Mercurial > repos > bgruening > antismash

comparison tool_dependencies.xml @ 25:99435bb90725 draft

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Uploaded
author bgruening
date Fri, 18 Oct 2013 03:35:17 -0400
parents b942dfd80819
children a5eb6fad2a76
comparison
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24:b942dfd80819 25:99435bb90725
5 </package> 5 </package>
6 <package name="hmmer" version="3.0"> 6 <package name="hmmer" version="3.0">
7 <repository changeset_revision="a44693e3a2c4" name="package_hmmer_3_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="a44693e3a2c4" name="package_hmmer_3_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="muscle" version="3.8.31"> 9 <package name="muscle" version="3.8.31">
10 <repository changeset_revision="ce304c51f69b" name="package_muscle_3_8_31" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="83bd107a5300" name="package_muscle_3_8_31" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
11 </package> 11 </package>
12 <package name="biopython" version="1.62"> 12 <package name="biopython" version="1.62">
13 <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 13 <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" />
14 </package> 14 </package>
15 15
16 <package name="helperlibs" version="0.1.2"> 16 <package name="helperlibs" version="0.1.2">
17 <install version="1.0"> 17 <install version="1.0">
18 <actions> 18 <actions>
19 <action type="download_by_url">https://pypi.python.org/packages/source/h/helperlibs/helperlibs-0.1.2.tar.gz</action> 19 <action type="download_by_url">https://pypi.python.org/packages/source/h/helperlibs/helperlibs-0.1.2.tar.gz</action>
20 <action type="make_directory">$INSTALL_DIR/lib/python</action> 20 <action type="make_directory">$INSTALL_DIR/lib/python</action>
21 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action> 21 <action type="shell_command">
22 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
23 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
24 </action>
22 <action type="set_environment"> 25 <action type="set_environment">
23 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> 26 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
24 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 27 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
25 </action> 28 </action>
26 </actions> 29 </actions>
33 <package name="cssselect" version="0.9"> 36 <package name="cssselect" version="0.9">
34 <install version="1.0"> 37 <install version="1.0">
35 <actions> 38 <actions>
36 <action type="download_by_url">https://pypi.python.org/packages/source/c/cssselect/cssselect-0.9.tar.gz</action> 39 <action type="download_by_url">https://pypi.python.org/packages/source/c/cssselect/cssselect-0.9.tar.gz</action>
37 <action type="make_directory">$INSTALL_DIR/lib/python</action> 40 <action type="make_directory">$INSTALL_DIR/lib/python</action>
38 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action> 41 <action type="shell_command">
42 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
43 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
44 </action>
39 <action type="set_environment"> 45 <action type="set_environment">
40 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> 46 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
41 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 47 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
42 </action> 48 </action>
43 </actions> 49 </actions>
50 <package name="pyquery" version="1.2.6"> 56 <package name="pyquery" version="1.2.6">
51 <install version="1.0"> 57 <install version="1.0">
52 <actions> 58 <actions>
53 <action type="download_by_url">https://github.com/gawel/pyquery/archive/1.2.6.tar.gz</action> 59 <action type="download_by_url">https://github.com/gawel/pyquery/archive/1.2.6.tar.gz</action>
54 <action type="make_directory">$INSTALL_DIR/lib/python</action> 60 <action type="make_directory">$INSTALL_DIR/lib/python</action>
55 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action> 61 <action type="shell_command">
62 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
63 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
64 </action>
56 <action type="set_environment"> 65 <action type="set_environment">
57 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> 66 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
58 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 67 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
59 </action> 68 </action>
60 </actions> 69 </actions>
67 <package name="straight.plugin" version="1.4.0-post-1"> 76 <package name="straight.plugin" version="1.4.0-post-1">
68 <install version="1.0"> 77 <install version="1.0">
69 <actions> 78 <actions>
70 <action type="download_by_url">https://pypi.python.org/packages/source/s/straight.plugin/straight.plugin-1.4.0-post-1.tar.gz</action> 79 <action type="download_by_url">https://pypi.python.org/packages/source/s/straight.plugin/straight.plugin-1.4.0-post-1.tar.gz</action>
71 <action type="make_directory">$INSTALL_DIR/lib/python</action> 80 <action type="make_directory">$INSTALL_DIR/lib/python</action>
72 <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action> 81 <action type="shell_command">
82 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
83 python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
84 </action>
73 <action type="set_environment"> 85 <action type="set_environment">
74 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> 86 <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
75 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 87 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
76 </action> 88 </action>
77 </actions> 89 </actions>
81 </readme> 93 </readme>
82 </package> 94 </package>
83 <package name="antismash" version="2.0.2"> 95 <package name="antismash" version="2.0.2">
84 <install version="1.0"> 96 <install version="1.0">
85 <actions_group> 97 <actions_group>
86 98 <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. -->
87 <!-- Download the binaries for antiSMASH compatible with 64-bit OSX. -->
88 <actions architecture="x86_64" os="darwin"> 99 <actions architecture="x86_64" os="darwin">
89 <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action> 100 <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action>
90 <action type="move_directory_files"> 101 <action type="move_directory_files">
91 <source_directory>.</source_directory> 102 <source_directory>.</source_directory>
92 <destination_directory>$INSTALL_DIR</destination_directory> 103 <destination_directory>$INSTALL_DIR</destination_directory>
107 do not offer the option for genprediction and do not install glimmer and Co. 118 do not offer the option for genprediction and do not install glimmer and Co.
108 For that reason deactivate the check. 119 For that reason deactivate the check.
109 --> 120 -->
110 <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/False/g' $INSTALL_DIR/run_antismash.py</action> 121 <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/False/g' $INSTALL_DIR/run_antismash.py</action>
111 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action> 122 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
112 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>n&gt; 123 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
113 </actions> 124 </actions>
114 125
115 <!-- Download the binaries for antiSMASH compatible with 64-bit OSX. --> 126 <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. -->
116 <actions architecture="i386" os="darwin"> 127 <actions architecture="i386" os="darwin">
117 <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action> 128 <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action>
118 <action type="move_directory_files"> 129 <action type="move_directory_files">
119 <source_directory>.</source_directory> 130 <source_directory>.</source_directory>
120 <destination_directory>$INSTALL_DIR</destination_directory> 131 <destination_directory>$INSTALL_DIR</destination_directory>
207 </action> 218 </action>
208 </actions_group> 219 </actions_group>
209 </install> 220 </install>
210 <readme> 221 <readme>
211 AntiSmash installation with all dependencies. 222 AntiSmash installation with all dependencies.
223 Java needs to be installed.
212 </readme> 224 </readme>
213 </package> 225 </package>
214 </tool_dependency> 226 </tool_dependency>