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