Mercurial > repos > wolma > package_python3_zlib_dependent_1_0
changeset 6:79f0803e3bbb draft
Uploaded
| author | wolma |
|---|---|
| date | Wed, 13 Aug 2014 08:30:38 -0400 |
| parents | f16443335cba |
| children | 5cfafaafa263 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 130 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Aug 13 08:30:38 2014 -0400 @@ -0,0 +1,130 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="zlib" version="1.2.8"> + <repository changeset_revision="9d017266c41e" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + + <package name="python3" version="3.4.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://www.python.org/ftp/python/3.4.1/Python-3.4.1.tgz</action> + + <action type="set_environment_for_install"> + <repository changeset_revision="9d017266c41e" name="package_zlib_1_2_8" owner="wolma" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="zlib" version="1.2.8" /> + </repository> + </action> + + <action type="shell_command"> + # The python build system doesn't check CPATH / C(PLUS)_INCLUDE_PATH which is set by the depended-upon + # tool definitions for these sources, but it does check CPPFLAGS / LDFLAGS + # Currently not whitespace-safe, I haven't found a way yet to quote the *FLAGS values so that they are + # correctly recognized by both the python build process and the compiler. But as galaxy itself isn't + # whitespace-safe either it doesn't really matter (currently). + oldifs="$IFS" + IFS=":" + for p in $CPLUS_INCLUDE_PATH + do + CPPFLAGS="$CPPFLAGS -I$p" + done + for p in $LD_LIBRARY_PATH + do + LDFLAGS="$LDFLAGS -L$p" + done + IFS="$oldifs" + export CPPFLAGS + export LDFLAGS + + # Clear variables that may be used in Galaxy's extenal python 2 environment + unset PYTHONPATH + unset PYTHONHOME + + ./configure --prefix="$INSTALL_DIR" --with-ensurepip \ + && make \ + && make install + </action> + + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable> + <!-- clear PYTHONPATH, otherwise we will get Galaxy's Python 2 libraries in the Python 3 path. --> + <environment_variable action="set_to" name="PYTHONPATH" /> + <environment_variable action="set_to" name="PYTHONHOME">$INSTALL_DIR</environment_variable> + <environment_variable action="prepend_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig</environment_variable> + </action> + </actions> + </install> + + <readme> + Python 3.4.1 + + The Python programming language version 3. + + http://www.python.org + + + A lean build of python 3.4.1. It does not include modules with external dependencies except for the zlib module, which requires the zlib library installed on your system. For a build with more such modules included look at https://toolshed.g2.bx.psu.edu/view/jankanis/package_python3_4 written by jankanis, of which this package is a shameless plagiarism. + + Python as of version 3.3 includes a built-in virtual environment manager. To create a python 3 virtual env, include the following actions in your tool_dependencies.xml, e.g. for a package MY_TOOL_venv: + + <action type="set_environment_for_install"> + <repository name="python3" owner="wolma"> + <package name="python3" version="3.4.1" /> + </repository> + <!-- other install time dependencies --> + </action> + + <action type="shell_command"> + # Unset any saved environment settings from parent virtual + # environments, e.g. for python 2 or if Galaxy itself is running + # from within a virtual environment. + unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME + # Create virtual environment MY_TOOL_venv + pyvenv MY_TOOL_venv + # install python packages + MY_TOOL_venv/bin/pip3 install {{NEEDED_PYTHON_PACKAGES}} + </action> + + <action type="set_environment"> + + <!-- Setting the PYTHONPATH correctly can be a bit tricky, because you must + make sure that the runtime PYTHONPATH from galaxy itself is not + included, as it probably points to python 2 code that can crash a + program if python 3 tries to load it. + + If you only use a single virtual environment that is created + specifically for a tool you are creating, you can just use a set_to + like below. + + If you create a virtual environment installation that is meant to be + reused by other packages, the virtual environment should probably + prepend its site-packages to the PYTHONPATH since a tool could be + using python modules from several virtual environments. But in such a + scenario the tool that uses these virtual environments should also + depend directly on the python3 package, and this dependency should be + listed before any virtual environment dependencies. This ensures that + the python3 environment settings that clear PYTHONPATH are sourced + first so galaxy's runtime PYTHONPATH is excluded. Virtual environments + can then prepend their PYTHONPATHs to each other. --> + <environment_variable name="PYTHONPATH" action="set_to">$INSTALL_DIR/MY_TOOL_venv/lib/python3.4/site-packages</environment_variable> + <!-- All that is really needed to use a specific virtual environment is that the + python interpreter in that environment is used, so add it to PATH --> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/MY_TOOL_venv/bin</environment_variable> + <!-- Clear incoming PYTHONHOME just like the venv's 'activate' command does --> + <environment_variable name="PYTHONHOME" action="set_to"></environment_variable> + <!-- To find shared libraries for python built-in modules such as libssl or libsqlite3 + we need to re-export LD_LIBRARY_PATH --> + <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LD_LIBRARY_PATH]</environment_variable> + </action> + + + Then, in your MY_TOOL.xml add the following requirement: + + <requirements> + <requirement name="package" version="XXX">MY_TOOL_venv</requirement> + </requirements> + + </readme> + + </package> +</tool_dependency>