47,674 Adding new row (or updating an existing row) for repository 'blast_datatypes' in the tool_shed_repository table, status set to 'New'. tool_shed.util.shed_util_common DEBUG 2013-08-20 23:34:47,886 Adding new row (or updating an existing row) for repository 'package_blast_plus_2_2_26' in the tool_shed_repository table, status set to 'New'. Warning: local() encountered an error (return code 64) while executing ' if [[ $(uname) == Linux ]]; then export FILENAME=ncbi-blast-2.2.26+-ia32-linux.tar.gz; fi if [[ $(arch) == x86_64 ]]; then export FILENAME=ncbi-blast-2.2.26+-x64-linux.tar.gz; fi if [[ $(uname) == Darwin ]]; then export FILENAME=ncbi-blast-2.2.26+-universal-macosx.tar.gz; fi echo Fetching $FILENAME if [[ $(uname) == Linux ]]; then wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi if [[ $(uname) == Darwin ]]; then curl -O ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi tar -zxvf $FILENAME echo Downloaded and decompressed ' Thanks Dave, I've made a note on this Trello card about exposing the log information of unsuccessful builds on the Tool Shed, https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-packages Can you tell me what version of Linux this is, and which shell? $ uname ... $ arch ... $ echo $0 ... That might give me a clue about the nature of the failure. My hunch is that I am using something bash specific. The simplest solution would be if you could run each of these command by hand to see if it triggers the same error: if [[ $(uname) == Linux ]]; then export FILENAME=ncbi-blast-2.2.26+-ia32-linux.tar.gz; fi if [[ $(arch) == x86_64 ]]; then export FILENAME=ncbi-blast-2.2.26+-x64-linux.tar.gz; fi if [[ $(uname) == Darwin ]]; then export FILENAME=ncbi-blast-2.2.26+-universal-macosx.tar.gz; fi echo Fetching $FILENAME if [[ $(uname) == Linux ]]; then wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi if [[ $(uname) == Darwin ]]; then curl -O ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi tar -zxvf $FILENAME echo Downloaded and decompressed Thanks, 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] Workflow import is not working, KeyError: 'header_lines'
On Wed, Aug 21, 2013 at 8:25 AM, Dannon Baker dannon.ba...@gmail.com wrote: Hey Peter, I've reproduced this here, thanks. Unfortunately this got missed previously, once we had the import itself working. To be clear, though, the workflow itself is still completely functional, imports and runs, and the only issue is the inability to view the svg? Via the Tool Shed I couldn't see the import workflow action... from memory it was on the broken SVG page? I could manually import the workflow from the *.ga file on disk, and it runs OK. I think what's causing this is that generate_workflow_image uses completely separate workflow modules which didn't have my previous fixes applied. This should be refactored so we don't have duplicated code sitting around, but I'll go ahead and patch it to get it working again shortly. Sounds good. On Wed, Aug 21, 2013 at 1:47 PM, Dannon Baker dannon.ba...@gmail.com wrote: Quick followup on this one -- had you manually tweaked this workflow prior to upload? I see all of the tool identifiers are the short form 'signalp3' and not the long-form toolshed included versions. These are not tweaked - it is an old workflow created with manually installed tools which therefore have the short form identifiers. This is something Galaxy may need to continue to support for backwards compatibility with old workflows supplied as supplementary files etc. I'm attempting to update the workflow to use the new long-form toolshed identifiers (although this has the minor downside of no longer being portable between different Tool Sheds). 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] Workflow import is not working, KeyError: 'header_lines'
On Wed, Aug 21, 2013 at 9:10 AM, Peter Cock p.j.a.c...@googlemail.comwrote: Via the Tool Shed I couldn't see the import workflow action... from memory it was on the broken SVG page? Yep, that's where it was. These are not tweaked - it is an old workflow created with manually installed tools which therefore have the short form identifiers. This is something Galaxy may need to continue to support for backwards compatibility with old workflows supplied as supplementary files etc. I'm attempting to update the workflow to use the new long-form toolshed identifiers (although this has the minor downside of no longer being portable between different Tool Sheds). Ok, thanks for the extra info, just wanted to make sure I knew what I was dealing with :) ___ 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] Duplicated entries in Manage installed tool shed repositories table
Thanks Peter, As soon as I can get the steps to produce white ghost, I'll get a fix committed - I've not been able to produce one yet. Greg Von Kuster On Aug 21, 2013, at 5:41 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Aug 20, 2013 at 8:34 PM, Greg Von Kuster g...@bx.psu.edu wrote: Peter and Ross, I've not been able to reproduce this behavior, most likely because I am not following the precise steps you've used when you see it. Can you clarify what you do when you encounter it? Thanks! Greg Von Kuster If it happens to me again, I'll try to narrow down what triggered it. Meanwhile this sounds like another white ghost tool stuck in the new state: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016193.html 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] Error granting permissions on new Tool Shed repository
I've made a note on the Trello issue Ross filed for this,
https://trello.com/c/SqrjrnNg/986
On Wed, Aug 7, 2013 at 4:16 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
This is a known issue ( not a Tool Shed issue, but a Galaxy issue )
related to the Select list that gets automatically populated with the
Select one option. You have to actually click the x on this option
to eliminate it. Again, this feature is inherited from Galaxy, so it's
not specific to the tool shed. I haven't had time to track it down
and fix it since I'm under water with just the tool shed.
Greg Von Kuster
On Aug 7, 2013, at 11:12 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Greg, Dave,
While logged into the Test Tool Shed as 'iuc', I just created
a new (empty) repository:
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26
See background discussion on this thread:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/015890.html
As 'iuc', I then tried to grant write access to myself ('peterjc')
and Bjoern ('bgruening') as we are both IUC members and
working on the Galaxy BLAST+ project:
https://github.com/peterjc/galaxy_blast
The default dummy entry Select One entry was still being
displayed. I clicked 'Grant Access' and got this error:
Internal Server Error
Galaxy was unable to sucessfully complete your request
URL:
http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=2f85dfc5735b60ae
Module galaxy.web.framework.middleware.error:149 in __call__
app_iter = self.application(environ, sr_checker)
Module paste.debug.prints:106 in __call__
environ, self.app)
Module paste.wsgilib:543 in intercept_output
app_iter = application(environ, replacement_start_response)
Module paste.recursive:84 in __call__
return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
body = method( trans, **kwargs )
Module galaxy.web.framework:98 in decorator
return func( self, trans, *args, **kwargs )
Module galaxy.webapps.tool_shed.controllers.repository:2072 in
manage_repository
user = trans.sa_session.query( trans.model.User ).get(
trans.security.decode_id( user_id ) )
Module galaxy.web.security:60 in decode_id
return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( ! )
)
Module encodings.hex_codec:42 in hex_decode
output = binascii.a2b_hex(input)
TypeError: Non-hexadecimal digit found
extra data
full traceback
text version
This may be an intermittent problem due to load or other unpredictable
factors, reloading the page may address the problem.
--
I tried again but explicitly removed the dummy entry Select One
and it seemed to have worked.
I am running Firefox v22.0 on Mac OS X.
Regards,
Peter
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Re: [galaxy-dev] One installable revision is not working for orphan-tool-dependencies - Was: Action type 'template_command' on galaxy-dist?
Hello Bjoern, On Aug 21, 2013, at 2:51 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Greg, a first test seems to work as expected for me, will test again with the whole CTB. Great - thanks! If I understood your commit you are searching now for the next valid 'installable' revision, aka a revision with metadata. Yes, this is correct. Does it make sense to have revisions for Tool dependency definition. Only one valid revision should be possible, per definition or? So we could skip that revision the system entirely for Tool dependency definition, or? No, this is not a good approach. It is important to check for a valid ( i.e., installable ) changeset revision for all repositories, even those of type tool_dependency_definition. If a tool_dependency_definition repository does not have a tip that is installable, it should be handled just like other repositores that do not have an installable revision. In addition to the error handling that will result from checking for validity, the framework supporting repository revisions is less fragile and easier to maintain if exceptions like this for repository types are not introduced. Thanks for the fast fix! Bjoern Thanks! Greg Von Kuster Hello Bjoern, This issue should be resolved in change set 10412:29ab5a6d75a7, whcih is currently running on both tool sheds. No changes should be necessary to any of your current dependency definition files. This changeset was committed to the stable branch, so production Galaxy environments can be safely updated as well. Of course, tracking central in Galaxy environments will get the fix as usual. Thanks very much for reporting this! Greg Von Kuster On Aug 15, 2013, at 9:01 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Dave, the bug is unfortunately still present in the latest Galaxy version. If you try to install http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 you will end up with an error, because numpy is not found. That error appears because scipy was uploaded and afterwards numpy was changed. The consequence is that scipy references on old (not installable) version of numpy and crashes. I would expect that scipy is always looking for the latest version of numpy regardless of what is specified in the numpy XML file. Is that assumption wrong? That would raise the question if revisions are still needed for orphan-tool-dependencies or 'Tool dependency definition'. Is that bug easy to fix? Or do I need to upload all my repositories in the right order again? That would be the consequence, because otherwise I do not get the revision tag updated. Thanks! Bjoern Peter, Björn, The August Galaxy release is out, and the template_command is now in the stable repository and branch. Regarding matplotlib and numpy, I currently only see matplotlib depending on the 74c21f9bdc39 revision of numpy. Is this still an issue, or has it been resolved? --Dave B. On 8/12/13 11:36:00.000, Bjoern Gruening wrote: On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote: On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote: Maybe I should retitle this thread... On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Thank you - installing the NumPy package now works for me, http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 I'm moving on to something odd with matplotlib instead... Peter There are currently two revisions to the main Tool Shed package for numpy, http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 Rev 0: c75482be1d3a - needs not-yet-released features Rev 1: 74c21f9bdc39 - simplified I'm trying to install a package dependent on this via matplotlib - but installing the matplotlib package fails: http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_2 This is something odd, why does it think it needs to install the rev 0 c75482be1d3a version of package_numpy_1_7? See screenshot, except here: Repository dependencies - installation of these additional repositories is required Name RevisionOwner Installation status package_freetype_2_4 8761091302c4iuc Installed package_numpy_1_7 74c21f9bdc39iuc Installed package_numpy_1_7 c75482be1d3aiuc Uninstalled Yes, the matplotlib tool_dependencies.xml does list the original revision: package name=numpy version=1.7.1 repository changeset_revision=c75482be1d3a name=package_numpy_1_7 owner=iuc prior_installation_required=True toolshed=http://toolshed.g2.bx.psu.edu; / /package package name=freetype version=2.4.11 repository changeset_revision=8761091302c4 name=package_freetype_2_4 owner=iuc prior_installation_required=True toolshed=http://toolshed.g2.bx.psu.edu; / /package But I thought as a Tool dependency definition
Re: [galaxy-dev] Error granting permissions on new Tool Shed repository
Thanks Peter, I've added some comments as well, and relabeld the Trello card as
trivial bug: Using Galaxy select lists fail unless the Select one option
removed first.
since this is not a tool shed issue, but a Selectlist issue in the Galaxy
formbuilder framework. The tool shed simply inherits this problem from there.
https://trello.com/c/SqrjrnNg/986-trivial-bug-toolshed-adding-a-user-using-the-grant-authority-to-make-changes-section-of-repository-management-fails-unless-selec
Greg Von Kuster
On Aug 21, 2013, at 9:21 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
I've made a note on the Trello issue Ross filed for this,
https://trello.com/c/SqrjrnNg/986
On Wed, Aug 7, 2013 at 4:16 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
This is a known issue ( not a Tool Shed issue, but a Galaxy issue )
related to the Select list that gets automatically populated with the
Select one option. You have to actually click the x on this option
to eliminate it. Again, this feature is inherited from Galaxy, so it's
not specific to the tool shed. I haven't had time to track it down
and fix it since I'm under water with just the tool shed.
Greg Von Kuster
On Aug 7, 2013, at 11:12 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Greg, Dave,
While logged into the Test Tool Shed as 'iuc', I just created
a new (empty) repository:
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26
See background discussion on this thread:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/015890.html
As 'iuc', I then tried to grant write access to myself ('peterjc')
and Bjoern ('bgruening') as we are both IUC members and
working on the Galaxy BLAST+ project:
https://github.com/peterjc/galaxy_blast
The default dummy entry Select One entry was still being
displayed. I clicked 'Grant Access' and got this error:
Internal Server Error
Galaxy was unable to sucessfully complete your request
URL:
http://testtoolshed.g2.bx.psu.edu/repository/manage_repository?id=2f85dfc5735b60ae
Module galaxy.web.framework.middleware.error:149 in __call__
app_iter = self.application(environ, sr_checker)
Module paste.debug.prints:106 in __call__
environ, self.app)
Module paste.wsgilib:543 in intercept_output
app_iter = application(environ, replacement_start_response)
Module paste.recursive:84 in __call__
return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
body = method( trans, **kwargs )
Module galaxy.web.framework:98 in decorator
return func( self, trans, *args, **kwargs )
Module galaxy.webapps.tool_shed.controllers.repository:2072 in
manage_repository
user = trans.sa_session.query( trans.model.User ).get(
trans.security.decode_id( user_id ) )
Module galaxy.web.security:60 in decode_id
return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( !
) )
Module encodings.hex_codec:42 in hex_decode
output = binascii.a2b_hex(input)
TypeError: Non-hexadecimal digit found
extra data
full traceback
text version
This may be an intermittent problem due to load or other unpredictable
factors, reloading the page may address the problem.
--
I tried again but explicitly removed the dummy entry Select One
and it seemed to have worked.
I am running Firefox v22.0 on Mac OS X.
Regards,
Peter
___
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___
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Re: [galaxy-dev] Workflow import is not working, KeyError: 'header_lines'
Hey Peter, The reason it's actually failing has to do with the tool Filter1, and your particular version of the filter tool not having the header lines parameter. This was added in 8678:a14006775b08. In this instance, we should have just used the default value. Once all tools and versions are in the toolshed, this sort of thing shouldn't crop up because you'll have the correct version available. I've committed a temporary fix in 10423:3c60f6a7dedc. On Wed, Aug 21, 2013 at 9:14 AM, Dannon Baker dannon.ba...@gmail.comwrote: On Wed, Aug 21, 2013 at 9:10 AM, Peter Cock p.j.a.c...@googlemail.comwrote: Via the Tool Shed I couldn't see the import workflow action... from memory it was on the broken SVG page? Yep, that's where it was. These are not tweaked - it is an old workflow created with manually installed tools which therefore have the short form identifiers. This is something Galaxy may need to continue to support for backwards compatibility with old workflows supplied as supplementary files etc. I'm attempting to update the workflow to use the new long-form toolshed identifiers (although this has the minor downside of no longer being portable between different Tool Sheds). Ok, thanks for the extra info, just wanted to make sure I knew what I was dealing with :) ___ 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] Workflow import is not working, KeyError: 'header_lines'
n Wed, Aug 21, 2013 at 2:59 PM, Dannon Baker dannon.ba...@gmail.com wrote: Hey Peter, The reason it's actually failing has to do with the tool Filter1, and your particular version of the filter tool not having the header lines parameter. This was added in 8678:a14006775b08. In this instance, we should have just used the default value. Yes - I realised later that the header_lines was from the Filter1 tool, http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016224.html Once all tools and versions are in the toolshed, this sort of thing shouldn't crop up because you'll have the correct version available. I was under the impression at GCC2013 that Galaxy would continue to keep a set of 'core' tools with no dependencies (like Filter1), but perhaps the goal is more a set of tools installed from the Tool Shed by default? I've committed a temporary fix in 10423:3c60f6a7dedc. Thanks, 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] Editing workflow - automatic update changes not saved?
Hi all, I'm trying to update one of my saved workflows which was created using an old version of the filter tool BEFORE this tool had the option Number of header lines to skip. In order to get rid of the nag message on using the tool, I want to re-save the workflow using the default 0 for this. This missing parameter was also causing problems trying to import the *.ga file for this old workflow, http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016223.html The (now out of date) copy of the Workflow is on the Tool Shed, but to update it I am working on the same Galaxy instance used to create it (where TMHMM and SignalP were manually installed and have been updated since): http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow 1. Log into Galaxy 2. Click on workflows (top menu) 3. Find my workflow, select Edit from the dropdown menu 4. Observe warning: Workflow loaded with changes Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save. Step 3: Filter No value found for 'Number of header lines to skip', used default Step 6: Filter No value found for 'Number of header lines to skip', used default 5. Click on these workflow steps, verify this new parameter is set to zero. 6. Save the workflow, observe blue progress bar pops up. 7. Close the workflow 9. Save the workflow to disk as a *.ga file 8. Open the workflow again for editing Expected result: New parameter recorded, and tool versions updated. Actual result: No change, same warning appears. No sign of the new setting in the freshly save *.ga file. Tool versions not changed. Workaround: Change the default values to one (1), save, close, reopen, no warning, change values back to zero (0), save, close, reopen, Happy. Is this simply a bug where the workflow editor wrongly assumes no changes have been made (despite there being two major types of change - the new header_lines parameter, and the versions of the tools)? 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] Passing user_email to a data source
Hi, I didn't know this was possible, thanks! Unfortunately I can't use this in my case because I can only use param with type=hidden for a data source... Anthony On 21/08/2013 08:51, Hans-Rudolf Hotz wrote: Hi Anthony I doubt it will solve your problem, but just as a general hint: you can use the email address for filtering. In our case, the user gets a different list of groups he/she can select from, eg: param name=group type=select label=Select your group options from_file=access_to_miseq column name=email index=0/ column name=value index=1/ filter type=static_value name=external_source_filter value=$__user_email__ column=0/ /options /param and our file '~/tool-data/access_to_miseq' looks like: 1...@fmi.chgbioinfo 1...@fmi.chgfungen 1...@fmi.chgmeier ## a...@fmi.chgfungen ## 1...@fmi.chgfungen 1...@fmi.chgmeier Regards, Hans-Rudolf On 08/20/2013 05:51 PM, Anthony Bretaudeau wrote: Hello, I'm trying to add a new data source to my Galaxy instance, using synchronous data depositing. The data source needs to know the email address of the user who tries to import data to the Galaxy server. I would have like to write something like that: inputs action=https://example.com/my/data/source; check_values=false method=get displayBrowse the XX data source $GALAXY_URL/display param name=user_email type=hidden value=$__user_email__ / /inputs Then Galaxy would have generated this url: https://example.com/my/data/source?GALAXY_URL=httpuser_email=t...@example.com But this doesn't work, because the $__user_email__ seems to be available only in command tag. I end up with this url which is useless: https://example.com/my/data/source?GALAXY_URL=httpuser_email=$__user_email__ Is there any way to do what I need to do? It would be great if variables were available in param tags too. Otherwise, maybe I could write a custom tool type to do this. Is there any guideline for this? I have seen someone talking about that a few months ago, but with no answer: http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-September/011258.html Thanks for your help Regards Anthony Bretaudeau ___ 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] Non-ascii characters in password break Galaxy login
Hi all, I've seen several unicode issues reported recently, so here is another one: I just tried to log in and naively copy and pasted my password from one browser to another: This upset Galaxy, 143.234.100.162 - - [21/Aug/2013:15:47:55 +0100] POST /galaxy/user/login?use_panels=False HTTP/1.1 500 - http://xxx/galaxy/user/login; Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 5.1; Trident/4.0; .NET CLR 1.1.4322; .NET CLR 2.0.50727; .NET CLR 3.0.4506.2152; .NET CLR 3.5.30729; .NET4.0C; .NET4.0E) Error - type 'exceptions.UnicodeEncodeError': 'ascii' codec can't encode characters in position 0-7: ordinal not in range(128) URL: http://ppserver/galaxy/user/login?use_panels=False File '/mnt/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/mnt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/mnt/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/mnt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/mnt/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/mnt/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/user.py', line 438 in login message, status, user, success = self.__validate_login( trans, **kwd ) File '/mnt/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/user.py', line 485 in __validate_login elif not user.check_password( password ): File '/mnt/galaxy/galaxy-dist/lib/galaxy/model/__init__.py', line 100 in check_password return galaxy.security.passwords.check_password( cleartext, self.password ) File '/mnt/galaxy/galaxy-dist/lib/galaxy/security/passwords.py', line 30 in check_password if hashlib.sha1( guess ).hexdigest() == hashed: UnicodeEncodeError: 'ascii' codec can't encode characters in position 0-7: ordinal not in range(128) 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] JSON error trying to update Tool Shed workflow
Hi Peter, You are probably using a mac if you are seeing this, so can you check to see if your .ga file permissions include an @ sign? This an Apple osx issue, and you'll need to do the following: xattr -d com.apple.quarantine name of your exported.ga file When you do this, it will fix the permissions, and uploading to the tool shed should work. Greg Von Kuster On Aug 21, 2013, at 11:23 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I was trying to update this workflow repository on the Test Tool Shed, http://testtoolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow Attempting to upload the tar-ball appeared to fail as follows: URL: http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=eb13e537583cdf2a Module galaxy.web.framework.middleware.error:149 in __call__ app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ environ, self.app) Module paste.wsgilib:543 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request body = method( trans, **kwargs ) Module galaxy.web.framework:98 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.webapps.tool_shed.controllers.upload:203 in upload metadata_util.set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=content_alert_str, **kwd ) Module tool_shed.util.metadata_util:1850 in set_repository_metadata_due_to_new_tip error_message, status = set_repository_metadata( trans, repository, content_alert_str=content_alert_str, **kwd ) Module tool_shed.util.metadata_util:1779 in set_repository_metadata persist=False ) Module tool_shed.util.metadata_util:698 in generate_metadata_for_changeset_revision exported_workflow_dict = json.from_json_string( workflow_text ) Module simplejson:384 in loads Module simplejson.decoder:402 in decode Module simplejson.decoder:420 in raw_decode JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0) Confusingly the changes seem to get uploaded anyway but seems to have generated a dummy file _secreted_protein_workflow.ga (note the leading underscore) http://testtoolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=36b2c2b5051eid=eb13e537583cdf2a Not realising this, I recreated and reupload the tarball (which worked and removed the phantom file): http://testtoolshed.g2.bx.psu.edu/repository/view_changeset?ctx_str=f32581ab2c35id=eb13e537583cdf2a The tar-ball (re)created for the upload was created using: $ tar -cf secreted_protein_workflow_v0.0.2.tar.gz README.rst repository_dependencies.xml secreted_protein_workflow.ga I don't have the first tar-ball anymore, but I also don't have any file named _secreted_protein_workflow.ga with a leading underscore in my working directory so I am pretty sure this was created by the Tool Shed somehow. 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/ ___ 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] JSON error trying to update Tool Shed workflow
On Wed, Aug 21, 2013 at 4:30 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, You are probably using a mac if you are seeing this, so can you check to see if your .ga file permissions include an @ sign? Yes, I am, and yes, they have an '@' sign. This an Apple osx issue, and you'll need to do the following: xattr -d com.apple.quarantine name of your exported.ga file $ xattr -d com.apple.quarantine secreted_protein_workflow.ga xattr: secreted_protein_workflow.ga: No such xattr: com.apple.quarantine Odd. Anyway, '@' sign gone. When you do this, it will fix the permissions, and uploading to the tool shed should work. It looks like my second upload attempt already solved this. I don't quite understand what went wrong on the Tool Shed, but is this something you need to handle gracefully? Thanks, 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] Embedding a help text in a Workflow?
On Mon, Aug 19, 2013 at 3:34 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Filed on Trello, https://trello.com/c/HaQnZGvW/1060-embedding-help-text-in-workflows-ideally-rich-text-with-markup Peter On Fri, May 10, 2013 at 5:07 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote: Do you think we could add a new 'rich text' field for a workflow free text help / readme file? Annotations will support HTML, and it's always been the long-term plan that they will include HTML. What's missing is a nice editor for creating HTML annotations. I've taken advantage of this to add a sentence to my workflow annotation with a URL to the Tool Shed where the user can read the full README file. This is a reasonable compromise for now - the annotation needs to be short as it is shown at the top of the page when running a workflow. See: http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow/72f03c2102ee I presume this HTML field gets sanitised (to avoid security exploits), so the user text can't do anything too complicated. Right now actually editing this field is quite painful (and assumes you know raw HTML in order to do any formatting at all), but it works :) 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] Embedding a help text in a Workflow?
On Wed, Aug 21, 2013 at 5:40 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Aug 19, 2013 at 3:34 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Filed on Trello, https://trello.com/c/HaQnZGvW/1060-embedding-help-text-in-workflows-ideally-rich-text-with-markup Peter On Fri, May 10, 2013 at 5:07 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote: Do you think we could add a new 'rich text' field for a workflow free text help / readme file? Annotations will support HTML, and it's always been the long-term plan that they will include HTML. What's missing is a nice editor for creating HTML annotations. I've taken advantage of this to add a sentence to my workflow annotation with a URL to the Tool Shed where the user can read the full README file. This is a reasonable compromise for now - the annotation needs to be short as it is shown at the top of the page when running a workflow. See: http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow/72f03c2102ee I presume this HTML field gets sanitised (to avoid security exploits), so the user text can't do anything too complicated. Right now actually editing this field is quite painful (and assumes you know raw HTML in order to do any formatting at all), but it works :) Bug report for Greg/Dave, filed here: https://trello.com/c/2crUDlsr/1073-workflow-annotation-not-rendered-as-html-on-tool-shed The workflow annotation is isn't rendered as HTML on the Tool Shed :( e.g. http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow or http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow 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] Bismark issue
Hi Shane, please find a new bismark version with an updated dependency on samtools 0.1.19 here: http://toolshed.g2.bx.psu.edu/view/bgruening/bismark Thanks for reporting that issue, Bjoern I've had a bit of a time trying to get Bismark working on our Galaxy instance. The install doesn't work because of the dependency on samtools 0.1.18 but in fact it requires samtools 0.1.19. I have a build of that installed as standard on our system so putting a symlink to that in the place of the samtools built for the bismark wrapper makes it work - I was seeing issues where the BAM file wasn't created and noticed in Bjoern's readme.rst that said it required samtools 0.1.19 or later. Shane -- For urgent cases, contact supp...@biomatters.com Dr Shane Sturrock shane.sturr...@biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand ___ 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] One installable revision is not working for orphan-tool-dependencies - Was: Action type 'template_command' on galaxy-dist?
Hi Greg, seems to work fine! Hello Bjoern, On Aug 21, 2013, at 2:51 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Greg, a first test seems to work as expected for me, will test again with the whole CTB. Great - thanks! If I understood your commit you are searching now for the next valid 'installable' revision, aka a revision with metadata. Yes, this is correct. Just a thought ... is it really the next or the top (valid)? Does it make sense to have revisions for Tool dependency definition. Only one valid revision should be possible, per definition or? So we could skip that revision the system entirely for Tool dependency definition, or? No, this is not a good approach. It is important to check for a valid ( i.e., installable ) changeset revision for all repositories, even those of type tool_dependency_definition. If a tool_dependency_definition repository does not have a tip that is installable, it should be handled just like other repositores that do not have an installable revision. In addition to the error handling that will result from checking for validity, the framework supporting repository revisions is less fragile and easier to maintain if exceptions like this for repository types are not introduced. Ah ok, yes that makes sense. Also if it is not installable, it probably should not be possible to upload it, or? Thanks for the clarification. Bjoern Thanks for the fast fix! Bjoern Thanks! Greg Von Kuster Hello Bjoern, This issue should be resolved in change set 10412:29ab5a6d75a7, whcih is currently running on both tool sheds. No changes should be necessary to any of your current dependency definition files. This changeset was committed to the stable branch, so production Galaxy environments can be safely updated as well. Of course, tracking central in Galaxy environments will get the fix as usual. Thanks very much for reporting this! Greg Von Kuster On Aug 15, 2013, at 9:01 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Dave, the bug is unfortunately still present in the latest Galaxy version. If you try to install http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 you will end up with an error, because numpy is not found. That error appears because scipy was uploaded and afterwards numpy was changed. The consequence is that scipy references on old (not installable) version of numpy and crashes. I would expect that scipy is always looking for the latest version of numpy regardless of what is specified in the numpy XML file. Is that assumption wrong? That would raise the question if revisions are still needed for orphan-tool-dependencies or 'Tool dependency definition'. Is that bug easy to fix? Or do I need to upload all my repositories in the right order again? That would be the consequence, because otherwise I do not get the revision tag updated. Thanks! Bjoern Peter, Björn, The August Galaxy release is out, and the template_command is now in the stable repository and branch. Regarding matplotlib and numpy, I currently only see matplotlib depending on the 74c21f9bdc39 revision of numpy. Is this still an issue, or has it been resolved? --Dave B. On 8/12/13 11:36:00.000, Bjoern Gruening wrote: On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote: On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote: Maybe I should retitle this thread... On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Thank you - installing the NumPy package now works for me, http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 I'm moving on to something odd with matplotlib instead... Peter There are currently two revisions to the main Tool Shed package for numpy, http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 Rev 0: c75482be1d3a - needs not-yet-released features Rev 1: 74c21f9bdc39 - simplified I'm trying to install a package dependent on this via matplotlib - but installing the matplotlib package fails: http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_2 This is something odd, why does it think it needs to install the rev 0 c75482be1d3a version of package_numpy_1_7? See screenshot, except here: Repository dependencies - installation of these additional repositories is required Name RevisionOwner Installation status package_freetype_2_4 8761091302c4iuc Installed package_numpy_1_7 74c21f9bdc39iuc Installed package_numpy_1_7 c75482be1d3aiuc Uninstalled Yes, the matplotlib tool_dependencies.xml does list the original revision: package name=numpy version=1.7.1 repository changeset_revision=c75482be1d3a
Re: [galaxy-dev] [galaxy-iuc] Duplicated entries in Manage installed tool shed repositories table
We should create a Tool Shed Hackathon, I'm an expert in producing 'white ghosts' :) Thanks Peter, As soon as I can get the steps to produce white ghost, I'll get a fix committed - I've not been able to produce one yet. Greg Von Kuster On Aug 21, 2013, at 5:41 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Aug 20, 2013 at 8:34 PM, Greg Von Kuster g...@bx.psu.edu wrote: Peter and Ross, I've not been able to reproduce this behavior, most likely because I am not following the precise steps you've used when you see it. Can you clarify what you do when you encounter it? Thanks! Greg Von Kuster If it happens to me again, I'll try to narrow down what triggered it. Meanwhile this sounds like another white ghost tool stuck in the new state: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016193.html Peter ___ galaxy-iuc mailing list galaxy-...@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-iuc ___ 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] One installable revision is not working for orphan-tool-dependencies - Was: Action type 'template_command' on galaxy-dist?
Hello Bjoern, On Aug 21, 2013, at 1:27 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Greg, seems to work fine! Hello Bjoern, On Aug 21, 2013, at 2:51 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Greg, a first test seems to work as expected for me, will test again with the whole CTB. Great - thanks! If I understood your commit you are searching now for the next valid 'installable' revision, aka a revision with metadata. Yes, this is correct. Just a thought ... is it really the next or the top (valid)? In the case of repositories of type tool_dependency_definition, if the repository is associated with an installable revision, it will always be the tip. So in these cases, next will be tip or None, in which case an error has been encountered and should be handled as usual. Does it make sense to have revisions for Tool dependency definition. Only one valid revision should be possible, per definition or? So we could skip that revision the system entirely for Tool dependency definition, or? No, this is not a good approach. It is important to check for a valid ( i.e., installable ) changeset revision for all repositories, even those of type tool_dependency_definition. If a tool_dependency_definition repository does not have a tip that is installable, it should be handled just like other repositores that do not have an installable revision. In addition to the error handling that will result from checking for validity, the framework supporting repository revisions is less fragile and easier to maintain if exceptions like this for repository types are not introduced. Ah ok, yes that makes sense. Also if it is not installable, it probably should not be possible to upload it, or? It has always been possible to upload changeset revisions with invalid contents. The tool shed will simply attempt to communicate the reason the contents are invalid. I'm not sure this case should be handled differently. Thanks for the clarification. Bjoern Thanks for the fast fix! Bjoern Thanks! Greg Von Kuster Hello Bjoern, This issue should be resolved in change set 10412:29ab5a6d75a7, whcih is currently running on both tool sheds. No changes should be necessary to any of your current dependency definition files. This changeset was committed to the stable branch, so production Galaxy environments can be safely updated as well. Of course, tracking central in Galaxy environments will get the fix as usual. Thanks very much for reporting this! Greg Von Kuster On Aug 15, 2013, at 9:01 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Dave, the bug is unfortunately still present in the latest Galaxy version. If you try to install http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12 you will end up with an error, because numpy is not found. That error appears because scipy was uploaded and afterwards numpy was changed. The consequence is that scipy references on old (not installable) version of numpy and crashes. I would expect that scipy is always looking for the latest version of numpy regardless of what is specified in the numpy XML file. Is that assumption wrong? That would raise the question if revisions are still needed for orphan-tool-dependencies or 'Tool dependency definition'. Is that bug easy to fix? Or do I need to upload all my repositories in the right order again? That would be the consequence, because otherwise I do not get the revision tag updated. Thanks! Bjoern Peter, Björn, The August Galaxy release is out, and the template_command is now in the stable repository and branch. Regarding matplotlib and numpy, I currently only see matplotlib depending on the 74c21f9bdc39 revision of numpy. Is this still an issue, or has it been resolved? --Dave B. On 8/12/13 11:36:00.000, Bjoern Gruening wrote: On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote: On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote: Maybe I should retitle this thread... On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Thank you - installing the NumPy package now works for me, http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 I'm moving on to something odd with matplotlib instead... Peter There are currently two revisions to the main Tool Shed package for numpy, http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7 Rev 0: c75482be1d3a - needs not-yet-released features Rev 1: 74c21f9bdc39 - simplified I'm trying to install a package dependent on this via matplotlib - but installing the matplotlib package fails: http://toolshed.g2.bx.psu.edu/view/iuc/package_matplotlib_1_2 This is something odd, why does it think it needs to install the rev 0 c75482be1d3a version of package_numpy_1_7? See
[galaxy-dev] Why does my trackster complain about not being able to display BED files?
Hi,I am using the latest version of galaxy at my local installation and I try to use trackster to display a simple BED file, but it invariably complains about not having a converter for this datatype and it tells me to check mydatatypes_conf.xml which I did (not sure what I should be looking for, but this is the section on BED files...Am I missing a converter? And why would a BED file even needed to be converted?ThanksThon datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true" converter file="bed_to_gff_converter.xml" target_datatype="gff"/ converter file="interval_to_coverage.xml" target_datatype="coverage"/ converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/ converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/ converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/ converter file="bed_to_fli_converter.xml" target_datatype="fli"/ !-- display file="ucsc/interval_as_bed.xml" / -- !-- display file="genetrack.xml" / -- display file="igb/bed.xml" / /datatype datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true" converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/ /datatype datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" / !-- datatype extension="bed6" type="galaxy.datatypes.interval:Bed6" converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/ /datatype -- datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" / datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true" converter file="len_to_linecount.xml" target_datatype="linecount" / /datatype datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" dis___ 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] Why does my trackster complain about not being able to display BED files?
Hi Anthonius, Do you have the BEDTools installed and its directory added to your PATH environment variable? Trackster uses compressed file formats to reduce the amount of data transfers. I hope this helps, Sam On Wed, Aug 21, 2013 at 4:11 PM, Anthonius deBoer thondeb...@me.com wrote: Hi, I am using the latest version of galaxy at my local installation and I try to use trackster to display a simple BED file, but it invariably complains about not having a converter for this datatype and it tells me to check my datatypes_conf.xml which I did (not sure what I should be looking for, but this is the section on BED files... Am I missing a converter? And why would a BED file even needed to be converted? Thanks Thon datatype extension=bed type=galaxy.datatypes.interval:Bed display_in_upload=true converter file=bed_to_gff_converter.xml target_datatype=gff/ converter file=interval_to_coverage.xml target_datatype=coverage/ converter file=bed_to_bgzip_converter.xml target_datatype=bgzip/ converter file=bed_to_tabix_converter.xml target_datatype=tabix depends_on=bgzip/ converter file=bed_to_summary_tree_converter.xml target_datatype=summary_tree/ converter file=bed_to_fli_converter.xml target_datatype=fli/ !-- display file=ucsc/interval_as_bed.xml / -- !-- display file=genetrack.xml / -- display file=igb/bed.xml / /datatype datatype extension=bedgraph type=galaxy.datatypes.interval:BedGraph display_in_upload=true converter file=bedgraph_to_bigwig_converter.xml target_datatype=bigwig/ /datatype datatype extension=bedstrict type=galaxy.datatypes.interval:BedStrict / !-- datatype extension=bed6 type=galaxy.datatypes.interval:Bed6 converter file=bed_to_genetrack_converter.xml target_datatype=genetrack/ /datatype -- datatype extension=bed12 type=galaxy.datatypes.interval:Bed12 / datatype extension=len type=galaxy.datatypes.chrominfo:ChromInfo display_in_upload=true converter file=len_to_linecount.xml target_datatype=linecount / /datatype datatype extension=bigbed type=galaxy.datatypes.binary:BigBed mimetype=application/octet-stream dis ___ 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] Bismark issue
Hi Bjoern, I've upgraded our machine and confirmed it now works fine. Thanks for that! Shane On 22/08/2013, at 5:17 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Shane, please find a new bismark version with an updated dependency on samtools 0.1.19 here: http://toolshed.g2.bx.psu.edu/view/bgruening/bismark Thanks for reporting that issue, Bjoern I've had a bit of a time trying to get Bismark working on our Galaxy instance. The install doesn't work because of the dependency on samtools 0.1.18 but in fact it requires samtools 0.1.19. I have a build of that installed as standard on our system so putting a symlink to that in the place of the samtools built for the bismark wrapper makes it work - I was seeing issues where the BAM file wasn't created and noticed in Bjoern's readme.rst that said it required samtools 0.1.19 or later. Shane -- For urgent cases, contact supp...@biomatters.com Dr Shane Sturrock shane.sturr...@biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand ___ 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/ -- For urgent cases, contact supp...@biomatters.com Dr Shane Sturrock shane.sturr...@biomatters.com Senior Scientist Tel: +64 (0) 9 379 5064 76 Anzac Ave Auckland New Zealand smime.p7s Description: S/MIME cryptographic 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/
[galaxy-dev] error installing dependency for tool shed repository.
I've just created a repository in the sandbox and have been trying to test the installation of a dependency my tool needs. The tool needs the python module requests and I've written code. I get an error: STDERR python: can't open file 'setup.py': [Errno 2] No such file or directory I've modeled my code on examples I've found in the tool shed. I've replaced the requests module with other python modules and these are installed ok. I can also download and manually install requests with python setup.py install Any suggestions as to what I may be doing wrong? tool_dependencies.xml: ?xml version=1.0? tool_dependency package name=requests version=1.2.3 install version=1.0 actions action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/requests-1.2.3.tar.gz/action action type=make_directory$INSTALL_DIR/lib/python/action action type=make_directory$INSTALL_DIR/bin/action action type=set_environment environment_variable name=PYTHONPATH action=append_to$INSTALL_DIR/lib/python/environment_variable environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action action type=shell_commandpython setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action /actions /install readme /readme /package /tool_dependency ingTest.xml: tool id=ingTest name=ingTest version=1.0 descriptionTesting Tool Shed/description requirements requirement type=package version=1.2.3requests/requirement /requirements command interpreter=python /command inputs /inputs outputs /outputs help .. class:: infomark /help /tool Thanks, -Curt Curt Palm Data Engineer INGENUITY SYSTEMS | www.ingenuity.com 1700 Seaport Blvd., 3rd Floor | Redwood City, CA 94063 650.381.5084 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?
Yep...$ bedtools --versionbedtools v2.17.0ThonOn Aug 21, 2013, at 01:40 PM, sam guerler aysam.guer...@gmail.com wrote:Hi Anthonius,Do you have the BEDTools installed and its directory added to your PATH environment variable? Trackster uses compressed file formats to reduce the amount of data transfers.I hope this helps,SamOn Wed, Aug 21, 2013 at 4:11 PM, Anthonius deBoer thondeb...@me.com wrote:Hi,I am using the latest version of galaxy at my local installation and I try to use trackster to display a simple BED file, but it invariably complains about not having a converter for this datatype and it tells me to check mydatatypes_conf.xml which I did (not sure what I should be looking for, but this is the section on BED files...Am I missing a converter? And why would a BED file even needed to be converted?ThanksThon datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true" converter file="bed_to_gff_converter.xml" target_datatype="gff"/ converter file="interval_to_coverage.xml" target_datatype="coverage"/ converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/ converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/ converter file="bed_to_summary_tree_converter.xml" target_datatype="summary_tree"/ converter file="bed_to_fli_converter.xml" target_datatype="fli"/ !-- display file="ucsc/interval_as_bed.xml" / -- !-- display file="genetrack.xml" / -- display file="igb/bed.xml" / /datatype datatype extension="bedgraph" type="galaxy.datatypes.interval:BedGraph" display_in_upload="true" converter file="bedgraph_to_bigwig_converter.xml" target_datatype="bigwig"/ /datatype datatype extension="bedstrict" type="galaxy.datatypes.interval:BedStrict" / !-- datatype extension="bed6" type="galaxy.datatypes.interval:Bed6" converter file="bed_to_genetrack_converter.xml" target_datatype="genetrack"/ /datatype -- datatype extension="bed12" type="galaxy.datatypes.interval:Bed12" / datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true" converter file="len_to_linecount.xml" target_datatype="linecount" / /datatype datatype extension="bigbed" type="galaxy.datatypes.binary:BigBed" mimetype="application/octet-stream" dis___ 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] error installing dependency for tool shed repository.
Curt, I tried installing the ingtest repository on a local instance of Galaxy, and the requests python module installed without errors. Which revision of Galaxy are you trying to install this repository into, and what kind of environment are you running on that system? --Dave B. On 2013-08-21 19:12, Curt Palm wrote: I've just created a repository in the sandbox and have been trying to test the installation of a dependency my tool needs. The tool needs the python module requests and I've written code. I get an error: STDERR python: can't open file 'setup.py': [Errno 2] No such file or directory I've modeled my code on examples I've found in the tool shed. I've replaced the requests module with other python modules and these are installed ok. I can also download and manually install requests with python setup.py install Any suggestions as to what I may be doing wrong? tool_dependencies.xml: ?xml version=1.0? tool_dependency package name=requests version=1.2.3 install version=1.0 actions action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/requests-1.2.3.tar.gz/action action type=make_directory$INSTALL_DIR/lib/python/action action type=make_directory$INSTALL_DIR/bin/action action type=set_environment environment_variable name=PYTHONPATH action=append_to$INSTALL_DIR/lib/python/environment_variable environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action action type=shell_commandpython setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action /actions /install readme /readme /package /tool_dependency ingTest.xml: tool id=ingTest name=ingTest version=1.0 descriptionTesting Tool Shed/description requirements requirement type=package version=1.2.3requests/requirement /requirements command interpreter=python /command inputs /inputs outputs /outputs help .. class:: infomark /help /tool Thanks, -Curt Curt Palm Data Engineer INGENUITY SYSTEMS | www.ingenuity.com 1700 Seaport Blvd., 3rd Floor | Redwood City, CA 94063 650.381.5084 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] error installing dependency for tool shed repository.
Hi Dave, I made changes giving the suggestions of Ross, I got a different error and that gave me insight as to what was going on. I uploaded new xml: ?xml version=1.0? tool_dependency package name=requests version=1.2.3 install version=1.0 actions action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/re quests-1.2.3.tar.gz/action action type=make_directory$INSTALL_DIR/lib/python/action action type=shell_commandexport PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python amp;amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action action type=set_environment environment_variable name=PYTHONPATH action=append_to$INSTALL_DIR/lib/python/environment_variable environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme /readme /package /tool_dependency And this worked for me. I'm thinking you may have downloaded after I made the changes. -Curt On 8/21/13 6:01 PM, Dave Bouvier d...@bx.psu.edu wrote: Curt, I tried installing the ingtest repository on a local instance of Galaxy, and the requests python module installed without errors. Which revision of Galaxy are you trying to install this repository into, and what kind of environment are you running on that system? --Dave B. Try moving the action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/re quests-1.2.3.tar.gz/action line so it's the one before action type=shell_commandpython setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action I think I've been bitten by this - it seems download_by_url changes the current path but only temporarily so you need to run setup.py immediately as the next step? If this works, please confirm to the entire list - I'm sending this to you just in case I'm full of it :) On Thu, Aug 22, 2013 at 9:12 AM, Curt Palm cp...@ingenuity.com wrote: I've just created a repository in the sandbox and have been trying to test the installation of a dependency my tool needs. The tool needs the python module requests and I've written code. I get an error: STDERR python: can't open file 'setup.py': [Errno 2] No such file or directory I've modeled my code on examples I've found in the tool shed. I've replaced the requests module with other python modules and these are installed ok. I can also download and manually install requests with python setup.py install Any suggestions as to what I may be doing wrong? -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J On 2013-08-21 19:12, Curt Palm wrote: I've just created a repository in the sandbox and have been trying to test the installation of a dependency my tool needs. The tool needs the python module requests and I've written code. I get an error: STDERR python: can't open file 'setup.py': [Errno 2] No such file or directory I've modeled my code on examples I've found in the tool shed. I've replaced the requests module with other python modules and these are installed ok. I can also download and manually install requests with python setup.py install Any suggestions as to what I may be doing wrong? tool_dependencies.xml: ?xml version=1.0? tool_dependency package name=requests version=1.2.3 install version=1.0 actions action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/ requests-1.2.3.tar.gz/action action type=make_directory$INSTALL_DIR/lib/python/action action type=make_directory$INSTALL_DIR/bin/action action type=set_environment environment_variable name=PYTHONPATH action=append_to$INSTALL_DIR/lib/python/environment_variable environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action action type=shell_commandpython setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action /actions /install readme /readme /package /tool_dependency ingTest.xml: tool id=ingTest name=ingTest version=1.0 descriptionTesting Tool Shed/description requirements requirement type=package version=1.2.3requests/requirement /requirements command interpreter=python /command inputs /inputs outputs /outputs help .. class:: infomark /help /tool Thanks, -Curt Curt Palm Data Engineer INGENUITY SYSTEMS | www.ingenuity.com 1700 Seaport Blvd., 3rd Floor | Redwood City,
Re: [galaxy-dev] error installing dependency for tool shed repository.
Curt, I'm happy to hear that everything is now working. If you encounter any further issues, please don't hesitate to contact us. --Dave B. On 2013-08-21 21:31, Curt Palm wrote: Hi Dave, I made changes giving the suggestions of Ross, I got a different error and that gave me insight as to what was going on. I uploaded new xml: ?xml version=1.0? tool_dependency package name=requests version=1.2.3 install version=1.0 actions action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/re quests-1.2.3.tar.gz/action action type=make_directory$INSTALL_DIR/lib/python/action action type=shell_commandexport PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python amp;amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action action type=set_environment environment_variable name=PYTHONPATH action=append_to$INSTALL_DIR/lib/python/environment_variable environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme /readme /package /tool_dependency And this worked for me. I'm thinking you may have downloaded after I made the changes. -Curt On 8/21/13 6:01 PM, Dave Bouvier d...@bx.psu.edu wrote: Curt, I tried installing the ingtest repository on a local instance of Galaxy, and the requests python module installed without errors. Which revision of Galaxy are you trying to install this repository into, and what kind of environment are you running on that system? --Dave B. Try moving the action type=download_by_urlhttp://pypi.python.org/packages/source/r/requests/re quests-1.2.3.tar.gz/action line so it's the one before action type=shell_commandpython setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin/action I think I've been bitten by this - it seems download_by_url changes the current path but only temporarily so you need to run setup.py immediately as the next step? If this works, please confirm to the entire list - I'm sending this to you just in case I'm full of it :) On Thu, Aug 22, 2013 at 9:12 AM, Curt Palm cp...@ingenuity.com wrote: I've just created a repository in the sandbox and have been trying to test the installation of a dependency my tool needs. The tool needs the python module requests and I've written code. I get an error: STDERR python: can't open file 'setup.py': [Errno 2] No such file or directory I've modeled my code on examples I've found in the tool shed. I've replaced the requests module with other python modules and these are installed ok. I can also download and manually install requests with python setup.py install Any suggestions as to what I may be doing wrong? ___ 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/
