Mercurial > repos > wolma > mimodd

comparison tool_dependencies.xml @ 19:8f108b41a149 draft

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Uploaded
author wolma
date Tue, 26 Apr 2016 15:27:13 -0400
parents 2742ad4d1608
children aba6d9b1c1f1
comparison
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18:2742ad4d1608 19:8f108b41a149
24 </action> 24 </action>
25 <action type="shell_command">python3 -m venv --without-pip $INSTALL_DIR/MiModD_venv</action> 25 <action type="shell_command">python3 -m venv --without-pip $INSTALL_DIR/MiModD_venv</action>
26 <!-- remove the plain python symlink from the venv to avoid its 26 <!-- remove the plain python symlink from the venv to avoid its
27 accidental use by Galaxy, MiModD uses python3 explicitly --> 27 accidental use by Galaxy, MiModD uses python3 explicitly -->
28 <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action> 28 <action type="shell_command">rm $INSTALL_DIR/MiModD_venv/bin/python</action>
29 <action type="shell_command">. $INSTALL_DIR/MiModD_venv/bin/activate</action>
30 29
31 <!-- download and install setuptools (required to install rpy2) --> 30 <!-- download and install setuptools (required to install rpy2) -->
32 <action type="download_file" sha256sum="7b2a76ec3aeb6dc95ae66eab173e7b46e26436c5ba4ee94744f2360bce493b25">https://depot.galaxyproject.org/software/setuptools/setuptools_18.2_src_all.tar.bz2</action> 31 <action type="download_file" sha256sum="7b2a76ec3aeb6dc95ae66eab173e7b46e26436c5ba4ee94744f2360bce493b25">https://depot.galaxyproject.org/software/setuptools/setuptools_18.2_src_all.tar.bz2</action>
33 <action type="shell_command">tar -xjf setuptools_18.2_src_all.tar.bz2</action> 32 <action type="shell_command">tar -xjf setuptools_18.2_src_all.tar.bz2</action>
34 <action type="change_directory">pypa-setuptools-1a981f2e5031</action> 33 <action type="change_directory">pypa-setuptools-1a981f2e5031</action>
35 <action type="shell_command">python3 setup.py install</action> 34 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
36 <action type="change_directory">$TMP_WORK_DIR</action> 35 <action type="change_directory">$TMP_WORK_DIR</action>
37 36
38 <!-- download and install six (required by rpy2) --> 37 <!-- download and install six (required by rpy2) -->
39 <action type="download_file" sha256sum="e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5">https://depot.galaxyproject.org/software/six/six_1.9.0_src_all.tar.gz</action> 38 <action type="download_file" sha256sum="e24052411fc4fbd1f672635537c3fc2330d9481b18c0317695b46259512c91d5">https://depot.galaxyproject.org/software/six/six_1.9.0_src_all.tar.gz</action>
40 <action type="shell_command">tar -xzf six_1.9.0_src_all.tar.gz</action> 39 <action type="shell_command">tar -xzf six_1.9.0_src_all.tar.gz</action>
41 <action type="change_directory">six-1.9.0</action> 40 <action type="change_directory">six-1.9.0</action>
42 <action type="shell_command">python3 setup.py install</action> 41 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
43 <action type="change_directory">$TMP_WORK_DIR</action> 42 <action type="change_directory">$TMP_WORK_DIR</action>
44 43
45 <!-- download and install rpy2 --> 44 <!-- download and install rpy2 -->
46 <action type="download_file" sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441">https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz</action> 45 <action type="download_file" sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441">https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz</action>
47 <action type="shell_command">tar -xzf rpy2_2.7.5_src_all.tar.gz</action> 46 <action type="shell_command">tar -xzf rpy2_2.7.5_src_all.tar.gz</action>
55 </repository> 54 </repository>
56 </action> 55 </action>
57 <action type="shell_command"> 56 <action type="shell_command">
58 export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" &amp;&amp; 57 export LDFLAGS="-L$READLINE_LIB_PATH -lreadline" &amp;&amp;
59 export CPPFLAGS="-I$READLINE_INCLUDE_PATH" &amp;&amp; 58 export CPPFLAGS="-I$READLINE_INCLUDE_PATH" &amp;&amp;
60 python3 setup.py install 59 $INSTALL_DIR/MiModD_venv/bin/python3 setup.py install
61 </action> 60 </action>
62 <action type="change_directory">$TMP_WORK_DIR</action> 61 <action type="change_directory">$TMP_WORK_DIR</action>
63 62
64 <!-- download and install MiModD --> 63 <!-- download and install MiModD -->
65 <action type="download_file">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action> 64 <action type="download_file">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.7.2.tar.gz</action>
69 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 68 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
70 <package name="zlib" version="1.2.8" /> 69 <package name="zlib" version="1.2.8" />
71 </repository> 70 </repository>
72 </action> 71 </action>
73 <!-- install MiModD placing the entry script mimodd into the venv's bin directory --> 72 <!-- install MiModD placing the entry script mimodd into the venv's bin directory -->
74 <action type="shell_command">python3 setup.py install</action> 73 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 setup.py install</action>
75 <!-- make MiModD's wrapped binaries executable --> 74 <!-- make MiModD's wrapped binaries executable -->
76 <action type="chmod"><file mode="755">$INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</file></action> 75 <action type="chmod"><file mode="755">$INSTALL_DIR/MiModD_venv/lib/python3.4/site-packages/MiModD/bin/*</file></action>
77 <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself --> 76 <!-- run MiModD's __first_run__ module once to give the package a chance to configure itself -->
78 <action type="shell_command">python3 -m MiModD.__first_run__</action> 77 <action type="shell_command">$INSTALL_DIR/MiModD_venv/bin/python3 -m MiModD.__first_run__</action>
79 78
80 <action type="set_environment"> 79 <action type="set_environment">
81 <!-- make the mimodd entry script discoverable --> 80 <!-- make the mimodd entry script discoverable -->
82 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable> 81 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/MiModD_venv/bin</environment_variable>
83 <!-- clear $PYTHONPATH and $PYTHONHOME --> 82 <!-- clear $PYTHONPATH and $PYTHONHOME -->