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Repository clc_assembly_cell
Owner: peterjc
Synopsis: Galaxy wrapper for the CLC Assembly Cell suite from CLCBio
This is a wrapper for the commercial "CLC Assembly Cell" suite from CLCBio which
includes a de novo assembler and read mapper.

http://www.clcbio.com/products/clc-assembly-cell/
Type: unrestricted
Revision: 5:31a9169b6222
This revision can be installed: True
Times cloned / installed: 538

Repository README files - may contain important installation or license information

Galaxy wrapper for the CLC Assembly Cell suite from CLCbio

This wrapper is copyright 2013-2017 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).
v0.0.4
  • Bug fix for <version_command> to capture tool version.
v0.0.5
  • Support the -u or --discardunmapped option to discard unmapped reads in the CLC Mapper wrapper.
  • Bug fix to use the $CLC_ASSEMBLY_CELL environment variable when calling clc_cas_to_sam in the CLC MApper wrapper.
v0.0.6
  • Update tool XML for optional vs required parameters.
  • Update URLs in documentation.
v0.0.7
  • Use <command detect_errors="aggressive"> (internal change only).
  • Single quote command line arguments (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_update -t testtoolshed --check_diff tools/clc_assembly_cell/
...

or:

$ planemo shed_update -t toolshed --check_diff tools/clc_assembly_cell/
...

To just build and check the tar ball, use:

$ planemo shed_upload --tar_only 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.

Dependencies of this repository

Repository package_samtools_0_1_19 revision c9bd782f5342 owned by iuc

Name Version Type
samtools 0.1.19 package

Contents of this repository

Name Description Version Minimum Galaxy Version
Maps reads giving a SAM/BAM file 0.0.7 16.01
Assembles reads giving a FASTA file 0.0.7 16.01

Categories
Assembly - Tools for working with assemblies
Next Gen Mappers - Tools for the analysis and handling of Next Gen sequencing data
SAM - Tools for manipulating alignments in the SAM format