# HG changeset patch
# User bitlab
# Date 1570452237 14400
# Node ID 0589a1c5f33a2663d04a0375296311a26d595d6d
# Parent  5ce7e50f159b8e76298ca6281bbf929c1798df2c
Fixed absolute paths

diff -r 5ce7e50f159b -r 0589a1c5f33a chromeister/chromeister.xml
--- a/chromeister/chromeister.xml	Tue Dec 18 06:59:41 2018 -0500
+++ b/chromeister/chromeister.xml	Mon Oct 07 08:43:57 2019 -0400
@@ -7,7 +7,7 @@
       <param name="kmer" type="integer" value="32" label="Kmer" help="Seed size used to find unique hits" />
       <param name="diffuse" type="integer" value="4" label="Difusse value" help="Level of the heuristic subsampling employed" />
    </inputs>
-   <command>cp $query "${query.name}"; cp $db "${db.name}"; (/home/galaxy-bitlab/galaxy/tools/chromeister/bin/CHROMEISTER -query "${query.name}" -db "${db.name}" -dimension $dimension -kmer $kmer -diffuse $diffuse -out "${query.name}"-"${db.name}".mat) &amp;>/dev/null ; rm "${query.name}"; rm "${db.name}"; Rscript /home/galaxy-bitlab/galaxy/tools/chromeister/bin/compute_score.R  "${query.name}"-"${db.name}".mat $dimension; mv "${query.name}"-"${db.name}".mat $output; mv "${query.name}"-"${db.name}".mat.filt.png $outputIMAGEN ; mv "${query.name}"-"${db.name}".mat.events.txt $outputEVENTS; rm hits-XY-"${query.name}"-"${db.name}".mat.hits</command>
+   <command>make all -C ${__tool_directory__}/src ; cp $query "${query.name}"; cp $db "${db.name}"; (${__tool_directory__}/bin/CHROMEISTER -query "${query.name}" -db "${db.name}" -dimension $dimension -kmer $kmer -diffuse $diffuse -out "${query.name}"-"${db.name}".mat) &amp;>/dev/null ; rm "${query.name}"; rm "${db.name}"; Rscript ${__tool_directory__}/bin/compute_score.R  "${query.name}"-"${db.name}".mat $dimension; mv "${query.name}"-"${db.name}".mat $output; mv "${query.name}"-"${db.name}".mat.filt.png $outputIMAGEN ; mv "${query.name}"-"${db.name}".mat.events.txt $outputEVENTS; rm hits-XY-"${query.name}"-"${db.name}".mat.hits</command>
   <outputs>
       <data name="output" format="txt" label="Comparison matrix"/>
       <data name="outputIMAGEN" format="png" label="Comparison dotplot"/>