Mercurial > repos > peterjc > clc_assembly_cell
annotate tools/clc_assembly_cell/README.rst @ 3:9fe1a922353b draft
v0.0.5 option to discard unmapped read; env var bugfix
author | peterjc |
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date | Wed, 11 May 2016 06:49:58 -0400 |
parents | 139b6f0a0bb5 |
children | 46a667b5e19e |
rev | line source |
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0 | 1 Galaxy wrapper for the CLC Assembly Cell suite from CLCbio |
2 ========================================================== | |
3 | |
1 | 4 This wrapper is copyright 2013-2015 by Peter Cock, The James Hutton Institute |
0 | 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 | |
1 | 28 This Galaxy wrapper was written and tested using CLC Assembly Cell v4.1.0, |
29 specifically ``clc_assember`` and ``clc_mapper`` binaries for 64 bit Linux | |
30 which report version 4.10.86742 at the command line. | |
0 | 31 |
32 | |
33 Automated Installation | |
34 ====================== | |
35 | |
36 This should be straightforward, Galaxy should automatically download and | |
37 install the wrapper from the Galaxy Tool Shed. However, you will need to | |
38 manually install the CLC Assembly Cell software, and setup the environment | |
39 variable ``$CLC_ASSEMBLY_CELL`` to the directory containing the binaries | |
1 | 40 (in particular, binaries ``clc_assembler``, ``clc_mapper`` and |
41 ``clc_cas_to_sam``). For example:: | |
42 | |
43 $ export CLC_ASSEMBLY_CELL=/opt/clcbio/clc-assembly-cell-4.1.0-linux_64/ | |
0 | 44 |
1 | 45 If your CLC Bio licence is restricted to specific machines on your cluster, |
46 use Galaxy's job configuration settings to ensure CLC jobs are only sent | |
47 to those licenced computers. For SGE, we use the ``-l hostname="..."`` | |
48 option to do this. Alternatively your cluster administrator might setup | |
49 a dedicated job queue. | |
0 | 50 |
51 | |
52 Manual Installation | |
53 =================== | |
54 | |
55 First install the CLC Assembly Cell sortware as described above. | |
56 | |
57 To install the wrapper copy or move the following files under the Galaxy tools | |
58 folder, e.g. in a ``tools/clcbio/`` folder: | |
59 | |
1 | 60 * ``clc_assembler.xml`` (Galaxy tool definition) |
61 * ``clc_mapper.xml`` (Galaxy tool definition) | |
62 * ``README.rst`` (this file) | |
0 | 63 |
64 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer | |
65 the tools. Just all these line, for example next to other assembly tools:: | |
66 | |
67 <tool file="clc_assembly_cell/clc_assembler.xml" /> | |
68 <tool file="clc_assembly_cell/clc_mapper.xml" /> | |
69 | |
70 If you wish to run the unit tests, also move/copy the ``test-data/`` files | |
71 under Galaxy's ``test-data/`` folder. Then run:: | |
72 | |
73 $ ./run_tests.sh -id clc_assembler | |
74 $ ./run_tests.sh -id clc_mapper | |
75 | |
76 That's it. | |
77 | |
78 | |
79 History | |
80 ======= | |
81 | |
82 ======= ====================================================================== | |
83 Version Changes | |
84 ------- ---------------------------------------------------------------------- | |
85 v0.0.1 - Initial public release. | |
86 v0.0.2 - Actually use the ``$CLC_ASSEMBLY_CELL`` environment variable. | |
87 - Enable and fixed the tests. | |
1 | 88 v0.0.3 - Reorder XML elements (internal change only). |
89 - Added citation tags. | |
90 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). | |
2 | 91 v0.0.4 - Bug fix for ``<version_command>`` to capture tool version. |
3
9fe1a922353b
v0.0.5 option to discard unmapped read; env var bugfix
peterjc
parents:
2
diff
changeset
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92 v0.0.5 - Support the ``-u`` or ``--discardunmapped`` option to discard |
9fe1a922353b
v0.0.5 option to discard unmapped read; env var bugfix
peterjc
parents:
2
diff
changeset
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93 unmapped reads in the CLC Mapper wrapper. |
9fe1a922353b
v0.0.5 option to discard unmapped read; env var bugfix
peterjc
parents:
2
diff
changeset
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94 - Bug fix to use the ``$CLC_ASSEMBLY_CELL`` environment variable when |
9fe1a922353b
v0.0.5 option to discard unmapped read; env var bugfix
peterjc
parents:
2
diff
changeset
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95 calling ``clc_cas_to_sam`` in the CLC MApper wrapper. |
0 | 96 ======= ====================================================================== |
97 | |
98 | |
99 Developers | |
100 ========== | |
101 | |
102 Development is on this itHub repository: | |
103 https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell | |
104 | |
1 | 105 For pushing a release to the test or main "Galaxy Tool Shed", use the following |
106 Planemo commands (which requires you have set your Tool Shed access details in | |
107 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: | |
108 | |
2 | 109 $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/ |
1 | 110 ... |
111 | |
112 or:: | |
0 | 113 |
2 | 114 $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/ |
1 | 115 ... |
116 | |
117 To just build and check the tar ball, use:: | |
0 | 118 |
1 | 119 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/clc_assembly_cell/ |
120 ... | |
121 $ tar -tzf shed_upload.tar.gz | |
122 test-data/NC_010642.fna | |
0 | 123 tools/clc_assembly_cell/README.rst |
124 tools/clc_assembly_cell/clc_assembler.xml | |
125 tools/clc_assembly_cell/clc_mapper.xml | |
126 tools/clc_assembly_cell/tool_dependencies.xml | |
127 | |
128 | |
129 Licence (MIT) | |
130 ============= | |
131 | |
132 Permission is hereby granted, free of charge, to any person obtaining a copy | |
133 of this software and associated documentation files (the "Software"), to deal | |
134 in the Software without restriction, including without limitation the rights | |
135 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
136 copies of the Software, and to permit persons to whom the Software is | |
137 furnished to do so, subject to the following conditions: | |
138 | |
139 The above copyright notice and this permission notice shall be included in | |
140 all copies or substantial portions of the Software. | |
141 | |
142 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
143 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
144 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
145 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
146 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
147 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
148 THE SOFTWARE. | |
149 | |
150 NOTE: This is the licence for the Galaxy Wrapper only. The CLCbio tools are | |
151 commercial, and are available and licenced separately. |