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"?>
    <package name="blast+" version="2.2.26+">
        <install version="1.0">
                <action type="shell_command">cd c++ &amp;&amp;
./configure --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make
                <action type="set_environment">
                    <environment_variable name="PATH"

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):

<?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" />

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
    <!-- 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"
        <requirement type="binary">blastn</requirement>
        <requirement type="package" version="2.2.26+">blast+</requirement>

The package name and version still match the (relocated)
tool_dependencies.xml file, so this should be OK, right?


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