# HG changeset patch
# User iuc
# Date 1544793205 18000
# Node ID f18f0b887c31ccd2fe116e5186c76cdeb6a94078
# Parent  382a4c19007f085ea01e500b2637a514623f5f20
planemo upload commit 99b8e51a68074a214ca4415a635a426e80e4129b

diff -r 382a4c19007f -r f18f0b887c31 busco.xml
--- a/busco.xml	Fri Oct 20 03:54:35 2017 -0400
+++ b/busco.xml	Fri Dec 14 08:13:25 2018 -0500
@@ -9,16 +9,16 @@
 
         &&
 
+        if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which run_BUSCO.py)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
+        cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
+        export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
+
         #if $adv.aug_prediction.augustus_mode == 'history':
             ## Using an augustus model from history, we need to unzip it and let augustus find it
 
-            cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
-
             mkdir -p 'augustus_dir/species/' &&
 
             tar -C 'augustus_dir/species/' -xzvf '${adv.aug_prediction.augustus_model}' > /dev/null &&
-
-            export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
         #end if
 
         run_BUSCO.py
diff -r 382a4c19007f -r f18f0b887c31 tool-data/busco.loc.sample
--- a/tool-data/busco.loc.sample	Fri Oct 20 03:54:35 2017 -0400
+++ b/tool-data/busco.loc.sample	Fri Dec 14 08:13:25 2018 -0500
@@ -5,9 +5,14 @@
 #
 # Datasets can be retrieved from http://busco.ezlab.org/frame_wget.html
 #
-# "/some/path/arthropoda/" would be the last column in the line
-# If this were for the mm10 mouse genome, the resulting entry would look like:
+# "/some/path/datasets/" would be the last column in the line
+# If this were for the /some/path/lineage/cyanobacteria_odb9/ reference dataset:
 #
-#arthropoda_2.0	arthropoda_2.0	/some/path/arthropoda/
+# $ ls /some/path/datasets/cyanobacteria_odb9/
+#   ancestral  ancestral_variants  dataset.cfg  hmms  info  lengths_cutoff  prfl  scores_cutoff
+#
+# the resulting entry would look like:
+#
+#cyanobacteria_odb9	cyanobacteria	/some/path/datasets/
 #
 #