diff --git a/jbrowse/resources/views/begin.html b/jbrowse/resources/views/begin.html index 9032801a3..50c216bb6 100644 --- a/jbrowse/resources/views/begin.html +++ b/jbrowse/resources/views/begin.html @@ -1,9 +1,9 @@ The JBrowse module is part of DISCVR-Seq. It provides a wrapper around the JBrowse Genome Browser, which lets users rapidly take data generated or uploaded into DISCRV-Seq and view it using JBrowse. -The module ships with a version of JBrowse, meaning very little extra configuration is required in order to start using these tools. The primary reasons we created this wrapper around JBrowse are: +The module ships with a version of JBrowse 2, meaning very little extra configuration is required in order to start using these tools. The primary reasons we created this wrapper around JBrowse are:

\ No newline at end of file diff --git a/jbrowse/src/org/labkey/jbrowse/JBrowseManager.java b/jbrowse/src/org/labkey/jbrowse/JBrowseManager.java index ec0f92945..c1039d844 100644 --- a/jbrowse/src/org/labkey/jbrowse/JBrowseManager.java +++ b/jbrowse/src/org/labkey/jbrowse/JBrowseManager.java @@ -236,7 +236,19 @@ public static class TestCase extends Assert public void testJBrowseCli() throws Exception { File exe = JBrowseManager.get().getJbrowseCli(); - String output = new SimpleScriptWrapper(_log).executeWithOutput(Arrays.asList(exe.getPath(), "help")); + SimpleScriptWrapper wrapper = new SimpleScriptWrapper(_log); + wrapper.setThrowNonZeroExits(false); + + String output = wrapper.executeWithOutput(Arrays.asList(exe.getPath(), "help")); + if (wrapper.getLastReturnCode() != 0) + { + _log.error("Non-zero exit from testJBrowseCli: " + wrapper.getLastReturnCode()); + wrapper.getCommandsExecuted().forEach(_log::error); + _log.error("output: "); + _log.error(output); + + throw new RuntimeException("Non-zero exit running testJBrowseCli: " + wrapper.getLastReturnCode()); + } assertTrue("Malformed output", output.contains("Add an assembly to a JBrowse 2 configuration")); }