Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

7 Aug 2013

      On Wed, Aug 7, 2013 at 3:54 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
...
On Wed, Aug 7, 2013 at 3:36 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
...
Hi Peter,
On Aug 7, 2013, at 10:26 AM, Peter Cock <p.j.a.cock@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++ &&
./configure --prefix=$INSTALL_DIR && make && make
install</action>
                <action type="set_environment">
                    <environment_variable name="PATH"
action="prepend_to">$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):

<?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