Mercurial > repos > peterjc > get_orfs_or_cdss
changeset 5:a119cd123b2d draft
Uploaded v0.0.5b, README style
| author | peterjc |
|---|---|
| date | Wed, 24 Jul 2013 10:34:47 -0400 |
| parents | 26ce6e046040 |
| children | 2dedcbc5f4b6 |
| files | tools/filters/get_orfs_or_cdss.rst tools/filters/get_orfs_or_cdss.txt |
| diffstat | 2 files changed, 120 insertions(+), 111 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/filters/get_orfs_or_cdss.rst Wed Jul 24 10:34:47 2013 -0400 @@ -0,0 +1,120 @@ +Galaxy tool to find ORFs or simple CDSs +======================================= + +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 (using Biopython library functions) +to search nucleotide sequences for open reading frames (ORFs) or coding +sequences (CDSs) where the first potential start codon is used. See the +help text in the XML file for more information. + +This tool is available from the Galaxy Tool Shed at: + +* http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss + +See also the EMBOSS tool ``getorf`` which offers similar functionality and +has also been wrapped for use within Galaxy. + + +Automated Installation +====================== + +This should be straightforward using the Galaxy Tool Shed, which should be +able to automatically install the dependency on Biopython, and then install +this tool and run its unit tests. + + +Manual Installation +=================== + +There are just two files to install to use this tool from within Galaxy: + +* get_orfs_or_cdss.py (the Python script) +* get_orfs_or_cdss.xml (the Galaxy tool definition) + +If you are installing this manually (rather than via the Tool Shed), the +suggested location is in the Galaxy folder tools/filters next to the tool +for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL. +You will also need to modify the tools_conf.xml file to tell Galaxy to offer the +tool. One suggested location is in the filters section. Simply add the line:: + + <tool file="filters/get_orfs_or_cdss.xml" /> + +You will also need to install Biopython 1.54 or later. If you want to run +the unit tests, include this line in tools_conf.xml.sample and the sample +FASTA files under the test-data directory. Then:: + + ./run_functional_tests.sh -id get_orfs_or_cdss + +That's it. + + +History +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +v0.0.1 - Initial version. +v0.0.2 - Correct labelling issue on reverse strand. + - Use the new <stdio> settings in the XML wrappers to catch errors +v0.0.3 - Include unit tests. + - Record Python script version when run from Galaxy. +v0.0.4 - Link to Tool Shed added to help text and this documentation. +v0.0.5 - Automated intallation of the Biopython dependency. + - Use reStructuredText for this README file. +======= ====================================================================== + + +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 get_orfs_or_cdss.tar.gz tools/filters/get_orfs_or_cdss.* tools/filters/repository_dependencies.xml test-data/get_orf_input*.fasta test-data/Ssuis.fasta + +Check this worked:: + + $ tar -tzf get_orfs_or_cdss.tar.gz + filter/get_orfs_or_cdss.py + filter/get_orfs_or_cdss.rst + filter/get_orfs_or_cdss.xml + tools/filters/repository_dependencies.xml + test-data/get_orf_input.fasta + test-data/get_orf_input.Suis_ORF.nuc.fasta + test-data/get_orf_input.Suis_ORF.prot.fasta + test-data/get_orf_input.t11_nuc_out.fasta + test-data/get_orf_input.t11_open_nuc_out.fasta + test-data/get_orf_input.t11_open_prot_out.fasta + test-data/get_orf_input.t11_prot_out.fasta + test-data/get_orf_input.t1_nuc_out.fasta + test-data/get_orf_input.t1_prot_out.fasta + test-data/Ssuis.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/filters/get_orfs_or_cdss.txt Mon Jun 24 02:23:51 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,111 +0,0 @@ -Galaxy tool to find ORFs or simple CDSs -======================================= - -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 (using Biopython library functions) -to search nucleotide sequences for open reading frames (ORFs) or coding -sequences (CDSs) where the first potential start codon is used. See the -help text in the XML file for more information. - -This tool is available from the Galaxy Tool Shed at: -http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss - - -Automated Installation -====================== - -This should be straightforward using the Galaxy Tool Shed, which should be -able to automatically install the dependency on Biopython, and then install -this tool and run its unit tests. - - -Manual Installation -=================== - -There are just two files to install to use this tool from within Galaxy: - -* get_orfs_or_cdss.py (the Python script) -* get_orfs_or_cdss.xml (the Galaxy tool definition) - -If you are installing this manually (rather than via the Tool Shed), the -suggested location is in the Galaxy folder tools/filters next to the tool -for calling sff_extract.py for converting SFF to FASTQ or FASTA + QUAL. -You will also need to modify the tools_conf.xml file to tell Galaxy to offer the -tool. One suggested location is in the filters section. Simply add the line: - -<tool file="filters/get_orfs_or_cdss.xml" /> - -You will also need to install Biopython 1.54 or later. If you want to run -the unit tests, include this line in tools_conf.xml.sample and the sample -FASTA files under the test-data directory. Then: - -./run_functional_tests.sh -id get_orfs_or_cdss - -That's it. - - -History -======= - -v0.0.1 - Initial version. -v0.0.2 - Correct labelling issue on reverse strand. - - Use the new <stdio> settings in the XML wrappers to catch errors -v0.0.3 - Include unit tests. - - Record Python script version when run from Galaxy. -v0.0.4 - Link to Tool Shed added to help text and this documentation. -v0.0.5 - Automated intallation of the Biopython dependency. - - -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 get_orfs_or_cdss.tar.gz tools/filters/get_orfs_or_cdss.* tools/filters/repository_dependencies.xml test-data/get_orf_input*.fasta test-data/Ssuis.fasta - -Check this worked: - -$ tar -tzf get_orfs_or_cdss.tar.gz -filter/get_orfs_or_cdss.py -filter/get_orfs_or_cdss.txt -filter/get_orfs_or_cdss.xml -tools/filters/repository_dependencies.xml -test-data/get_orf_input.fasta -test-data/get_orf_input.Suis_ORF.nuc.fasta -test-data/get_orf_input.Suis_ORF.prot.fasta -test-data/get_orf_input.t11_nuc_out.fasta -test-data/get_orf_input.t11_open_nuc_out.fasta -test-data/get_orf_input.t11_open_prot_out.fasta -test-data/get_orf_input.t11_prot_out.fasta -test-data/get_orf_input.t1_nuc_out.fasta -test-data/get_orf_input.t1_prot_out.fasta -test-data/Ssuis.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.