Re: [galaxy-dev] how to manage multiple tool versions
Hi Bjoern, Thanks for the note, and sorry I could not type your name in the original alphabet -- it looks Icelandic. :-) I'll follow your instructions and see how it goes. Best, Rui On Fri, Mar 7, 2014 at 7:17 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi Rui, if you want to use only the local installation and not the toolshed one, go to the toolshed installation inside your galaxy and remove under manage tool dependencies the dependency on macs2. As soon as you get rid of the dependency the local installation is used. Cheers, Bjoern P.S. There is also a MACS2 version now for testing Am 08.03.2014 00:48, schrieb ruiwang.sz: Hi Guys, I'm sorry to post multiple times for the same question. Now I removed all the specifics of my problem and I only want someone to point me to the right documentation. Admins, I know you are busy, but don't you want more people to benefit from this platform? When galaxy upgraded it started using the tool_shed version of the tool and killed the tools we installed ourselves. Right now we have both versions. How should we manage this situation properly if we don't want the tool_shed version and want to keep using what we had before? Nate said that MACS came with galaxy before. I didn't know that. From the day we started using MACS it was installed by ourselves. Not sure if that caused the problem. Thanks, Rui ___ 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] upload error
Hi John, Thanks for the note. Please see inline. On Fri, Mar 7, 2014 at 7:18 PM, John Chilton jmchil...@gmail.com wrote: Hmm... I am not certain but it sounds like the migration script ripped something out of your Galaxy tool panel that you did not want it to? This is unfortunate - but I don't think it would happen again now that the migration process is complete. Some future update to Galaxy may include additional migrations scripts but now that macs is out it won't ever be migrated again. imagine you can just update your tool_conf.xml file to point to your existing macs wrapper you set up manually and you can either leave the devteam version of macs in place or uninstall it if you prefer your own. Is it not this easy? Yes that's what I thought, but I was worrying that if I remove devteam version of macs from the migrated_tool.conf, I might break something potentially useful for galaxy. Mainly, I try not to manually change things since that would not be maintainable over time. That's why I was asking how to handle this properly. It's great to have your confirmation that it works this way. :-) Thanks, Rui ___ 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] upload error
Awesome. How is the upload behaving? Are you still having issues with it? M. On Sat, Mar 8, 2014 at 12:20 PM, ruiwang.sz ruiwang...@gmail.com wrote: Hi John, Thanks for the note. Please see inline. On Fri, Mar 7, 2014 at 7:18 PM, John Chilton jmchil...@gmail.com wrote: Hmm... I am not certain but it sounds like the migration script ripped something out of your Galaxy tool panel that you did not want it to? This is unfortunate - but I don't think it would happen again now that the migration process is complete. Some future update to Galaxy may include additional migrations scripts but now that macs is out it won't ever be migrated again. imagine you can just update your tool_conf.xml file to point to your existing macs wrapper you set up manually and you can either leave the devteam version of macs in place or uninstall it if you prefer your own. Is it not this easy? Yes that's what I thought, but I was worrying that if I remove devteam version of macs from the migrated_tool.conf, I might break something potentially useful for galaxy. Mainly, I try not to manually change things since that would not be maintainable over time. That's why I was asking how to handle this properly. It's great to have your confirmation that it works this way. :-) Thanks, Rui ___ 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/
