Mercurial > repos > pjbriggs > pal_finder

annotate tool_dependencies.xml @ 3:e1a14ed7a9d6 draft

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Updated to version 0.02.04.4 (new pal_filter script)
author pjbriggs
date Wed, 24 Feb 2016 08:25:17 -0500
parents b6ccc7dd7b02
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0
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="pal_finder" version="0.02.04">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">http://sourceforge.net/projects/palfinder/files/pal_finder_v0.02.04.tar.gz</action>
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7 <action type="move_file">
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8 <source>pal_finder_v0.02.04.pl</source>
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9 <destination>$INSTALL_DIR/bin</destination>
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10 </action>
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11 <action type="move_file">
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12 <source>config.txt</source>
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13 <destination>$INSTALL_DIR/data</destination>
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14 </action>
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15 <action type="move_file">
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16 <source>simple.ref</source>
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17 <destination>$INSTALL_DIR/data</destination>
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18 </action>
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19 <action type="set_environment">
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20 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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21 </action>
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22 <action type="set_environment">
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23 <environment_variable name="PALFINDER_SCRIPT_DIR" action="set_to">$INSTALL_DIR/bin</environment_variable>
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24 </action>
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25 <action type="set_environment">
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26 <environment_variable name="PALFINDER_DATA_DIR" action="set_to">$INSTALL_DIR/data</environment_variable>
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27 </action>
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28 </actions>
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29 </install>
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30 <readme>pal_finder also needs Perl</readme>
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31 </package>
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32 <package name="perl" version="5.16.3">
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33 <install version="1.0">
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34 <actions>
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35 <!-- install perl -->
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36 <action type="download_by_url">http://www.cpan.org/src/5.0/perl-5.16.3.tar.gz</action>
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37 <action type="shell_command">./Configure -des -Dprefix=$INSTALL_DIR -Dstartperl='#!/usr/bin/env perl'</action>
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38 <action type="make_install" />
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39 <action type="set_environment">
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40 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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41 </action>
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42 </actions>
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43 </install>
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44 <readme>
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45 Perl 5 is a highly capable, feature-rich programming language with over 25 years of
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46 development:
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47
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48 http://www.perl.org/
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49 </readme>
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50 </package>
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51 <package name="primer3_core" version="2.0.0">
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52 <install version="1.0">
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53 <actions>
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54 <action type="download_by_url">https://sourceforge.net/projects/primer3/files/primer3/2.0.0-alpha/primer3-2.0.0-alpha.tar.gz</action>
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55 <action type="shell_command">make -C src -f Makefile</action>
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56 <action type="move_file">
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57 <source>src/primer3_core</source>
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58 <destination>$INSTALL_DIR/bin</destination>
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59 </action>
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60 <action type="set_environment">
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61 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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62 </action>
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63 </actions>
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64 </install>
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65 <readme>primer3_core</readme>
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66 </package>
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67 <package name="biopython" version="1.65">
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68 <install version="1.0">
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69 <actions>
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70 <action type="shell_command">pip install --install-option "--prefix=$INSTALL_DIR" https://pypi.python.org/packages/source/b/biopython/biopython-1.65.tar.gz</action>
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71 <action type="set_environment">
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72 <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python2.7/site-packages</environment_variable>
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73 <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib64/python2.7/site-packages</environment_variable>
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74 </action>
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75 </actions>
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76 </install>
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77 <readme>BioPython 1.65</readme>
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78 </package>
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79 <package name="pandaseq" version="2.8.1">
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80 <install version="1.0">
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81 <actions>
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82 <action type="download_by_url">https://github.com/neufeld/pandaseq/archive/v2.8.1.tar.gz</action>
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83 <action type="shell_command">./autogen.sh</action>
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84 <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
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85 <action type="shell_command">make</action>
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86 <action type="shell_command">make install</action>
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87 <action type="set_environment">
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88 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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89 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
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90 </action>
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91 </actions>
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92 </install>
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93 <readme>PANDASeq 2.8.1
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94
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95 PANDASEQ is a program to align Illumina reads, optionally
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96 with PCR primers embedded in the sequence, and reconstruct
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97 an overlapping sequence.
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98
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99 https://github.com/neufeld/pandaseq
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100 </readme>
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101 </package>
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102 </tool_dependency>