Mercurial > repos > peterjc > clc_assembly_cell
view tools/clc_assembly_cell/README.rst @ 4:95a5f56a24eb draft
planemo upload for https://github.com/peterjc/pico_galaxy/tools/clc_assembly_cell/28b690151fe39a4e66133d37a625d348a1900b5d
author | peterjc |
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date | Tue, 12 May 2015 12:15:25 -0400 |
parents | 93ef6468b288 |
children | 40badce80899 |
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Galaxy wrapper for the CLC Assembly Cell suite from CLCbio ========================================================== This wrapper is copyright 2013-2015 by Peter Cock, The James Hutton Institute (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. CLC Assembly Cell is the commercial command line assembly suite from CLCbio. It uses SIMD instructions to parallelize and accelerate their assembly algorithms, and is also very memory efficient making it an appealing choice for complex genomes where the RAM requirements exclude other popular tools. For more information: http://www.clcbio.com/products/clc-assembly-cell/ You can download the CLC Assembly Cell User Manual here, currently v4.2 http://www.clcbio.com/files/usermanuals/CLC_Assembly_Cell_User_Manual.pdf There is also an online manual here: http://clcsupport.com/clcassemblycell/current/index.php?manual=Introduction.html There is currently a free trial download here: http://www.clcbio.com/?action=transfer_user&productVersion=4.2&productID=6982&productName=CLC+Assembly+Cell&nonce=db842e3f95 This wrapper is available from the Galaxy Tool Shed at: http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell This Galaxy wrapper was written and tested using CLC Assembly Cell v4.1.0, specifically ``clc_assember`` and ``clc_mapper`` binaries for 64 bit Linux which report version 4.10.86742 at the command line. Automated Installation ====================== This should be straightforward, Galaxy should automatically download and install the wrapper from the Galaxy Tool Shed. However, you will need to manually install the CLC Assembly Cell software, and setup the environment variable ``$CLC_ASSEMBLY_CELL`` to the directory containing the binaries (in particular, binaries ``clc_assembler``, ``clc_mapper`` and ``clc_cas_to_sam``). For example:: $ export CLC_ASSEMBLY_CELL=/opt/clcbio/clc-assembly-cell-4.1.0-linux_64/ If your CLC Bio licence is restricted to specific machines on your cluster, use Galaxy's job configuration settings to ensure CLC jobs are only sent to those licenced computers. For SGE, we use the ``-l hostname="..."`` option to do this. Alternatively your cluster administrator might setup a dedicated job queue. Manual Installation =================== First install the CLC Assembly Cell sortware as described above. To install the wrapper copy or move the following files under the Galaxy tools folder, e.g. in a ``tools/clcbio/`` folder: * ``clc_assembler.xml`` (Galaxy tool definition) * ``clc_mapper.xml`` (Galaxy tool definition) * ``README.rst`` (this file) You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tools. Just all these line, for example next to other assembly tools:: <tool file="clc_assembly_cell/clc_assembler.xml" /> <tool file="clc_assembly_cell/clc_mapper.xml" /> If you wish to run the unit tests, also move/copy the ``test-data/`` files under Galaxy's ``test-data/`` folder. Then run:: $ ./run_tests.sh -id clc_assembler $ ./run_tests.sh -id clc_mapper That's it. History ======= ======= ====================================================================== Version Changes ------- ---------------------------------------------------------------------- v0.0.1 - Initial public release. v0.0.2 - Actually use the ``$CLC_ASSEMBLY_CELL`` environment variable. - Enable and fixed the tests. v0.0.3 - Reorder XML elements (internal change only). - Added citation tags. - Planemo for Tool Shed upload (``.shed.yml``, internal change only). ======= ====================================================================== Developers ========== Development is on this itHub repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell For pushing a release to the test or main "Galaxy Tool Shed", use the following Planemo commands (which requires you have set your Tool Shed access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/ ... or:: $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/ ... To just build and check the tar ball, use:: $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/clc_assembly_cell/ ... $ tar -tzf shed_upload.tar.gz test-data/NC_010642.fna 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 Licence (MIT) ============= Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. NOTE: This is the licence for the Galaxy Wrapper only. The CLCbio tools are commercial, and are available and licenced separately.