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 > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
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