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comparison tool_dependencies.xml @ 3:039ef13e3676 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
author bgruening
date Sun, 01 Nov 2015 10:34:34 -0500
parents 548537fc2577
children
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2:548537fc2577 3:039ef13e3676
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="openbabel" version="2.3.2"> 3 <package name="eigen2" version="2.0.17">
4 <repository changeset_revision="e5ef70185d24" name="package_openbabel_2_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="a270fba04f3a" name="package_eigen_2_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="graphicsmagick" version="1.3.18"> 6 <package name="confab" version="1.0.1">
7 <repository changeset_revision="ef238a8bdc1d" name="package_graphicsmagick_1_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="osra" version="2.0.0">
10 <install version="1.0"> 7 <install version="1.0">
11 <actions> 8 <actions>
12 <!-- first action is always downloading --> 9 <action type="download_by_url">https://github.com/bgruening/confab/archive/1.0.1.tar.gz</action>
13 <action type="download_by_url">http://downloads.sourceforge.net/project/osra/osra/2.0.0/osra-2.0.0.tgz</action>
14 10
15 <!-- populate the environment variables from the dependend repos --> 11 <!-- populate the environment variables from the dependend repos -->
16 <action type="set_environment_for_install"> 12 <action type="set_environment_for_install">
17 <repository changeset_revision="e5ef70185d24" name="package_openbabel_2_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 13 <repository changeset_revision="a270fba04f3a" name="package_eigen_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
18 <package name="openbabel" version="2.3.2" /> 14 <package name="eigen2" version="2.0.17" />
19 </repository>
20 <repository changeset_revision="ef238a8bdc1d" name="package_graphicsmagick_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
21 <package name="graphicsmagick" version="1.3.18" />
22 </repository> 15 </repository>
23 </action> 16 </action>
24 17
25 <!--compiling potrace-1.11 --> 18 <action type="shell_command">cmake . -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DEIGEN2_INCLUDE_DIR=$EIGEN2_SOURCE_PATH</action>
26 <action type="download_file">http://potrace.sourceforge.net/download/1.11/potrace-1.11.tar.gz</action>
27 <action type="shell_command">tar xfvz potrace-1.11.tar.gz &amp;&amp; cd potrace-1.11 &amp;&amp; ./configure --with-libpotrace --prefix=$INSTALL_DIR/potrace/build &amp;&amp; make &amp;&amp; make install</action>
28
29 <!--compiling gocr 0.50patched -->
30 <!-- not yet possible
31 <action type="download_file">http://www-e.uni-magdeburg.de/jschulen/ocr/gocr-0.50.tar.gz</action>
32 <action type="shell_command">tar xfvz gocr-0.50.tar.gz &amp;&amp; cd gocr-0.50 &amp;&amp; ./configure -|-prefix=$INSTALL_DIR/gocr/build &amp;&amp; make libs &amp;&amp; make all install</action>
33 -->
34 <action type="download_file">http://downloads.sourceforge.net/project/osra/gocr-patched/gocr-0.50pre-patched.tgz</action>
35 <action type="shell_command">tar xfvz gocr-0.50pre-patched.tgz &amp;&amp; cd gocr-0.50pre-patched &amp;&amp; ./configure --prefix=$INSTALL_DIR/gocr/build &amp;&amp; make libs &amp;&amp; make all install</action>
36
37
38 <!--compiling tclap 1.2.1 -->
39 <action type="download_file">http://downloads.sourceforge.net/project/tclap/tclap-1.2.1.tar.gz</action>
40 <action type="shell_command">tar xfvz tclap-1.2.1.tar.gz &amp;&amp; cd tclap-1.2.1 &amp;&amp; ./configure --prefix=$INSTALL_DIR/tclap/build &amp;&amp; make &amp;&amp; make install</action>
41
42 <!--compiling ocrad 0.21 -->
43 <action type="download_file">http://mirror.checkdomain.de/gnu/ocrad/ocrad-0.21.tar.gz</action>
44 <action type="shell_command">tar xfvz ocrad-0.21.tar.gz &amp;&amp; cd ocrad-0.21 &amp;&amp; ./configure --prefix=$INSTALL_DIR/ocrad/build &amp;&amp; make &amp;&amp; make install</action>
45
46 <!--compiling cuneiform 1.1.0 -->
47 <action type="download_file">https://launchpad.net/cuneiform-linux/1.1/1.1/+download/cuneiform-linux-1.1.0.tar.bz2</action>
48 <action type="shell_command">tar xfvj cuneiform-linux-1.1.0.tar.bz2 &amp;&amp; cd cuneiform-linux-1.1.0 &amp;&amp; mkdir build &amp;&amp; cd build &amp;&amp; cmake .. -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR/cuneiform/build/ &amp;&amp; make &amp;&amp; make install</action>
49
50 <!--And finally OSRA 1.4.0-->
51 <!-- Extending the PATH is needed for OSRA -->
52 <action type="shell_command">export PATH=$PATH:$GRAPHICSMAGICK_ROOT_DIR/bin/ &amp;&amp;
53 ./configure --with-tclap-include=$INSTALL_DIR/tclap/build/include/ --with-potrace-include=$INSTALL_DIR/potrace/build/include/ --with-potrace-lib=$INSTALL_DIR/potrace/build/lib/ --with-gocr-include=$INSTALL_DIR/gocr/build/include/gocr/ --with-gocr-lib=$INSTALL_DIR/gocr/build/lib/ --with-ocrad-include=$INSTALL_DIR/ocrad/build/include/ --with-ocrad-lib=$INSTALL_DIR/ocrad/build/lib/ --with-cuneiform-include=$INSTALL_DIR/cuneiform/build/include/ --with-cuneiform --with-cuneiform-lib=$INSTALL_DIR/cuneiform/build/install/lib/ --with-openbabel-include=$OPENBABEL_INCLUDE_DIR/openbabel-2.0/ --with-openbabel-lib=$OPENBABEL_LIB_DIR --with-graphicsmagick-lib=$GRAPHICSMAGICK_ROOT_DIR/lib/ --with-graphicsmagick-include=$GRAPHICSMAGICK_ROOT_DIR/include/GraphicsMagick/ --prefix=$INSTALL_DIR </action>
54 <action type="shell_command">make</action> 19 <action type="shell_command">make</action>
55 <action type="shell_command">make install</action> 20 <action type="shell_command">make install</action>
56
57 <action type="shell_command">rm $INSTALL_DIR/tclap/ -r</action>
58 <!--<action type="shell_command">rm $INSTALL_DIR/openbabel/ -r</action>-->
59 <action type="shell_command">rm $INSTALL_DIR/gocr/ -r</action>
60 <action type="shell_command">rm $INSTALL_DIR/ocrad/ -r</action>
61 <action type="shell_command">rm $INSTALL_DIR/cuneiform/ -r</action>
62
63 <action type="set_environment"> 21 <action type="set_environment">
64 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[GRAPHICSMAGICK_ROOT_DIR]/lib/</environment_variable>
65 <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/potrace/build/lib/</environment_variable>
66 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 22 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
67 <!-- OSRA_DATA_FILES is only used by the galaxy wrapper and is not part of OSRA --> 23 <environment_variable action="set_to" name="BABEL_DATADIR">$INSTALL_DIR/share/openbabel</environment_variable>
68 <environment_variable action="set_to" name="OSRA_DATA_FILES">$INSTALL_DIR/share</environment_variable> 24 <environment_variable action="set_to" name="BABEL_LIBDIR">$INSTALL_DIR/lib/openbabel/2.2.99</environment_variable>
69 </action> 25 </action>
70 </actions> 26 </actions>
71 </install> 27 </install>
72 <readme>We still have a handfull of requirements</readme> 28 <readme>Compiling Confab requires g++, CMake 2.4+. Optional but required for a few features is libxml2 and zlib.</readme>
73 </package> 29 </package>
74 </tool_dependency> 30 </tool_dependency>