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 |
|
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.
|