From dan@bx.psu.edu Wed Apr  9 11:14:20 2014
From: Daniel Blankenberg <dan@bx.psu.edu>
To: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Data Tables and *.loc files: Using named columns
	versus from_data_table
Date: Wed, 09 Apr 2014 11:14:18 -0400
Message-ID: <4A1994A3-412D-478E-B9D2-36B71F1EE998@bx.psu.edu>
In-Reply-To:
 <CAKVJ-_613PO6n3-FuxcxWa-Tp-C3VAMRuxb63szc=VWZLtURbw@mail.gmail.com>
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Hi Peter,

Having a standalone repository that just contained the tool data table and .l=
oc file that could be a dependency of other repositories would be a good way =
to go here. Unfortunately, this isn=E2=80=99t supported right now. I=E2=80=99=
ve opened a trello card for this: https://trello.com/c/VZxV08Qt

However, even though you currently need to include the tool data table defini=
tion and .loc sample in each repository in order for the tool to be valid, it=
 is still a best practice to use tool data tables.


Thanks,

Dan

On Apr 9, 2014, at 7:04 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:

> Hi all,
>=20
> In discussion about adding an NCBI BLAST data manager
> https://github.com/peterjc/galaxy_blast/issues/22 based on
> Dan's example, Michael Li has suggested using the new(ish)
> Data Table functionality of Galaxy for using *.loc files:
> https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables
>=20
> Currently the BLAST+ wrappers access the blastdb.loc file
> for picking a system installed nucleotide BLAST database
> like this:
>=20
>    <param name=3D"database" type=3D"select" label=3D"Nucleotide BLAST datab=
ase">
>        <options from_file=3D"blastdb.loc">
>            <column name=3D"value" index=3D"0"/>
>            <column name=3D"name" index=3D"1"/>
>            <column name=3D"path" index=3D"2"/>
>        </options>
>    </param>
>=20
> See https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_pl=
us/ncbi_macros.xml
>=20
> With the from_data_table feature this which would be much shorter:
>=20
>    <param name=3D"database" type=3D"select" label=3D"Nucleotide BLAST datab=
ase">
>        <options from_data_table=3D"blastdb" />
>    </param>
>=20
> For this to work, the column information must instead be
> defined centrally in ``tool_data_table_conf.xml`` (via a
> ``tool_data_table_conf.xml.sample`` file), e.g.
>=20
>    <table name=3D"blastdb" comment_char=3D"#">
>        <columns>value, name, path</columns>
>        <file path=3D"tool-data/blastdb.loc" />
>    </table>
>=20
> For simple tools this seems quite neat, but within a single tool
> suite using XML macros seems equally effective for centrally
> defining the columns in the *.loc files (we do this currently).
>=20
> However, what worries me is the data table XML configuration
> file adds a new complexity for dependency management between
> different ToolShed repositories using a *.loc file (like the *.loc
> files for BLAST databases).
>=20
> For the BLAST database *.loc files, the simplest solution seems
> to be not to use the Data Tables feature (as we do now).
>=20
> The next best solution seems to be to put the sample *.loc files
> and associated data table definition XML files into a shared
> ToolShed repository (called called blast_data_tables, or
> blast_databases?) which would be declared as a dependency
> of anything using the BLAST database *.loc files (e.g. the
> BLAST+ wrappers and any data managers).
>=20
> [This would be like the existing blast_datatypes ToolShed
> repository which is a declared dependency of many tools
> using BLAST]
>=20
> Is that a good plan? What benefits does it have over simply
> not using the Data Table functionality?
>=20
> Thanks,
>=20
> Peter
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>=20
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