diff --git a/docs/tutorial/data_files/volvox_microarray.bw.conf b/docs/tutorial/data_files/volvox_microarray.bw.conf new file mode 100644 index 0000000000..7d9c50b778 --- /dev/null +++ b/docs/tutorial/data_files/volvox_microarray.bw.conf @@ -0,0 +1,8 @@ +#configuration snippet for the volvox bigwig test track +{ + "label": "volvox_microarray.bw", + "key": "volvox_microarray.bw", + "urlTemplate": "../../raw/volvox/volvox_microarray.bw", + "type": "JBrowse/View/Track/Wiggle", + "storeClass": "JBrowse/Store/BigWig" +} diff --git a/setup.sh b/setup.sh index a33f7f4a1a..e36c8bb0ec 100755 --- a/setup.sh +++ b/setup.sh @@ -30,9 +30,9 @@ echo -n "Formatting Volvox example data ..."; rm -rf sample_data/json/volvox; bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa --out sample_data/json/volvox; bin/biodb-to-json.pl -v --conf docs/tutorial/conf_files/volvox.json --out sample_data/json/volvox; + bin/add-track-json.pl sample_data/raw/volvox/volvox_microarray.bw.conf sample_data/json/volvox/trackList.json bin/generate-names.pl -v --out sample_data/json/volvox; - # also recreate some symlinks used by tests and such if [ -d sample_data/json/modencode ]; then mkdir -p sample_data/json/modencode/tracks; diff --git a/tests/selenium_tests/volvox_biodb_test.py b/tests/selenium_tests/volvox_biodb_test.py index e9e568ad31..5f848d21c0 100644 --- a/tests/selenium_tests/volvox_biodb_test.py +++ b/tests/selenium_tests/volvox_biodb_test.py @@ -14,18 +14,7 @@ def setUp( self ): call( "bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa --out sample_data/json/volvox/", shell=True ) call( "bin/biodb-to-json.pl --conf docs/tutorial/conf_files/volvox.json --out sample_data/json/volvox/", shell=True ) call( "bin/wig-to-json.pl --out sample_data/json/volvox/ --wig docs/tutorial/data_files/volvox_microarray.wig", shell=True ) - - # add a definition for the volvox bigwig test track - addtrack = subprocess.Popen( ["bin/add-track-json.pl","sample_data/json/volvox/trackList.json"], stdin=PIPE ); - addtrack.stdin.write("""{ - "label": "volvox_microarray.bw", - "key": "volvox_microarray.bw", - "urlTemplate": "../../raw/volvox/volvox_microarray.bw", - "type": "JBrowse/View/Track/Wiggle", - "storeClass": "JBrowse/Store/BigWig" - }""") - addtrack.stdin.close() - + call( "bin/add-track-json.pl sample_data/raw/volvox/volvox_microarray.bw.conf sample_data/json/volvox/trackList.json", shell=True ) call( "bin/generate-names.pl --dir sample_data/json/volvox/", shell=True ) super( AbstractVolvoxBiodbTest, self ).setUp()