Mercurial > repos > peterjc > mira_assembler
changeset 9:b1d60b46d282 draft
Uploaded v0.0.8 take 3, citation information added, commented out test
| author | peterjc |
|---|---|
| date | Wed, 11 Sep 2013 06:21:44 -0400 |
| parents | da604cc07658 |
| children | 84cb67beb1ea |
| files | tools/mira_3_4/README.rst tools/mira_3_4/mira.txt tools/mira_3_4/mira.xml |
| diffstat | 3 files changed, 141 insertions(+), 116 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mira_3_4/README.rst Wed Sep 11 06:21:44 2013 -0400 @@ -0,0 +1,119 @@ +Galaxy tool to wrap the MIRA sequence assembly program (v3.4) +============================================================= + +This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute +(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. +See the licence text below (MIT licence). + +This tool is a short Python script (to collect the MIRA output and move it +to where Galaxy expects the files, and convert MIRA's TCS file into a tab +separated file for use in Galaxy). + +It is available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler + + +Automated Installation +====================== + +This should be straightforward, Galaxy should automatically download and +install the precompiled binary for MIRA v3.4.0 for the Galaxy wrapper, +and run any tests. + + +Manual Installation +=================== + +There are just two Galaxy files to install: + +* mira.py (the Python script) +* mira.xml (the Galaxy tool definition) + +The suggested location is a new tools/mira_3_4 folder. You will also need to +modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do +this to tools_conf.xml.sample in order to run any tests:: + + <tool file="mira_3_4/mira.xml" /> + +You will also need to install MIRA, we used version 3.4.1.1. See: + +* http://chevreux.org/projects_mira.html +* http://sourceforge.net/projects/mira-assembler/ + +WARNING: This tool was developed to construct viral genome assembly and +mapping pipelines, for which the run time and memory requirements are +negligible. For larger tasks, be aware that MIRA can require vast amounts +of RAM and run-times of over a week are possible. This tool wrapper makes +no attempt to spot and reject such large jobs. + + +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v0.0.1 - Initial version (working prototype, using MIRA 3.2.1) +v0.0.2 - Improve capture of stdout/stderr (should see it as it runs) +v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later + (some other switches changed, e.g. -OUT rrol to rrot, which + means the wrapper no longer works with MIRA 3.2.x) + - The contig summary file (TCS file) was removed in MIRA 3.4 + - Report all missing output files (not just first missing one) +v0.0.4 - Fix problem with backbone arguments inroduced in v0.0.3 +v0.0.5 - Implement the <version_command> tag to record the wrapper + version and the MIRA version being used. + - Check using MIRA 3.4 (later versions have a different API) +v0.0.6 - Tell MIRA to use /tmp for temporary files + - Tell MIRA to ignore long read names (otherwise it aborts) +v0.0.7 - Automated installation of the 64 bit Linux MIRA binary. +v0.0.8 - Basic unit test added (but commented out due to Galaxy issue). + - Link to Tool Shed added to help text and this documentation. + - Use reStructuredText for this README file. + - Adopted standard MIT licence. + - Updated citation information (Cock et al. 2013). +======= ====================================================================== + + +Developers +========== + +This script and related tools are being developed on the following hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/tools + +For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use +the following command from the Galaxy root folder:: + + $ tar -czf mira_wrapper.tar.gz tools/mira_3_4/README.rst tools/mira_3_4/mira.xml tools/mira_3_4/mira.py tools/mira_3_4/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta + +Check this worked: + + $ tar -tzf mira_wrapper.tar.gz + tools/mira_3_4/README.rst + tools/mira_3_4/mira.xml + tools/mira_3_4/mira.py + tools/mira_3_4/tool_dependencies.xml + test-data/tvc_mini.fastq + test-data/tvc_contigs.fasta + + +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.
--- a/tools/mira_3_4/mira.txt Thu May 02 12:40:04 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,112 +0,0 @@ -Galaxy tool to wrap the MIRA sequence assembly program (v3.4) -============================================================= - -This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute -(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. -See the licence text below. - -This tool is a short Python script (to collect the MIRA output and move it -to where Galaxy expects the files, and convert MIRA's TCS file into a tab -separated file for use in Galaxy). - -It is available from the Galaxy Tool Shed at: -http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler - - -Automated Installation -====================== - -This should be straightforward, Galaxy should automatically download and -install the precompiled binary for MIRA v3.4.0 for the Galaxy wrapper, -and run any tests. - - -Manual Installation -=================== - -There are just two Galaxy files to install: - -* mira.py (the Python script) -* mira.xml (the Galaxy tool definition) - -The suggested location is a new tools/mira_3_4 folder. You will also need to -modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do -this to tools_conf.xml.sample in order to run any tests: - -<tool file="mira_3_4/mira.xml" /> - -You will also need to install MIRA, we used version 3.4.1.1. See: - -http://chevreux.org/projects_mira.html -http://sourceforge.net/projects/mira-assembler/ - -WARNING: This tool was developed to construct viral genome assembly and -mapping pipelines, for which the run time and memory requirements are -negligible. For larger tasks, be aware that MIRA can require vast amounts -of RAM and run-times of over a week are possible. This tool wrapper makes -no attempt to spot and reject such large jobs. - - -History -======= - -v0.0.1 - Initial version (working prototype, using MIRA 3.2.1) -v0.0.2 - Improve capture of stdout/stderr (should see it as it runs) -v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later - (some other switches changed, e.g. -OUT rrol to rrot, which - means the wrapper no longer works with MIRA 3.2.x) - - The contig summary file (TCS file) was removed in MIRA 3.4 - - Report all missing output files (not just first missing one) -v0.0.4 - Fix problem with backbone arguments inroduced in v0.0.3 -v0.0.5 - Implement the <version_command> tag to record the wrapper - version and the MIRA version being used. - - Check using MIRA 3.4 (later versions have a different API) -v0.0.6 - Tell MIRA to use /tmp for temporary files - - Tell MIRA to ignore long read names (otherwise it aborts) -v0.0.7 - Automated installation of the 64 bit Linux MIRA binary. -v0.0.8 - Basic unit test added. - - Link to Tool Shed added to help text and this documentation. - - -Developers -========== - -This script and related tools are being developed on the following hg branch: -http://bitbucket.org/peterjc/galaxy-central/src/tools - -For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use -the following command from the Galaxy root folder: - -$ tar -czf mira_wrapper.tar.gz tools/mira_3_4/mira.* tools/mira_3_4/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta - -Check this worked: - -$ tar -tzf mira_wrapper.tar.gz -tools/mira_3_4/mira.py -tools/mira_3_4/mira.txt -tools/mira_3_4/mira.xml -tools/mira_3_4/tool_dependencies.xml -test-data/tvc_mini.fastq -test-data/tvc_contigs.fasta - - -Licence (MIT/BSD style) -======================= - -Permission to use, copy, modify, and distribute this software and its -documentation with or without modifications and for any purpose and -without fee is hereby granted, provided that any copyright notices -appear in all copies and that both those copyright notices and this -permission notice appear in supporting documentation, and that the -names of the contributors or copyright holders not be used in -advertising or publicity pertaining to distribution of the software -without specific prior permission. - -THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL -WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE -CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT -OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE -OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE -OR PERFORMANCE OF THIS SOFTWARE.
--- a/tools/mira_3_4/mira.xml Thu May 02 12:40:04 2013 -0400 +++ b/tools/mira_3_4/mira.xml Wed Sep 11 06:21:44 2013 -0400 @@ -139,9 +139,12 @@ <data name="out_log" format="txt" label="MIRA log" /> </outputs> <tests> - <test> <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses strain data and miraSearchESTSNPs. Here we just assemble it. --> +<!-- +Commenting out test until Galaxy framework is fixed, +https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests + <test> <param name="job_method" value="denovo" /> <param name="job_type" value="est" /> <param name="job_qual" value="accurate" /> @@ -153,6 +156,7 @@ <param name="condIonTorrent.use" value="false" /> <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" /> </test> +--> </tests> <help> @@ -160,14 +164,28 @@ Runs MIRA v3.4, collects the output, and throws away all the temporary files. +MIRA is an open source assembly tool capable of handling sequence data from +a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454 and also +Ion Torrent). + +It is particularly suited to small genomes such as bacteria. + **Citation** -If you use this tool in scientific work leading to a publication, please cite: +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: -Chevreux et al. (1999) Genome Sequence Assembly Using Trace Signals and Additional Sequence Information Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56. +Peter Cock, Bjoern Gruening, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Chevreux et al. (1999). +Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. +Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56. This wrapper is available to install into other Galaxy Instances via the Galaxy -Tool Shed at http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler +Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler </help> </tool>