Hello Kai,
There are many ways to script the command-line version of the contig
mover. One possibility would be to use find, e.g.:
find . -name "*.draft.fasta" -exec ./run_mcm.sh {} \;
you will need to make a 3 line script called run_mcm.sh with the
following contents:
#!/bin/bash
RESULTSDIR=`basename $1`
java -Xmx500m -cp Mauve.jar org.gel.mauve.contigs.ContigOrderer -output
$RESULTSDIR -ref reference.gbk -draft {}
and make the script executable first: chmod 755 run_mcm.sh
Note that you will likely need to provide the full path to Mauve.jar,
and run the script in the directory with your draft assemblies, which I
have assumed use filenames ending with .draft.fasta. Change as
appropriate.
Similar techniques could probably be used with GNU parallel to run the
contig mover in parallel...
Best,
-Aaron
On Fri, 2015-05-01 at 00:14 +1000, Zhou, K (mmb) wrote:
> Hi all,
>
>
> I wanna oder the contigs of multiple bacterial samples with one
> reference. I can do it one by one indeed by command line, but it's
> time comsuming. Could anyone tell me how can I run it in batch model?
>
>
> Thank you very much for your helps in advance!
>
>
> Kai Zhou
>
>
>
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Associate Professor, ithree institute
University of Technology Sydney
Australia
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