More debugging now of krona perl imports.

broadinstitute · May 1, 2016 · 6ea3030 · 6ea3030
1 parent 76b5d7d
commit 6ea3030
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/tools/krona.py b/tools/krona.py
@@ -29,6 +29,7 @@ def opt(self):
         bin_path = os.path.dirname(self.executable_path())
         # Get at the opt directory from the conda env root
         opt = os.path.abspath(join(bin_path, '..', 'opt', 'krona'))
+        util.misc.run_and_print(['ktGetLibPath'])
         return opt
 
     def import_taxonomy(self, input_tsvs, output, query_column=None, taxid_column=None,

diff --git a/travis/tests-long.sh b/travis/tests-long.sh
@@ -9,12 +9,11 @@ if [ $TRAVIS_PULL_REQUEST != "false" -o $TRAVIS_BRANCH = "master" -o -n "$TRAVIS
     nosetests -v \
         --logging-clear-handlers \
         --with-timer \
-        --with-xunit \
-        -w test/integration/
-        # --with-xunit --with-coverage \
-        # --cover-inclusive --cover-branches --cover-tests \
-        # --cover-package broad_utils,illumina,assembly,interhost,intrahost,metagenomics,ncbi,read_utils,reports,taxon_filter,tools,util \
-
+        --with-xunit --with-coverage \
+        --cover-inclusive --cover-branches --cover-tests \
+        --cover-package broad_utils,illumina,assembly,interhost,intrahost,metagenomics,ncbi,read_utils,reports,taxon_filter,tools,util \
+        test/integration/test_kraken.py
+    # -w test/integration
 else
     echo "This is not a pull request: skipping long running tests."
 fi