| Previous changeset 12:c2c70edb70eb (2016-04-25) Next changeset 14:5e9c1c67716b (2016-04-25) |
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Commit message:
Uploaded |
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modified:
tool_dependencies.xml |
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removed:
mimodd |
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| diff -r c2c70edb70eb -r f0b3871cb869 mimodd --- a/mimodd Mon Apr 25 17:26:32 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
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| b |
| diff -r c2c70edb70eb -r f0b3871cb869 tool_dependencies.xml --- a/tool_dependencies.xml Mon Apr 25 17:26:32 2016 -0400 +++ b/tool_dependencies.xml Mon Apr 25 17:27:25 2016 -0400 |
| [ |
| @@ -3,6 +3,12 @@ <package name="zlib" version="1.2.8"> <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> + <package name="R" version="3.2.1"> + <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="readline" version="6.2"> + <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> <package name="python3" version="3.4.1"> <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> @@ -10,27 +16,50 @@ <package name="mimodd" version="0.1.7.2"> <install version="1.0"> <actions> - <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action> + <!-- prepare a python3 venv to install into --> <action type="set_environment_for_install"> <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="python3" version="3.4.1" /> </repository> </action> + <action type="shell_command">python3 -m venv --without-pip $INSTALL_DIR/MiModD_venv</action> + <!-- remove the plain python symlink from the venv to avoid its + accidental use by Galaxy, MiModD uses python3 explicitly --> + <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action> + <action type="shell_command">. $INSTALL_DIR/MiModD_venv/bin/activate</action> + + <!-- download and install rpy2 --> + <action sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441" type="download_by_url"> + https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz + </action> + <action type="set_environment_for_install"> + <repository changeset_revision="52d6f646b3b5" name="package_readline_6_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="readline" version="6.2" /> + </repository> + <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="R" version="3.2.1" /> + </repository> + </action> + <action type="shell_command"> + export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" && + export CPPFLAGS="-I$READLINE_INCLUDE_PATH" && + python3 setup.py install + </action> + <action type="change_directory">$TMP_WORK_DIR</action> + + <!-- download and install MiModD --> + <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action> <action type="set_environment_for_install"> <repository changeset_revision="dce22a65bac2" name="package_zlib_1_2_8" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="zlib" version="1.2.8" /> </repository> </action> - <action type="shell_command">pyvenv --without-pip $INSTALL_DIR/MiModD_venv</action> - <!-- remove the plain python symlink from the venv to avoid its - accidental use by Galaxy, MiModD uses python3 explicitly --> - <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action> <!-- install MiModD placing the entry script mimodd into the venv's bin directory --> - <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action> + <action type="shell_command">python3 setup.py install</action> <!-- make MiModD's wrapped binaries executable --> - <action type="shell_command">chmod 755 $INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</action> + <action type="chmod"><file mode="755">$INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</file></action> <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself --> - <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action> + <action type="shell_command">python3 -m MiModD.__first_run__</action> <action type="set_environment"> <!-- make the mimodd entry script discoverable --> @@ -42,7 +71,6 @@ <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LD_LIBRARY_PATH]</environment_variable> </action> - </actions> </install> <readme> |