On Wed, Oct 30, 2013 at 4:03 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hello all,
> This is just to announce I am working on a wrapper for
> "CLC Assembly Cell" which is the CLCbio commercial
> command line assembly tool suite.
> http://www.clcbio.com/products/clc-assembly-cell/
> Our institute bought a licence primarily for use on plant
> genomes where other assemblers at the time required
> too much RAM to complete. This assembler is both fast
> and low memory, which can be very useful.
> Wrapper development here:
> https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell
> Prototype releases will be on the Test Tool Shed (soon):
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
> Stable Tool Shed releases will be here (later):
> http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
> I would be interested to hear from anyone else with access to
> a licensed copy of the tool interested in using it from Galaxy.
> e.g. Is it reasonable to assume the tools are on the $PATH,
> or is using a specific environment variable more helpful?

I've continued working on this and it seems to be working
quite nicely on the Illumina examples I have tried. I have
written a Galaxy wrapper for the clc_assembler command
line tool (FASTA/FASTQ reads to a FASTA assembly), plus
a combined wrapper for clc_mapper and clc_cas_to_sam
(FASTA/FASTQ reads plus FASTA assembly to a BAM
mapping file).

This avoids the issues with attempting to define a Galaxy
datatype for the CLCbio CAS file format - which is not self
contained and therefore does not fit Galaxy's data model.

I would prefer to have someone else test this on another
Galaxy instance before I post it to the main Tool Shed,
but any feedback would be welcome.


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