Hi Peter,

> On Wed, Aug 7, 2013 at 3:54 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> > On Wed, Aug 7, 2013 at 3:36 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> >> Hi Peter,
> >>
> >> On Aug 7, 2013, at 10:26 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> >>
> >>> Hi Greg et al,
> >>>
> >>> For the NCBI BLAST+ wrappers, Nicola has suggested we split
> >>> out the binaries themselves into a separate Tool Shed package,
> >>> e.g. package_blast_plus_2_2_26 and similar for the later releases.
> >>>
> >>> https://github.com/peterjc/galaxy_blast/issues/7
> >>>
> >>> I think this is a good idea.
> >>
> >> I agree.
> >
> > Excellent, we'll start work on that.
> >
> > ...
> >
> > OK then, I'll setup these using the current tool_dependencies.xml
> > from the ncbi_blast_plus suite (which right now is breaking on the
> > Tool Shed due to its copy of BOOST being updated), first:
> >
> >  - http://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_2_26
> >
> 
> Done, using just the tool_dependencies.xml file which was
> previously bundled within the ncbi_blast_plus Tool Shed repo:
> 
> <?xml version="1.0"?>
> <tool_dependency>
>     <package name="blast+" version="2.2.26+">
>         <install version="1.0">
>             <actions>
>                 <action
> type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz</action>
>                 <action type="shell_command">cd c++ &amp;&amp;
> ./configure --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make
> install</action>
>                 <action type="set_environment">
>                     <environment_variable name="PATH"
> action="prepend_to">$INSTALL_DIR/bin</environment_variable>
>                 </action>
>             </actions>
>         </install>
>         <readme>
>         ....
>         </readme>
>     </package>
> </tool_dependency>
> 
> Now, back in ncbi_blast_plus, I have revised the
> repository_dependencies.xml to declare this new
> repository dependency (the revision tag etc is missing
> to mean the latest version at upload is used):

Mh, I never tried that but I think that will not work. The blast
datatypes are ok to be included in repository_dependency.xml but the
package_blast_plus needs to be in tool_dependency.xml, imho.

<?xml version="1.0"?>
<tool_dependency>
    <package name="blast+" version="2.2.26+">
        <repository name="package_blast_plus_2_2_26" owner="iuc" />
    </package>
</tool_dependency>

If you have that you do not need to change your tools.

Hopefully I'm correct.
Bjoern


> <?xml version="1.0"?>
> <repositories description="This requires the BLAST datatype
> definitions (e.g. the BLAST XML format) and the BLAST+ binaries">
>     <repository name="blast_datatypes" owner="devteam" />
>     <repository name="package_blast_plus_2_2_26" owner="iuc" />
> </repositories>
> 
> Now do I need to change the individual tools at all? e.g.
> 
> <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.20">
>     <description>Search nucleotide database with nucleotide query
> sequence(s)</description>
>     <!-- If job splitting is enabled, break up the query file into parts -->
>     <parallelism method="multi" split_inputs="query"
> split_mode="to_size" split_size="1000" shared_inputs="subject,histdb"
> merge_outputs="output1"></parallelism>
>     <requirements>
>         <requirement type="binary">blastn</requirement>
>         <requirement type="package" version="2.2.26+">blast+</requirement>
>     </requirements>
>     ....
> 
> The package name and version still match the (relocated)
> tool_dependencies.xml file, so this should be OK, right?
> 
> Thanks,
> 
> 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/

Reply via email to