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v0.0.3 citation information and internal changes
author peterjc
date Wed, 05 Aug 2015 10:57:39 -0400
parents 0996169ac2e8
children 139b6f0a0bb5
comparison
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0:0996169ac2e8 1:5ae1c0312aaa
1 Galaxy wrapper for the CLC Assembly Cell suite from CLCbio 1 Galaxy wrapper for the CLC Assembly Cell suite from CLCbio
2 ========================================================== 2 ==========================================================
3 3
4 This wrapper is copyright 2013 by Peter Cock, The James Hutton Institute 4 This wrapper is copyright 2013-2015 by Peter Cock, The James Hutton Institute
5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. 5 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
6 See the licence text below. 6 See the licence text below.
7 7
8 CLC Assembly Cell is the commercial command line assembly suite from CLCbio. 8 CLC Assembly Cell is the commercial command line assembly suite from CLCbio.
9 It uses SIMD instructions to parallelize and accelerate their assembly 9 It uses SIMD instructions to parallelize and accelerate their assembly
23 http://www.clcbio.com/?action=transfer_user&productVersion=4.2&productID=6982&productName=CLC+Assembly+Cell&nonce=db842e3f95 23 http://www.clcbio.com/?action=transfer_user&productVersion=4.2&productID=6982&productName=CLC+Assembly+Cell&nonce=db842e3f95
24 24
25 This wrapper is available from the Galaxy Tool Shed at: 25 This wrapper is available from the Galaxy Tool Shed at:
26 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell 26 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
27 27
28 This Galaxy wrapper was written and tested using CLC Assembly Cell 28 This Galaxy wrapper was written and tested using CLC Assembly Cell v4.1.0,
29 version 4.10.86742 29 specifically ``clc_assember`` and ``clc_mapper`` binaries for 64 bit Linux
30 which report version 4.10.86742 at the command line.
30 31
31 32
32 Automated Installation 33 Automated Installation
33 ====================== 34 ======================
34 35
35 This should be straightforward, Galaxy should automatically download and 36 This should be straightforward, Galaxy should automatically download and
36 install the wrapper from the Galaxy Tool Shed. However, you will need to 37 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 manually install the CLC Assembly Cell software, and setup the environment
38 variable ``$CLC_ASSEMBLY_CELL`` to the directory containing the binaries 39 variable ``$CLC_ASSEMBLY_CELL`` to the directory containing the binaries
39 (and in particular, the ``clc_assembler`` binary). For example: 40 (in particular, binaries ``clc_assembler``, ``clc_mapper`` and
41 ``clc_cas_to_sam``). For example::
40 42
41 $ export CLC_ASSEMBLY_CELL=/opt/clcbio/clc-assembly-cell-4.1.0-linux_64/ 43 $ export CLC_ASSEMBLY_CELL=/opt/clcbio/clc-assembly-cell-4.1.0-linux_64/
44
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.
42 50
43 51
44 Manual Installation 52 Manual Installation
45 =================== 53 ===================
46 54
47 First install the CLC Assembly Cell sortware as described above. 55 First install the CLC Assembly Cell sortware as described above.
48 56
49 To install the wrapper copy or move the following files under the Galaxy tools 57 To install the wrapper copy or move the following files under the Galaxy tools
50 folder, e.g. in a ``tools/clcbio/`` folder: 58 folder, e.g. in a ``tools/clcbio/`` folder:
51 59
52 * clc_assembler.xml (Galaxy tool definition) 60 * ``clc_assembler.xml`` (Galaxy tool definition)
53 * clc_mapper.xml (Galaxy tool definition) 61 * ``clc_mapper.xml`` (Galaxy tool definition)
54 * README.rst (this file) 62 * ``README.rst`` (this file)
55 63
56 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer 64 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:: 65 the tools. Just all these line, for example next to other assembly tools::
58 66
59 <tool file="clc_assembly_cell/clc_assembler.xml" /> 67 <tool file="clc_assembly_cell/clc_assembler.xml" />
75 Version Changes 83 Version Changes
76 ------- ---------------------------------------------------------------------- 84 ------- ----------------------------------------------------------------------
77 v0.0.1 - Initial public release. 85 v0.0.1 - Initial public release.
78 v0.0.2 - Actually use the ``$CLC_ASSEMBLY_CELL`` environment variable. 86 v0.0.2 - Actually use the ``$CLC_ASSEMBLY_CELL`` environment variable.
79 - Enable and fixed the tests. 87 - Enable and fixed the tests.
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).
80 ======= ====================================================================== 91 ======= ======================================================================
81 92
82 93
83 Developers 94 Developers
84 ========== 95 ==========
85 96
86 Development is on this itHub repository: 97 Development is on this itHub repository:
87 https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell 98 https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell
88 99
89 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use 100 For pushing a release to the test or main "Galaxy Tool Shed", use the following
90 the following command from the Galaxy root folder:: 101 Planemo commands (which requires you have set your Tool Shed access details in
102 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
91 103
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 104 $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/
105 ...
93 106
94 Check this worked:: 107 or::
95 108
96 $ tar -tzf clcbio.tar.gz 109 $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/
110 ...
111
112 To just build and check the tar ball, use::
113
114 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/clc_assembly_cell/
115 ...
116 $ tar -tzf shed_upload.tar.gz
117 test-data/NC_010642.fna
97 tools/clc_assembly_cell/README.rst 118 tools/clc_assembly_cell/README.rst
98 tools/clc_assembly_cell/clc_assembler.xml 119 tools/clc_assembly_cell/clc_assembler.xml
99 tools/clc_assembly_cell/clc_mapper.xml 120 tools/clc_assembly_cell/clc_mapper.xml
100 tools/clc_assembly_cell/tool_dependencies.xml 121 tools/clc_assembly_cell/tool_dependencies.xml
101 test-data/NC_010642.fna
102 122
103 123
104 Licence (MIT) 124 Licence (MIT)
105 ============= 125 =============
106 126