Mercurial > repos > pjbriggs > pal_finder
annotate README.rst @ 9:b3ca3ece8a8b draft
WIP detect/trap "bad primer product range" errors.
| author | pjbriggs |
|---|---|
| date | Fri, 16 Jun 2017 09:12:09 -0400 |
| parents | 67ab365c29a7 |
| children | d26fb5260c67 |
| rev | line source |
|---|---|
| 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 | |
| 3 | 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 | |
| 3 | 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) | |
| 3 | 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 | |
| 5 | 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 | |
| 3 | 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 | |
| 5 | 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 ---------- ---------------------------------------------------------------------- | |
| 8 | 63 |
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b3ca3ece8a8b
WIP detect/trap "bad primer product range" errors.
pjbriggs
parents:
8
diff
changeset
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64 0.02.04.6 - Trap for errors in ``pal_finder_v0.02.04.pl`` resulting in bad |
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b3ca3ece8a8b
WIP detect/trap "bad primer product range" errors.
pjbriggs
parents:
8
diff
changeset
|
65 ranges being supplied to ``primer3_core`` for some reads via |
|
b3ca3ece8a8b
WIP detect/trap "bad primer product range" errors.
pjbriggs
parents:
8
diff
changeset
|
66 ``PRIMER_PRODUCT_RANGE_SIZE``. |
| 8 | 67 0.02.04.5 - Update to handle large output files which can sometimes be generated |
| 68 by the ``pal_finder_v0.02.04.pl`` or ``pal_filter.py`` scripts (logs | |
| 69 of hundreds of Gb's have been observed in production): log files | |
| 70 longer than 500 lines are now truncated to avoid downstream problems. | |
| 5 | 71 0.02.04.4 - Update to the filter script (``pal_filter.py``) which removes some |
| 72 columns from the output assembly file. | |
| 3 | 73 0.02.04.3 - Update to the Illumina filtering script from Graeme Fox (including |
| 74 new option to run ``PANDASeq`` assembly/QC steps), and corresponding | |
| 75 update to the tool; add support for input FASTQs to be a dataset | |
| 76 collection pair. | |
| 2 | 77 0.02.04.2 - Fix bug that causes tool to fail when prefix includes spaces; |
| 78 add explicit dependency on Perl 5.16.3. | |
| 0 | 79 0.02.04.1 - Add option to run Graeme Fox's ``pal_finder_filter.pl`` script to |
| 80 filter and sort the pal_finder output (Illumina input data only). | |
| 81 Update version number to reflect the pal_finder version. | |
| 82 0.0.6 - Allow input data to be either Illumina paired-end data in fastq | |
| 83 format or single-end 454 data in fasta format. | |
| 84 0.0.5 - Allow custom mispriming library to be specified; added | |
| 85 ``tool_dependencies.xml`` file to install pal_finder and primer3 | |
| 86 programs and configure environment for Galaxy automatically. | |
| 87 0.0.4 - Added more custom options for primer3_core for selecting primers on | |
| 88 size, GC and melting temperature criteria. | |
| 89 0.0.3 - Check that pal_finder script & config file, and primer3_core | |
| 90 executable are all available; move PRIMER_MIN_TM parameter to new | |
| 91 "custom" section for primer3 settings | |
| 92 0.0.2 - Updated pal_finder_wrapper.sh to allow locations of pal_finder Perl | |
| 93 script, data files and primer_core3 program to be set via environment | |
| 94 variables | |
| 95 0.0.1 - Initial version | |
| 96 ========== ====================================================================== | |
| 97 | |
| 98 | |
| 99 Developers | |
| 100 ========== | |
| 101 | |
| 102 This tool is developed on the following GitHub repository: | |
| 103 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/pal_finder | |
| 104 | |
| 105 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use | |
| 106 the ``package_pal_finder.sh`` script. | |
| 107 | |
| 108 | |
| 109 Licence (MIT) | |
| 110 ============= | |
| 111 | |
| 112 Permission is hereby granted, free of charge, to any person obtaining a copy | |
| 113 of this software and associated documentation files (the "Software"), to deal | |
| 114 in the Software without restriction, including without limitation the rights | |
| 115 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| 116 copies of the Software, and to permit persons to whom the Software is | |
| 117 furnished to do so, subject to the following conditions: | |
| 118 | |
| 119 The above copyright notice and this permission notice shall be included in | |
| 120 all copies or substantial portions of the Software. | |
| 121 | |
| 122 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| 123 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| 124 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
| 125 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| 126 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| 127 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
| 128 THE SOFTWARE. |