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++ &&
./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
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