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1 pal_finder: find microsatellite repeats and design PCR primers
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2 ==============================================================
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3
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4 Galaxy tool wrapper for the pal_finder microsatellite and PCR primer design script.
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5
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6 Automated installation
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7 ======================
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8
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9 Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
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10 the pal_finder and primer3_core programs (plus additional dependencies), and setting
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11 the appropriate environment variables.
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12
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13 Manual Installation
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14 ===================
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15
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16 There are three files to install:
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17
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18 - ``pal_finder_wrapper.xml`` (the Galaxy tool definition)
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19 - ``pal_finder_wrapper.sh`` (the shell script wrapper)
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20 - ``pal_finder_filter_and_assembly.py`` (filtering utility)
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21
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22 The suggested location is in a ``tools/pal_finder_wrapper/`` folder. You will then
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23 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
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24 by adding the line::
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25
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26 <tool file="pal_finder/pal_finder_wrapper.xml" />
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27
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28 You will also need to install the pal_finder and primer3 packages:
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29
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30 - ``pal_finder`` can be obtained from http://sourceforge.net/projects/palfinder/
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31 - ``Primer3`` version 2.0.0-alpha (see the pal_finder installation notes) can be
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32 obtained from http://primer3.sourceforge.net/releases.php
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33
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34 Additionally the filtering script needs ``BioPython`` and the ``PANDASeq`` program:
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35
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36 - ``BioPython`` can be obtained from https://pypi.python.org/packages/source/b/biopython/
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37 - ``PANDASeq`` version 2.8.1 can be obtained from https://github.com/neufeld/pandaseq/
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38
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39 The tool wrapper must be able to locate the ``pal_finder_v0.02.04.pl`` script, the
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40 example pal_finder ``config.txt`` and ``simple.ref`` data files, and the
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41 ``primer3_core`` program - the locations of these are taken from the following
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42 enviroment variables which you will need to set manually:
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43
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44 - ``PALFINDER_SCRIPT_DIR``: location of the pal_finder Perl script (defaults to /usr/bin)
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45 - ``PALFINDER_DATA_DIR``: location of the pal_finder data files (specifically config.txt
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46 and simple.ref; defaults to /usr/share/pal_finder_v0.02.04)
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47 - ``PRIMER3_CORE_EXE``: name of the primer3_core program, which should include the
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48 full path if it's not on the Galaxy user's PATH (defaults to primer3_core)
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49
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50 If you want to run the functional tests, copy the sample test files under
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51 sample test files under Galaxy's ``test-data/`` directory. Then::
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52
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53 ./run_tests.sh -id microsat_pal_finder
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54
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55 You will need to have set the environment variables above.
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56
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57 History
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58 =======
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59
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60 ========== ======================================================================
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61 Version Changes
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62 ---------- ----------------------------------------------------------------------
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63 0.02.04.4 - Update to the filter script (``pal_filter.py``) which removes some
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64 columns from the output assembly file.
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65 0.02.04.3 - Update to the Illumina filtering script from Graeme Fox (including
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66 new option to run ``PANDASeq`` assembly/QC steps), and corresponding
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67 update to the tool; add support for input FASTQs to be a dataset
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68 collection pair.
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69 0.02.04.2 - Fix bug that causes tool to fail when prefix includes spaces;
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70 add explicit dependency on Perl 5.16.3.
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71 0.02.04.1 - Add option to run Graeme Fox's ``pal_finder_filter.pl`` script to
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72 filter and sort the pal_finder output (Illumina input data only).
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73 Update version number to reflect the pal_finder version.
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74 0.0.6 - Allow input data to be either Illumina paired-end data in fastq
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75 format or single-end 454 data in fasta format.
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76 0.0.5 - Allow custom mispriming library to be specified; added
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77 ``tool_dependencies.xml`` file to install pal_finder and primer3
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78 programs and configure environment for Galaxy automatically.
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79 0.0.4 - Added more custom options for primer3_core for selecting primers on
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80 size, GC and melting temperature criteria.
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81 0.0.3 - Check that pal_finder script & config file, and primer3_core
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82 executable are all available; move PRIMER_MIN_TM parameter to new
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83 "custom" section for primer3 settings
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84 0.0.2 - Updated pal_finder_wrapper.sh to allow locations of pal_finder Perl
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85 script, data files and primer_core3 program to be set via environment
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86 variables
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87 0.0.1 - Initial version
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88 ========== ======================================================================
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89
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90
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91 Developers
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92 ==========
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93
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94 This tool is developed on the following GitHub repository:
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95 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/pal_finder
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96
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97 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
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98 the ``package_pal_finder.sh`` script.
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99
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100
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101 Licence (MIT)
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102 =============
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103
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104 Permission is hereby granted, free of charge, to any person obtaining a copy
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105 of this software and associated documentation files (the "Software"), to deal
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106 in the Software without restriction, including without limitation the rights
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107 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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108 copies of the Software, and to permit persons to whom the Software is
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109 furnished to do so, subject to the following conditions:
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110
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111 The above copyright notice and this permission notice shall be included in
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112 all copies or substantial portions of the Software.
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113
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114 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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115 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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116 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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117 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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118 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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119 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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120 THE SOFTWARE.
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