[galaxy-dev] testtoolshed : python-2.7 installation error
Hi, I get an installation error on the python 2.7 package in the test toolshed. I used the 'contact owner' function, but wanted to mention it here too, as there hasn't been reaction so far. Sorry for double posting if so. Error: tar (child): 5.2.tar.bz2: Cannot open: No such file or directory A similar error is in the Test run outputs. I believe it is related to the following (unnecessary) line in the tool_dependency.xml: action type=change_directory../action located just after the download_file action for the 5.2.tar.bz2 file. Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer ___ 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] testtoolshed : python-2.7 installation error
Hi Geert, Which tool is this? Peter On Thu, Aug 7, 2014 at 9:00 AM, Geert Vandeweyer geert.vandewey...@uantwerpen.be wrote: Hi, I get an installation error on the python 2.7 package in the test toolshed. I used the 'contact owner' function, but wanted to mention it here too, as there hasn't been reaction so far. Sorry for double posting if so. Error: tar (child): 5.2.tar.bz2: Cannot open: No such file or directory A similar error is in the Test run outputs. I believe it is related to the following (unnecessary) line in the tool_dependency.xml: action type=change_directory../action located just after the download_file action for the 5.2.tar.bz2 file. Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer ___ 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] testtoolshed : python-2.7 installation error
Hi Geert, are you talking about the package_python_* repository? Am 07.08.2014 um 10:00 schrieb Geert Vandeweyer: Hi, I get an installation error on the python 2.7 package in the test toolshed. I used the 'contact owner' function, but wanted to mention it here too, as there hasn't been reaction so far. Sorry for double posting if so. Oh this is interesting, because we did not get notified. It is from IUC correct? Error: tar (child): 5.2.tar.bz2: Cannot open: No such file or directory A similar error is in the Test run outputs. I believe it is related to the following (unnecessary) line in the tool_dependency.xml: action type=change_directory../action This can be. The cwd directory handling changed a lot in recent versions, due to bugs. And for a few repositories we still have the workarounds included. I will upload a new version without this workaround and see if it passes. located just after the download_file action for the 5.2.tar.bz2 file. Best, Geert ___ 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] testtoolshed : python-2.7 installation error
sorry about that confusion :-) Yes, I'm talking about the package_python_2.7 repository. The same error is also present in the test runs of the package_python_3* repo. Best, Geert On 08/07/2014 11:45 AM, Björn Grüning wrote: Hi Geert, are you talking about the package_python_* repository? Am 07.08.2014 um 10:00 schrieb Geert Vandeweyer: Hi, I get an installation error on the python 2.7 package in the test toolshed. I used the 'contact owner' function, but wanted to mention it here too, as there hasn't been reaction so far. Sorry for double posting if so. Oh this is interesting, because we did not get notified. It is from IUC correct? Error: tar (child): 5.2.tar.bz2: Cannot open: No such file or directory A similar error is in the Test run outputs. I believe it is related to the following (unnecessary) line in the tool_dependency.xml: action type=change_directory../action This can be. The cwd directory handling changed a lot in recent versions, due to bugs. And for a few repositories we still have the workarounds included. I will upload a new version without this workaround and see if it passes. located just after the download_file action for the 5.2.tar.bz2 file. Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer ___ 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] testtoolshed : python-2.7 installation error
Hi, I updated the python wrappers. Depending on your Galaxy version it should work now. @Greg, we still have the error that 'contact owner' does not seem to work :( Cheers, Bjoern Am 07.08.2014 um 12:11 schrieb Geert Vandeweyer: sorry about that confusion :-) Yes, I'm talking about the package_python_2.7 repository. The same error is also present in the test runs of the package_python_3* repo. Best, Geert On 08/07/2014 11:45 AM, Björn Grüning wrote: Hi Geert, are you talking about the package_python_* repository? Am 07.08.2014 um 10:00 schrieb Geert Vandeweyer: Hi, I get an installation error on the python 2.7 package in the test toolshed. I used the 'contact owner' function, but wanted to mention it here too, as there hasn't been reaction so far. Sorry for double posting if so. Oh this is interesting, because we did not get notified. It is from IUC correct? Error: tar (child): 5.2.tar.bz2: Cannot open: No such file or directory A similar error is in the Test run outputs. I believe it is related to the following (unnecessary) line in the tool_dependency.xml: action type=change_directory../action This can be. The cwd directory handling changed a lot in recent versions, due to bugs. And for a few repositories we still have the workarounds included. I will upload a new version without this workaround and see if it passes. located just after the download_file action for the 5.2.tar.bz2 file. Best, Geert ___ 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] changes to upload.py
I am concerned about having to merge those changes later on so thank you for confirming that. I was wondering if maybe these things were a moot point now. Certainly bam and sniff are built in? Here is additional code found in their older hack: if dataset.is_multi_byte: data_type = 'multi-byte char' ext = sniff.guess_ext( dataset.path, is_multi_byte=True ) # Is dataset content supported sniffable binary? elif check_bam( dataset.path ): ext = 'bam' data_type = 'bam' elif check_sff( dataset.path ): ext = 'sff' data_type = 'sff' elif check_celstgz( dataset.path ): ext = 'cels.tgz' data_type = 'cels.tgz' We have added info to the datatypes_conf.xml file for other data types they need to support in their tools so maybe I can just add this cels.tgz info there too. I will have to find someone who knows python better than I do to tell me what's going on in their additions to the upload.py file. Thanks, Dori -Original Message- From: Peter Cock [mailto:p.j.a.c...@googlemail.com] Sent: Thursday, August 07, 2014 11:35 AM To: Sajdak, Doris Cc: Galaxy Dev Subject: Re: [galaxy-dev] changes to upload.py On Thu, Aug 7, 2014 at 4:29 PM, Sajdak, Doris dj...@buffalo.edu wrote: I’m in an odd situation: I was given an older version of Galaxy with additional tools built into it by a new faculty member. He brought this from his former institutions and wanted us to run his Galaxy instance on our systems. We don’t want to support several instances so we agreed to put his tools into our Galaxy implementation. However, we are running into all kinds of snags. The latest issue is that we realized changes have been made to upload.py to allow for additional data types. Here’s an example of what I mean: def check_bam( temp_name ): return Bam().sniff( temp_name ) def check_sff( temp_name ): return Sff().sniff( temp_name ) def check_celstgz( temp_name ): return CelsTgz().sniff( temp_name ) While this doesn’t seem like a big deal to add those changes into our installation, I’m concerned that doing so will make us unable to update Galaxy in the future. Can you either confirm or deny that changes to upload.py on our system will be overwritten with Galaxy updates? Thanks, Dori That will cause you trouble with having to merge any future changes to upload.py as well. In this case, the sniffing should be handled via the Galaxy datatypes mechanism (see datatypes_conf.xml for instance), so these hacks may not be needed anymore? 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] The status is being set to Never installed
When I install a tool from the toolshed that has type=set_environment as a requirement, I get this in the main.log: Creating a new record for version None of tool dependency SCRIPT_PATH for revision 5fed38c7e063 of repository mirdeep2. The status is being set to Never installed. Consequently, nothing in the tool_dependency directory is created. The tool is shown to have missing dependencies in the 'Manage installed tool shed repositories' panel. Is there something special that must be done to allow a tool to have only an environment setting as a dependency? Is there something that can be done to fix the problem, other than going into the database and changing the tool_dependency.status from 'Never installed' to 'Installed' and manually creating the subdirectories? David Hoover, PhD Helix Systems Staff ___ 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] ToolShed error: samtools installation failure
That's correct -- none of them are run automatically. On Wed, Aug 6, 2014 at 3:08 PM, Beginner TI ruiwang...@gmail.com wrote: Ah, I think that I had a wrong impression before...so by default, the migration scripts listed here will NOT be executed, am I correct? I think that 'done' at the bottom made me think that it was executed... So it's the user's responsibility to execute those scripts, correct? Thanks, Rui The Emboss 5.0.0 tools have been eliminated from the distribution and the Emboss datatypes have been removed fromdatatypes_conf.xml.sample. You should remove the Emboss datatypes from your version of datatypes_conf.xml. Therepositories named emboss_5 and emboss_datatypes from the main Galaxy Tool Shed at http://toolshed.g2.bx.psu.eduwill be installed into your local Galaxy instance at the location discussed above by running the following command.vsh ./scripts/migrate_tools/0002_tools.sh^doneAfter the installation process finishes, you can start your Galaxy server. As part of this installation process,entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so thesetools will continue to be loaded into your tool panel. Because of this, existing entries for these files should beremoved from your file named ./tool_conf.xml, but only after the installation process finishes. On Wed, Aug 6, 2014 at 10:53 AM, Dannon Baker dannon.ba...@gmail.com wrote: Ahh, I think I see the issue. So, many galaxy tools are being migrated out of the distribution and to the toolshed -- you can find much more detailed information here: https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution The samtools wrappers were migrated in migration 8, I think, if that helps. Basically, there's a migration script that should have shown up in a terminal somewhere when you ran your galaxy instance after the update that will contain a reference to script(s) that you can run that'll take care of the migration. Let me know if you need more information, if the wiki page doesn't clear it up! -Dannon On Wed, Aug 6, 2014 at 1:36 PM, Beginner TI ruiwang...@gmail.com wrote: Hi Dannon, Thanks for the reply. Sorry for the duplicate. I was wondering that the original subject sounded like a user problem so I updated it... Actually we are having a little down time right now for a file system check. I'll try your suggestions asap and let you know. At the mean time, could you please elaborate this a little bit? I noticed that in the tool_conf.xml, not every tool is shown on the panel although they are all defined there in the same format. I also noticed that all the tool xml files, such as section id=samtools name=NGS: SAM Tools tool file=samtools/sam_bitwise_flag_filter.xml / tool file=samtools/sam2interval.xml / tool file=samtools/sam_to_bam.xml / tool file=samtools/bam_to_sam.xml / tool file=samtools/sam_merge.xml / tool file=samtools/samtools_mpileup.xml / tool file=samtools/sam_pileup.xml / tool file=samtools/pileup_parser.xml / tool file=samtools/pileup_interval.xml / tool file=samtools/samtools_flagstat.xml / tool file=samtools/samtools_rmdup.xml / tool file=samtools/samtools_slice_bam.xml / /section the directory samtools and all these xml files are no longer in the tools directory. seems that upgrade deleted them. is this correct? or they are moved to somewhere else? I looked around but didn't see. Based on this, I think that even I removed the tool_panel.xml file you mentioned, I will still not be able to restore samtools even I could see it...could you please let me know how I could configure this? Thanks, Rui On Wed, Aug 6, 2014 at 10:23 AM, Dannon Baker dannon.ba...@gmail.com wrote: Hi Rui, We'll definitely take a look. Please allow for a reasonable time period to pass before sending duplicate emails to the list asking for assistance. That said, does deleting your integrated_tool_panel.xml (this file is automatically regenerated by Galaxy, safe to remove it and restart) bring back your manually installed samtools? On Wed, Aug 6, 2014 at 1:08 PM, Beginner TI ruiwang...@gmail.com wrote: Could someone please take a look? Thanks, Rui On Tue, Aug 5, 2014 at 8:27 PM, Beginner TI ruiwang...@gmail.com wrote: Dear Admin, Since the upgrade, I lost the samtools that I installed myself. Although it is still in the tool_conf.xml, it does not show up on the panel. I tried to install from toolshed, but failed. Error messages pasted below. Could someone take a look? Thanks, Rui ⇝ AttributeError: 'NoneType' object has no attribute 'strip' URL: http://128.125.28.215/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=d2c3034af88d998dchangeset_revisions=af65bfb54977 Module
