On Mon, Nov 18, 2013 at 4:29 PM, Peter Cock email@example.com wrote:
On Mon, Nov 18, 2013 at 4:23 PM, Eric Kuyt firstname.lastname@example.org wrote:
Hi Peter, it turns out we only have a workbench licence, the clc_assembler packaged with the workbench is called ./clc_assembler_ilo
which has the man page below, do you think this is the same binary as the clc-assembly-cell assembler?
I will just try to link clc_assembler_ilo to my path and see what it does :)
Try creating a symlink named clc_assembler (or hacking my wrapper to look for clc_assembler_ilo instead of clc_assembler), but yes, it looks like the same tool under a different name (see below).
Interestingly yours is newer then ours, perhaps we need an update...
What about the clc_mapper and clc_cas_to_sam binaries which are used in my clc_mapper.xml wrapper? Are they there under different names too?
[I have no idea if the CLCbio workbench licence is intended to allow you to run the clc_assembler at the command line as well - you may need to double check that to be safe.]
Were you able to run the tools within the CLC workbench at the command line? This would be very encouraging for getting the most value-for-money out of existing CLCbio licences.