Re: [galaxy-dev] Question about composite blast datatypes
On Wed, Aug 13, 2014 at 7:22 PM, Eric Rasche rasche.e...@yandex.ru wrote: Hi Peter, I'm working on composite datatypes now (for PacBio SMRT cells). In the datatype I know I'll have files with variable names (e.g. .1, .2, .3) and after using the blast datattype as reference material, I noticed that you had commented out files with variable names from the datatype. Is there rationale behind that? Are we ensured that the entire directory will always be transferred so it's not a problem to not specify files as part of the datatype? Reference: https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatypes/blast.py#L232 Cheers, Eric Hi Eric, Edward Kirton wrote the original BLAST DB datatypes - I'm not sure how to nicely define open ended file lists for datatypes, but also the makeblastdb wrapper output does not have this problem (yet). If and when we try to support partitioned BLAST databases (with a *.nal or *.pal alias file) then this would be needed. I would think that the HTML composite datatype might be a better guide here, since you will order get lots of child files (images etc). My guess is the whole directory may be transferred anyway, but having undefined files could be a problem at some point... 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/
Re: [galaxy-dev] Question about composite blast datatypes
14.08.2014, 10:01, "Peter Cock" p.j.a.c...@googlemail.com:On Wed, Aug 13, 2014 at 7:22 PM, Eric Rasche rasche.e...@yandex.ru wrote: Hi Peter, I'm working on composite datatypes now (for PacBio SMRT cells). In the datatype I know I'll have files with variable names (e.g. .1, .2, .3) and after using the blast datattype as reference material, I noticed that you had commented out files with variable names from the datatype. Is there rationale behind that? Are we ensured that the entire directory will always be transferred so it's not a problem to not specify files as part of the datatype? Reference: https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatypes/blast.py#L232 Cheers, EricHi Eric,Edward Kirton wrote the original BLAST DB datatypes - I'm not surehow to nicely define open ended file lists for datatypes, but also themakeblastdb wrapper output does not have this problem (yet).If and when we try to support partitioned BLAST databases (with a*.nal or *.pal alias file) then this would be needed.I would think that the HTML composite datatype might be a betterguide here, since you will order get lots of child files (images etc).My guess is the whole directory may be transferred anyway, buthaving "undefined" files could be a problem at some point...Regards,PeterHi Peter, Okay, that generally answers that, I'm using the HTML datatype now, hopefully it'll accomplish what I want it to. Thanks for this information! Cheers,Eric -- Eric RascheProgrammer IICenter for Phage TechnologyTexas AM UnivesityCollege Station, TX 77843Ph: 4046922048 ___ 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] Question about composite blast datatypes
Hi Peter, I'm working on composite datatypes now (for PacBio SMRT cells). In the datatype I know I'll have files with variable names (e.g. .1, .2, .3) and after using the blast datattype as reference material, I noticed that you had commented out files with variable names from the datatype. Is there rationale behind that? Are we ensured that the entire directory will always be transferred so it's not a problem to not specify files as part of the datatype? Reference: https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatypes/blast.py#L232 Cheers,Eric -- Eric RascheProgrammer IICenter for Phage TechnologyTexas AM UnivesityCollege Station, TX 77843Ph: 4046922048 ___ 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/
