When I try to run planemo (v0.21.1) I get an error that seems to involve virtualenv. I followed the instructions for installing planemo using the traditional virtualenv and pip method:
planemo test --no_cleanup --install_galaxy --test_output /home/galaxy/files/013/dataset_13063.dat --test_data /home/galaxy/galaxy-functional-tests/ test.xml
git --git-dir /home/galaxy/.planemo/gx_repo fetch >/dev/null 2>&1
cd /tmp/tmpLNljIH; git clone --branch 'dev' '/home/galaxy/.planemo/gx_repo' 'galaxy-dev'; cd galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/galaxy/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /nfs/sw/.conda/envs/galaxy/bin/virtualenv -p /nfs/sw/.conda/envs/galaxy/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--skip-venv --dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}
Initialized empty Git repository in /tmp/tmpLNljIH/galaxy-dev/.git/
Running virtualenv with interpreter /nfs/sw/.conda/envs/galaxy/bin/python2.7
New python executable in .venv/bin/python2.7
Also creating executable in .venv/bin/python
.venv/bin/python2.7: error while loading shared libraries: libpython2.7.so.1.0: cannot open shared object file: No such file or directory
ERROR: The executable .venv/bin/python2.7 is not functioning
ERROR: It thinks sys.prefix is u'/tmp/tmpLNljIH/galaxy-dev' (should be u'/tmp/tm pLNljIH/galaxy-dev/.venv')
ERROR: virtualenv is not compatible with this system or executable
/bin/sh: .venv/bin/activate: No such file or directory
Testing using galaxy_root /tmp/tmpLNljIH/galaxy-dev
Testing tools with command [cd /tmp/tmpLNljIH/galaxy-dev; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--skip-venv --skip-common-startup"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv; else GALAXY_VIRTUAL_ENV=/home/galaxy/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /nfs/sw/.conda/envs/galaxy/bin/virtualenv -p /nfs/sw/.conda/envs/galaxy/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /remote/RMS/users/galaxy/files/013/dataset_13063.dat --xunit_report_file /tmp/tmpLNljIH/xunit.xml --structured_data_report_file /remote/home/galaxy/tool_test_output.json functional.test_toolbox ]
Set COMMON_STARTUP_ARGS to
/bin/sh: .venv/bin/activate: No such file or directory
Cannot locate xUnit report option for tests - update Galaxy for more detailed breakdown.
Warning: Problem with target Galaxy, it did not produce a structured test results files - summary information and planemo reports will be incorrect.
Can anyone give me any hints as to what is wrong?
Thanks!
I did some additional testing using planemo 0.14 and 0.21.1 and galaxy 15.07 and 15.10. Using planemo test only works when using the combination of planemo 0.14 and galaxy 15.07. Hope that helps?