Mercurial > repos > pjbriggs > pal_finder
annotate README.rst @ 1:771ebe02636f draft
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.
author | pjbriggs |
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date | Mon, 23 Mar 2015 07:01:37 -0400 |
parents | 3f908e7fff4f |
children | b6ccc7dd7b02 |
rev | line source |
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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 | |
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 ---------- ---------------------------------------------------------------------- | |
1
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
parents:
0
diff
changeset
|
57 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
parents:
0
diff
changeset
|
58 add explicit dependency on Perl 5.16.3. |
0 | 59 0.02.04.1 - Add option to run Graeme Fox's ``pal_finder_filter.pl`` script to |
60 filter and sort the pal_finder output (Illumina input data only). | |
61 Update version number to reflect the pal_finder version. | |
62 0.0.6 - Allow input data to be either Illumina paired-end data in fastq | |
63 format or single-end 454 data in fasta format. | |
64 0.0.5 - Allow custom mispriming library to be specified; added | |
65 ``tool_dependencies.xml`` file to install pal_finder and primer3 | |
66 programs and configure environment for Galaxy automatically. | |
67 0.0.4 - Added more custom options for primer3_core for selecting primers on | |
68 size, GC and melting temperature criteria. | |
69 0.0.3 - Check that pal_finder script & config file, and primer3_core | |
70 executable are all available; move PRIMER_MIN_TM parameter to new | |
71 "custom" section for primer3 settings | |
72 0.0.2 - Updated pal_finder_wrapper.sh to allow locations of pal_finder Perl | |
73 script, data files and primer_core3 program to be set via environment | |
74 variables | |
75 0.0.1 - Initial version | |
76 ========== ====================================================================== | |
77 | |
78 | |
79 Developers | |
80 ========== | |
81 | |
82 This tool is developed on the following GitHub repository: | |
83 https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/pal_finder | |
84 | |
85 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use | |
86 the ``package_pal_finder.sh`` script. | |
87 | |
88 | |
89 Licence (MIT) | |
90 ============= | |
91 | |
92 Permission is hereby granted, free of charge, to any person obtaining a copy | |
93 of this software and associated documentation files (the "Software"), to deal | |
94 in the Software without restriction, including without limitation the rights | |
95 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
96 copies of the Software, and to permit persons to whom the Software is | |
97 furnished to do so, subject to the following conditions: | |
98 | |
99 The above copyright notice and this permission notice shall be included in | |
100 all copies or substantial portions of the Software. | |
101 | |
102 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
103 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
104 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
105 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
106 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
107 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
108 THE SOFTWARE. |