search

ContentMine / phylotree

A repository for ami-phylotree development
0 stars 0 forks source link

How to run the new code/methods on a set of image files? #53

Open rossmounce opened 9 years ago

rossmounce commented 9 years ago

When I run 

mvn clean install

I can see exciting new NeXML output for one file / set of tests, output to this path:

./ami-plugin/target/phylo/image/003.pbm.png/
├── edited.nexml.xml
└── edited.nwk
0 directories, 2 files

How can, or should I run these methods on a set of input files? Previously I was running the below, but I have tried this and I don't get new style NeXML with cmphy namespace, edits and lookups:

#where ls.txt contains a list of input image files+paths to them, one per line
while read i ; do timeout 60s mvn exec:java  -Dexec.mainClass='org.xmlcml.ami2.plugins.phylotree.RunPhylo'  -Dexec.args=''"$i"' 50-output/'"$i"'' -e -X | tee $i.log ; done <ls.txt

I guess, I need to either amend RunPhylo, or exec a totally different java file?

petermr commented 9 years ago

This is run as a test and I need to customise it to run from the commandline and choose the appropriate output directory.

On Mon, Aug 24, 2015 at 11:02 PM, Ross Mounce notifications@github.com wrote:

When I run

mvn clean install

I can see exciting new NeXML output for one file / set of tests, output to this path:

./ami-plugin/target/phylo/image/003.pbm.png/ ├── edited.nexml.xml └── edited.nwk 0 directories, 2 files

How can, or should I run these methods on a set of input files? Previously I was running the below, but I have tried this and I don't get new style NeXML with cmphy namespace, edits and lookups:

where ls.txt contains a list of input image files+paths to them, one per line

while read i ; do timeout 60s mvn exec:java -Dexec.mainClass='org.xmlcml.ami2.plugins.phylotree.RunPhylo' -Dexec.args=''"$i"' 50-output/'"$i"'' -e -X | tee $i.log ; done <ls.txt

I guess, I need to either amend RunPhylo, or exec a totally different java file?

— Reply to this email directly or view it on GitHub https://github.com/ContentMine/phylotree/issues/53.

Peter Murray-Rust Reader in Molecular Informatics Unilever Centre, Dep. Of Chemistry University of Cambridge CB2 1EW, UK +44-1223-763069

rossmounce commented 9 years ago

I will read up on XSLT in the mean time