tool_dependencies.xml <action type="download_by_url"> regression?
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 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
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/
participants (2)
-
Bjoern Gruening -
Peter Cock