Mercurial > repos > wolma > mimodd

comparison tool_dependencies.xml @ 18:2742ad4d1608 draft

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rebase on package_python_3_4_lean
author wolma
date Tue, 26 Apr 2016 11:21:43 -0400
parents b658c34ee3fd
children 8f108b41a149
comparison
equal deleted inserted replaced
17:b658c34ee3fd 18:2742ad4d1608
7 <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="d0bf97420fb5" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="readline" version="6.3"> 9 <package name="readline" version="6.3">
10 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
11 </package> 11 </package>
12 <package name="python3" version="3.4.1"> 12 <package name="python3" version="3.4">
13 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 13 <repository changeset_revision="3956f4688295" name="package_python_3_4_x_lean" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
14 </package> 14 </package>
15 15
16 <package name="mimodd" version="0.1.7.2"> 16 <package name="mimodd" version="0.1.7.2">
17 <install version="1.0"> 17 <install version="1.0">
18 <actions> 18 <actions>
19 <!-- prepare a python3 venv to install into --> 19 <!-- prepare a python3 venv to install into -->
20 <action type="set_environment_for_install"> 20 <action type="set_environment_for_install">
21 <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu"> 21 <repository changeset_revision="3956f4688295" name="package_python_3_4_x_lean" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu">
22 <package name="python3" version="3.4.1" /> 22 <package name="python3" version="3.4" />
23 </repository> 23 </repository>
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> 29 <action type="shell_command">. $INSTALL_DIR/MiModD_venv/bin/activate</action>
30 30
31 <!-- download and install setuptools (required to install rpy2) -->
32 <action type="download_file" sha256sum="7b2a76ec3aeb6dc95ae66eab173e7b46e26436c5ba4ee94744f2360bce493b25">https://depot.galaxyproject.org/software/setuptools/setuptools_18.2_src_all.tar.bz2</action>
33 <action type="shell_command">tar -xjf setuptools_18.2_src_all.tar.bz2</action>
34 <action type="change_directory">pypa-setuptools-1a981f2e5031</action>
35 <action type="shell_command">python3 setup.py install</action>
36 <action type="change_directory">$TMP_WORK_DIR</action>
37
38 <!-- 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>
40 <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>
42 <action type="shell_command">python3 setup.py install</action>
43 <action type="change_directory">$TMP_WORK_DIR</action>
44
31 <!-- download and install rpy2 --> 45 <!-- download and install rpy2 -->
32 <action type="download_file" sha256sum="beb3445cfc3a0f9a36df7de6489d2a488a5ac113c471c448e46e6d9c47cb7840">https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz</action> 46 <action type="download_file" sha256sum="0d88f7fff21fbef523c8678ed8f850a36052edca4ce702c62f234fdcb52de441">https://depot.galaxyproject.org/software/rpy2/rpy2_2.7.5_src_all.tar.gz</action>
33 <action type="shell_command">tar -xzf 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>
34 <action type="change_directory">rpy2-2.7.5</action> 48 <action type="change_directory">rpy2-2.7.5</action>
35 <action type="set_environment_for_install"> 49 <action type="set_environment_for_install">
36 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 50 <repository changeset_revision="ca1a9400d4e1" name="package_readline_6_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
37 <package name="readline" version="6.3" /> 51 <package name="readline" version="6.3" />