Hi,

This tools has been passing its nightly tests fine,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus

However, there now appears to be a silent installation failure
(the install hasn't worked but there was no install error):

Automated tool test results
I think I can confirm that error (posted to IUC yesterday):
The following snipped used to work without the 'change_directory' action.

<tool_dependency>
    <package name="bzlib" version="1.0.6">
        <install version="1.0">
            <actions>
                <!-- first action is always downloading -->
                <action type="download_by_url">http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz</action>
                <action type="change_directory">bzip2-1.0.6</action>
                <action type="shell_command">make</action>
                <action type="shell_command">make install PREFIX=$INSTALL_DIR/bzlib</action>
                <action type="move_directory_files">
                    <source_directory>./</source_directory>
                    <destination_directory>$INSTALL_DIR/bzlib/source</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bzlib/bin</environment_variable>
                    <environment_variable name="BZLIB_LIB_DIR" action="set_to">$INSTALL_DIR/bzlib/lib</environment_variable>
                    <environment_variable name="BZLIB_INCLUDE_DIR" action="set_to">$INSTALL_DIR/bzlib/include</environment_variable>
                    <environment_variable name="BZLIB_SOURCE_DIR" action="set_to">$INSTALL_DIR/bzlib/source</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Compiling bzlib requires make and a C compiler. You can access bzlib with $BZLIB_LIB_DIR and $BZLIB_INCLUDE_DIR.</readme>
    </package>
</tool_dependency>


Tool test results
Automated test environment
Tests that failed
Tool id: nlstradamus
Tool version: nlstradamus
Test: test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/nlstradamus/nlstradamus/0.0.8)
Stderr:
Fatal error: Exit code 127 ()
/bin/sh: 1: NLStradamus: not found
Traceback:
Traceback (most recent call last):
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 171, in test_tool
    self.do_it( td, shed_tool_id=shed_tool_id )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 102, in do_it
    self.verify_dataset_correctness( outfile, hid=elem_hid,
maxseconds=testdef.maxseconds, attributes=attributes,
shed_tool_id=shed_tool_id )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 782, in verify_dataset_correctness
    self._assert_dataset_state( elem, 'ok' )
  File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 606, in _assert_dataset_state
    raise AssertionError( errmsg )
AssertionError: Expecting dataset state 'ok', but state is 'error'.
Dataset blurb: error

On the other hand, over on the main Tool Shed, with what should
be the same tool configuration, the install works (although there
is a new sniffer bug on the Galaxy side, see separate email):

http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus

Here's the tool_dependencies.xml file,

<?xml version="1.0"?>
<tool_dependency>
    <package name="NLStradamus" version="1.8">
        <install version="1.0">
            <actions>
                <action
type="download_by_url">http://www.moseslab.csb.utoronto.ca/NLStradamus/NLStradamus/NLStradamus.1.8.tar.gz</action>
<!-- Although v1.7 used a subfolder in the tar-ball, v1.8 did not -->
                <action type="shell_command">g++ NLStradamus.cpp -o
NLStradamus -O3</action>
                <action
type="move_file"><source>NLStradamus</source><destination>$INSTALL_DIR/</destination></action>
                <action type="set_environment">
                    <environment_variable name="PATH"
action="prepend_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
This downloads NLStradamus v1.8 from this folder,
http://www.moseslab.csb.utoronto.ca/NLStradamus/NLStradamus/

The C++ tool is compiled as described in the README_C.txt file, using
g++, and included in the $PATH.

The older slower Perl implementation is not installed.
        </readme>
    </package>
</tool_dependency>

My hunch is a subtle regression in the <action type="download_by_url">
(note in this case the tarball does not contain a sub-folder).

Peter
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