Mercurial > repos > pjbriggs > pal_finder
annotate README.rst @ 7:5e133b7b79a6 draft
Uploaded version 0.02.04.6 (uses conda dependency resolution).
author | pjbriggs |
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date | Mon, 19 Mar 2018 06:33:32 -0400 |
parents | a73c48890bde |
children | 4e625d3672ba |
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0 | 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 | |
2 | 10 the pal_finder and primer3_core programs (plus additional dependencies), and setting |
11 the appropriate environment variables. | |
0 | 12 |
13 Manual Installation | |
14 =================== | |
15 | |
2 | 16 There are three files to install: |
0 | 17 |
18 - ``pal_finder_wrapper.xml`` (the Galaxy tool definition) | |
19 - ``pal_finder_wrapper.sh`` (the shell script wrapper) | |
2 | 20 - ``pal_finder_filter_and_assembly.py`` (filtering utility) |
0 | 21 |
22 The suggested location is in a ``tools/pal_finder_wrapper/`` folder. You will then | |
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:: |
0 | 25 |
26 <tool file="pal_finder/pal_finder_wrapper.xml" /> | |
27 | |
28 You will also need to install the pal_finder and primer3 packages: | |
29 | |
30 - ``pal_finder`` can be obtained from http://sourceforge.net/projects/palfinder/ | |
31 - ``Primer3`` version 2.0.0-alpha (see the pal_finder installation notes) can be | |
32 obtained from http://primer3.sourceforge.net/releases.php | |
33 | |
2 | 34 Additionally the filtering script needs ``BioPython`` and the ``PANDASeq`` program: |
35 | |
36 - ``BioPython`` can be obtained from https://pypi.python.org/packages/source/b/biopython/ | |
37 - ``PANDASeq`` version 2.8.1 can be obtained from https://github.com/neufeld/pandaseq/ | |
38 | |
39 The tool wrapper must be able to locate the ``pal_finder_v0.02.04.pl`` script, the | |
40 example pal_finder ``config.txt`` and ``simple.ref`` data files, and the | |
41 ``primer3_core`` program - the locations of these are taken from the following | |
42 enviroment variables which you will need to set manually: | |
0 | 43 |
44 - ``PALFINDER_SCRIPT_DIR``: location of the pal_finder Perl script (defaults to /usr/bin) | |
45 - ``PALFINDER_DATA_DIR``: location of the pal_finder data files (specifically config.txt | |
46 and simple.ref; defaults to /usr/share/pal_finder_v0.02.04) | |
47 - ``PRIMER3_CORE_EXE``: name of the primer3_core program, which should include the | |
48 full path if it's not on the Galaxy user's PATH (defaults to primer3_core) | |
49 | |
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:: |
0 | 52 |
53 ./run_tests.sh -id microsat_pal_finder | |
54 | |
55 You will need to have set the environment variables above. | |
56 | |
57 History | |
58 ======= | |
59 | |
60 ========== ====================================================================== | |
61 Version Changes | |
62 ---------- ---------------------------------------------------------------------- | |
6 | 63 |
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5e133b7b79a6
Uploaded version 0.02.04.6 (uses conda dependency resolution).
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64 0.02.04.6 - Update to get dependencies using ``conda`` when installed from the |
5e133b7b79a6
Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
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65 toolshed (this removes the explicit dependency on Perl 5.16 |
5e133b7b79a6
Uploaded version 0.02.04.6 (uses conda dependency resolution).
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66 introduced in 0.02.04.2, as a result the outputs from the tool are |
5e133b7b79a6
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67 now non-deterministic in some cases). |
6 | 68 0.02.04.5 - Update to handle large output files which can sometimes be generated |
69 by the ``pal_finder_v0.02.04.pl`` or ``pal_filter.py`` scripts (logs | |
70 of hundreds of Gb's have been observed in production): log files | |
71 longer than 500 lines are now truncated to avoid downstream problems. | |
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72 0.02.04.4 - Update to the filter script (``pal_filter.py``) which removes some |
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73 columns from the output assembly file. |
2 | 74 0.02.04.3 - Update to the Illumina filtering script from Graeme Fox (including |
75 new option to run ``PANDASeq`` assembly/QC steps), and corresponding | |
76 update to the tool; add support for input FASTQs to be a dataset | |
77 collection pair. | |
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Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
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78 0.02.04.2 - Fix bug that causes tool to fail when prefix includes spaces; |
771ebe02636f
Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
pjbriggs
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79 add explicit dependency on Perl 5.16.3. |
0 | 80 0.02.04.1 - Add option to run Graeme Fox's ``pal_finder_filter.pl`` script to |
81 filter and sort the pal_finder output (Illumina input data only). | |
82 Update version number to reflect the pal_finder version. | |
83 0.0.6 - Allow input data to be either Illumina paired-end data in fastq | |
84 format or single-end 454 data in fasta format. | |
85 0.0.5 - Allow custom mispriming library to be specified; added | |
86 ``tool_dependencies.xml`` file to install pal_finder and primer3 | |
87 programs and configure environment for Galaxy automatically. | |
88 0.0.4 - Added more custom options for primer3_core for selecting primers on | |
89 size, GC and melting temperature criteria. | |
90 0.0.3 - Check that pal_finder script & config file, and primer3_core | |
91 executable are all available; move PRIMER_MIN_TM parameter to new | |
92 "custom" section for primer3 settings | |
93 0.0.2 - Updated pal_finder_wrapper.sh to allow locations of pal_finder Perl | |
94 script, data files and primer_core3 program to be set via environment | |
95 variables | |
96 0.0.1 - Initial version | |
97 ========== ====================================================================== | |
98 | |
99 | |
100 Developers | |
101 ========== | |
102 | |
103 This tool is developed on the following GitHub repository: | |
104 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/pal_finder | |
105 | |
106 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use | |
107 the ``package_pal_finder.sh`` script. | |
108 | |
109 | |
110 Licence (MIT) | |
111 ============= | |
112 | |
113 Permission is hereby granted, free of charge, to any person obtaining a copy | |
114 of this software and associated documentation files (the "Software"), to deal | |
115 in the Software without restriction, including without limitation the rights | |
116 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
117 copies of the Software, and to permit persons to whom the Software is | |
118 furnished to do so, subject to the following conditions: | |
119 | |
120 The above copyright notice and this permission notice shall be included in | |
121 all copies or substantial portions of the Software. | |
122 | |
123 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
124 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
125 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
126 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
127 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
128 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
129 THE SOFTWARE. |