Re: [galaxy-dev] How to enable auto option for newly added file formats
On Tue, Jun 25, 2013 at 8:28 AM, shashi shekhar me_shash...@yahoo.co.in wrote: Hi, yeah ..it is same thing... but i followed the galaxy -datatype(how to add new file format)tutorial ..but still my newly added file format is not working with auto option it always display txt format ..it is similar to txt format with some specific property .. Reagrds shashi So you've followed this: http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes Have you tested your sniff method works? Have you checked the order the file types are tested? Peter P.S. Don't forget to CC the mailing list. ___ 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] How to enable auto option for newly added file formats
Hi, yeah i followd this tutorial .. http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes yeah ,i have tested my sniff methods .it works fine .when i upload any pdb file by using the option file format (PDB ) , it works but with auto option it doesnot work regards shashi From: Peter Cock p.j.a.c...@googlemail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Galaxy Dev galaxy-...@bx.psu.edu Sent: Tuesday, 25 June 2013 1:14 PM Subject: Re: [galaxy-dev] How to enable auto option for newly added file formats On Tue, Jun 25, 2013 at 8:28 AM, shashi shekhar me_shash...@yahoo.co.in wrote: Hi, yeah ..it is same thing... but i followed the galaxy -datatype(how to add new file format)tutorial ..but still my newly added file format is not working with auto option it always display txt format ..it is similar to txt format with some specific property .. Reagrds shashi So you've followed this: http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes Have you tested your sniff method works? Have you checked the order the file types are tested? Peter P.S. Don't forget to CC the mailing list.___ 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] How to enable auto option for newly added file formats
Hi Shashi, can you try my molecule datatype repository? http://testtoolshed.g2.bx.psu.edu/view/bgruening/chemical_datatypes The source is here: https://github.com/bgruening/galaxytools/blob/master/chemicaltoolbox/datatypes/molecules.py I have also a PDB definition inluded maybe that works for you and we can join the effort. Thanks, Bjoern Hi, yeah i followd this tutorial .. http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes yeah ,i have tested my sniff methods .it works fine .when i upload any pdb file by using the option file format (PDB ) , it works but with auto option it doesnot work regards shashi __ From: Peter Cock p.j.a.c...@googlemail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Galaxy Dev galaxy-...@bx.psu.edu Sent: Tuesday, 25 June 2013 1:14 PM Subject: Re: [galaxy-dev] How to enable auto option for newly added file formats On Tue, Jun 25, 2013 at 8:28 AM, shashi shekhar me_shash...@yahoo.co.in wrote: Hi, yeah ..it is same thing... but i followed the galaxy -datatype(how to add new file format)tutorial ..but still my newly added file format is not working with auto option it always display txt format ..it is similar to txt format with some specific property .. Reagrds shashi So you've followed this: http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes Have you tested your sniff method works? Have you checked the order the file types are tested? Peter P.S. Don't forget to CC the mailing list. ___ 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] How to enable auto option for newly added file formats
Hi Björn, Thanks Björn for the reply , But pdb file format is working not working auto option ..it works with by selecting PDB file format option in galaxy ... do i have to modify any registry.py file or any other file ? i have included only init ,init_meta and sniff function in PDB ( txt ) in data.py file .. Regards shahsi From: Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de To: shashi shekhar me_shash...@yahoo.co.in Cc: Peter Cock p.j.a.c...@googlemail.com; Galaxy Dev galaxy-...@bx.psu.edu Sent: Tuesday, 25 June 2013 3:40 PM Subject: Re: [galaxy-dev] How to enable auto option for newly added file formats Hi Shashi, can you try my molecule datatype repository? http://testtoolshed.g2.bx.psu.edu/view/bgruening/chemical_datatypes The source is here: https://github.com/bgruening/galaxytools/blob/master/chemicaltoolbox/datatypes/molecules.py I have also a PDB definition inluded maybe that works for you and we can join the effort. Thanks, Bjoern Hi, yeah i followd this tutorial .. http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes yeah ,i have tested my sniff methods .it works fine .when i upload any pdb file by using the option file format (PDB ) , it works but with auto option it doesnot work regards shashi __ From: Peter Cock p.j.a.c...@googlemail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Galaxy Dev galaxy-...@bx.psu.edu Sent: Tuesday, 25 June 2013 1:14 PM Subject: Re: [galaxy-dev] How to enable auto option for newly added file formats On Tue, Jun 25, 2013 at 8:28 AM, shashi shekhar me_shash...@yahoo.co.in wrote: Hi, yeah ..it is same thing... but i followed the galaxy -datatype(how to add new file format)tutorial ..but still my newly added file format is not working with auto option it always display txt format ..it is similar to txt format with some specific property .. Reagrds shashi So you've followed this: http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes Have you tested your sniff method works? Have you checked the order the file types are tested? Peter P.S. Don't forget to CC the mailing list. ___ 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] How to enable auto option for newly added file formats
Am Dienstag, den 25.06.2013, 19:15 +0800 schrieb shashi shekhar: Hi Björn, Thanks Björn for the reply , But pdb file format is working not working auto option ..it works with by selecting PDB file format option in galaxy ... do i have to modify any registry.py file or any other file ? i have included only init ,init_meta and sniff function in PDB ( txt ) in data.py file .. Yes you have to modify the registry.py file. And you need to take care of the order of registered sniffers, these are crucial. Or you just install these data types from my tool shed repository :) Cheers, Bjoern Regards shahsi __ From: Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de To: shashi shekhar me_shash...@yahoo.co.in Cc: Peter Cock p.j.a.c...@googlemail.com; Galaxy Dev galaxy-...@bx.psu.edu Sent: Tuesday, 25 June 2013 3:40 PM Subject: Re: [galaxy-dev] How to enable auto option for newly added file formats Hi Shashi, can you try my molecule datatype repository? http://testtoolshed.g2.bx.psu.edu/view/bgruening/chemical_datatypes The source is here: https://github.com/bgruening/galaxytools/blob/master/chemicaltoolbox/datatypes/molecules.py I have also a PDB definition inluded maybe that works for you and we can join the effort. Thanks, Bjoern Hi, yeah i followd this tutorial .. http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes yeah ,i have tested my sniff methods .it works fine .when i upload any pdb file by using the option file format (PDB ) , it works but with auto option it doesnot work regards shashi __ From: Peter Cock p.j.a.c...@googlemail.com To: shashi shekhar me_shash...@yahoo.co.in Cc: Galaxy Dev galaxy-...@bx.psu.edu Sent: Tuesday, 25 June 2013 1:14 PM Subject: Re: [galaxy-dev] How to enable auto option for newly added file formats On Tue, Jun 25, 2013 at 8:28 AM, shashi shekhar me_shash...@yahoo.co.in wrote: Hi, yeah ..it is same thing... but i followed the galaxy -datatype(how to add new file format)tutorial ..but still my newly added file format is not working with auto option it always display txt format ..it is similar to txt format with some specific property .. Reagrds shashi So you've followed this: http://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes Have you tested your sniff method works? Have you checked the order the file types are tested? Peter P.S. Don't forget to CC the mailing list. ___ 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] How to enable auto option for newly added file formats
On Mon, Jun 24, 2013 at 3:39 PM, shashi shekhar me_shash...@yahoo.co.in wrote: Hi, I want to enable option auto option for some format ..how will i proceed . I have alreadu added the format in galaxy ., which works without auto option. Regards shashi Are you asking how to make Galaxy automatically recognise a new file type when uploading data into Galaxy? 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/
