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author pjbriggs
date Thu, 11 Dec 2014 09:23:24 -0500
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1 pal_finder: find microsatellite repeats and design PCR primers
2 ==============================================================
3
4 Galaxy tool wrapper for the pal_finder microsatellite and PCR primer design script.
5
6 Automated installation
7 ======================
8
9 Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
10 the pal_finder and primer3_core programs, and setting the appropriate environment
11 variables.
12
13 Manual Installation
14 ===================
15
16 There are two files to install:
17
18 - ``pal_finder_wrapper.xml`` (the Galaxy tool definition)
19 - ``pal_finder_wrapper.sh`` (the shell script wrapper)
20
21 The suggested location is in a ``tools/pal_finder_wrapper/`` folder. You will then
22 need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
23 by adding the line:
24
25 <tool file="pal_finder/pal_finder_wrapper.xml" />
26
27 You will also need to install the pal_finder and primer3 packages:
28
29 - ``pal_finder`` can be obtained from http://sourceforge.net/projects/palfinder/
30 - ``Primer3`` version 2.0.0-alpha (see the pal_finder installation notes) can be
31 obtained from http://primer3.sourceforge.net/releases.php
32
33 The tool wrapper must be able to locate the pal_finder Perl script, the example
34 pal_finder config.txt and simple.ref data files, and the primer3_core program - the
35 locations of these are taken from the following enviroment variables which you will
36 need to set manually:
37
38 - ``PALFINDER_SCRIPT_DIR``: location of the pal_finder Perl script (defaults to /usr/bin)
39 - ``PALFINDER_DATA_DIR``: location of the pal_finder data files (specifically config.txt
40 and simple.ref; defaults to /usr/share/pal_finder_v0.02.04)
41 - ``PRIMER3_CORE_EXE``: name of the primer3_core program, which should include the
42 full path if it's not on the Galaxy user's PATH (defaults to primer3_core)
43
44 If you want to run the functional tests, copy the sample test files under
45 sample test files under Galaxy's ``test-data/`` directory. Then:
46
47 ./run_tests.sh -id microsat_pal_finder
48
49 You will need to have set the environment variables above.
50
51 History
52 =======
53
54 ========== ======================================================================
55 Version Changes
56 ---------- ----------------------------------------------------------------------
57 0.02.04.1 - Add option to run Graeme Fox's ``pal_finder_filter.pl`` script to
58 filter and sort the pal_finder output (Illumina input data only).
59 Update version number to reflect the pal_finder version.
60 0.0.6 - Allow input data to be either Illumina paired-end data in fastq
61 format or single-end 454 data in fasta format.
62 0.0.5 - Allow custom mispriming library to be specified; added
63 ``tool_dependencies.xml`` file to install pal_finder and primer3
64 programs and configure environment for Galaxy automatically.
65 0.0.4 - Added more custom options for primer3_core for selecting primers on
66 size, GC and melting temperature criteria.
67 0.0.3 - Check that pal_finder script & config file, and primer3_core
68 executable are all available; move PRIMER_MIN_TM parameter to new
69 "custom" section for primer3 settings
70 0.0.2 - Updated pal_finder_wrapper.sh to allow locations of pal_finder Perl
71 script, data files and primer_core3 program to be set via environment
72 variables
73 0.0.1 - Initial version
74 ========== ======================================================================
75
76
77 Developers
78 ==========
79
80 This tool is developed on the following GitHub repository:
81 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/pal_finder
82
83 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
84 the ``package_pal_finder.sh`` script.
85
86
87 Licence (MIT)
88 =============
89
90 Permission is hereby granted, free of charge, to any person obtaining a copy
91 of this software and associated documentation files (the "Software"), to deal
92 in the Software without restriction, including without limitation the rights
93 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
94 copies of the Software, and to permit persons to whom the Software is
95 furnished to do so, subject to the following conditions:
96
97 The above copyright notice and this permission notice shall be included in
98 all copies or substantial portions of the Software.
99
100 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
101 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
102 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
103 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
104 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
105 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
106 THE SOFTWARE.