Mercurial > repos > peterjc > clc_assembly_cell
comparison tools/clc_assembly_cell/README.rst @ 0:0996169ac2e8 draft
Uploaded v0.0.2, previously only on the TestToolShed
author | peterjc |
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date | Fri, 21 Nov 2014 06:41:12 -0500 |
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children | 5ae1c0312aaa |
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1 Galaxy wrapper for the CLC Assembly Cell suite from CLCbio | |
2 ========================================================== | |
3 | |
4 This wrapper is copyright 2013 by Peter Cock, The James Hutton Institute | |
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. | |
6 See the licence text below. | |
7 | |
8 CLC Assembly Cell is the commercial command line assembly suite from CLCbio. | |
9 It uses SIMD instructions to parallelize and accelerate their assembly | |
10 algorithms, and is also very memory efficient making it an appealing choice | |
11 for complex genomes where the RAM requirements exclude other popular tools. | |
12 | |
13 For more information: | |
14 http://www.clcbio.com/products/clc-assembly-cell/ | |
15 | |
16 You can download the CLC Assembly Cell User Manual here, currently v4.2 | |
17 http://www.clcbio.com/files/usermanuals/CLC_Assembly_Cell_User_Manual.pdf | |
18 | |
19 There is also an online manual here: | |
20 http://clcsupport.com/clcassemblycell/current/index.php?manual=Introduction.html | |
21 | |
22 There is currently a free trial download here: | |
23 http://www.clcbio.com/?action=transfer_user&productVersion=4.2&productID=6982&productName=CLC+Assembly+Cell&nonce=db842e3f95 | |
24 | |
25 This wrapper is available from the Galaxy Tool Shed at: | |
26 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell | |
27 | |
28 This Galaxy wrapper was written and tested using CLC Assembly Cell | |
29 version 4.10.86742 | |
30 | |
31 | |
32 Automated Installation | |
33 ====================== | |
34 | |
35 This should be straightforward, Galaxy should automatically download and | |
36 install the wrapper from the Galaxy Tool Shed. However, you will need to | |
37 manually install the CLC Assembly Cell software, and setup the environment | |
38 variable ``$CLC_ASSEMBLY_CELL`` to the directory containing the binaries | |
39 (and in particular, the ``clc_assembler`` binary). For example: | |
40 | |
41 $ export CLC_ASSEMBLY_CELL=/opt/clcbio/clc-assembly-cell-4.1.0-linux_64/ | |
42 | |
43 | |
44 Manual Installation | |
45 =================== | |
46 | |
47 First install the CLC Assembly Cell sortware as described above. | |
48 | |
49 To install the wrapper copy or move the following files under the Galaxy tools | |
50 folder, e.g. in a ``tools/clcbio/`` folder: | |
51 | |
52 * clc_assembler.xml (Galaxy tool definition) | |
53 * clc_mapper.xml (Galaxy tool definition) | |
54 * README.rst (this file) | |
55 | |
56 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer | |
57 the tools. Just all these line, for example next to other assembly tools:: | |
58 | |
59 <tool file="clc_assembly_cell/clc_assembler.xml" /> | |
60 <tool file="clc_assembly_cell/clc_mapper.xml" /> | |
61 | |
62 If you wish to run the unit tests, also move/copy the ``test-data/`` files | |
63 under Galaxy's ``test-data/`` folder. Then run:: | |
64 | |
65 $ ./run_tests.sh -id clc_assembler | |
66 $ ./run_tests.sh -id clc_mapper | |
67 | |
68 That's it. | |
69 | |
70 | |
71 History | |
72 ======= | |
73 | |
74 ======= ====================================================================== | |
75 Version Changes | |
76 ------- ---------------------------------------------------------------------- | |
77 v0.0.1 - Initial public release. | |
78 v0.0.2 - Actually use the ``$CLC_ASSEMBLY_CELL`` environment variable. | |
79 - Enable and fixed the tests. | |
80 ======= ====================================================================== | |
81 | |
82 | |
83 Developers | |
84 ========== | |
85 | |
86 Development is on this itHub repository: | |
87 https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell | |
88 | |
89 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use | |
90 the following command from the Galaxy root folder:: | |
91 | |
92 $ tar -czf clcbio.tar.gz tools/clc_assembly_cell/README.rst tools/clc_assembly_cell/clc_assembler.xml tools/clc_assembly_cell/clc_mapper.xml tools/clc_assembly_cell/tool_dependencies.xml test-data/NC_010642.fna | |
93 | |
94 Check this worked:: | |
95 | |
96 $ tar -tzf clcbio.tar.gz | |
97 tools/clc_assembly_cell/README.rst | |
98 tools/clc_assembly_cell/clc_assembler.xml | |
99 tools/clc_assembly_cell/clc_mapper.xml | |
100 tools/clc_assembly_cell/tool_dependencies.xml | |
101 test-data/NC_010642.fna | |
102 | |
103 | |
104 Licence (MIT) | |
105 ============= | |
106 | |
107 Permission is hereby granted, free of charge, to any person obtaining a copy | |
108 of this software and associated documentation files (the "Software"), to deal | |
109 in the Software without restriction, including without limitation the rights | |
110 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
111 copies of the Software, and to permit persons to whom the Software is | |
112 furnished to do so, subject to the following conditions: | |
113 | |
114 The above copyright notice and this permission notice shall be included in | |
115 all copies or substantial portions of the Software. | |
116 | |
117 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
118 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
119 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
120 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
121 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
122 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
123 THE SOFTWARE. | |
124 | |
125 NOTE: This is the licence for the Galaxy Wrapper only. The CLCbio tools are | |
126 commercial, and are available and licenced separately. |