Mercurial > repos > jjohnson > snpeff
changeset 8:aecbd8878923
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 29 Nov 2013 09:29:05 -0500 |
| parents | 0ad9733e22a4 |
| children | f981ba577f2b |
| files | README readme.rst snpEff_macros.xml |
| diffstat | 3 files changed, 24 insertions(+), 38 deletions(-) [+] |
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--- a/README Fri Nov 29 09:27:22 2013 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -These are galaxy tools for SnpEff a variant annotation and effect prediction tool by Pablo Cingolani. -It annotates and predicts the effects of variants on genes (such as amino acid changes). -( http://snpeff.sourceforge.net/ ) - -This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift. - -This will use the default location for genome reference downloads from the snpEff.config: -data_dir = ~/snpEff/data/ -You can manually edit the installed snpEff.config and change the location, or you can create a symbolic link to the desired data location from ~/snpEff. - -The genome reference options used by the tools: - "SnpEff" snpEff.xml - "SnpEff Download" snpEff_download.xml -are taken from: tool-data/snpeffect_genomedb.loc - -There are 2 datamanagers to download and install prebuilt SnpEff Genome databases: - data_manager_snpeff_databases - generates a list of available SnpEff genome databases into the tool-data/snpeff_databases.loc - data_manager_snpeff_download - downloads a SnpEff genome database selected from: tool-data/snpeff_databases.loc and adds entries to snpeff_genomedb.loc,snpeff_regulationdb.loc,snpeff_annotations.loc - -SnpEff citation: -"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] - -SnpSift citation: -"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Fri Nov 29 09:29:05 2013 -0500 @@ -0,0 +1,24 @@ +These are galaxy tools for SnpEff a variant annotation and effect prediction tool by Pablo Cingolani. +It annotates and predicts the effects of variants on genes (such as amino acid changes). +( http://snpeff.sourceforge.net/ ) + +This repository contains a tool_dependencies.xml file that will attempt to automatically install SnpEff and SnpSift. + +This will use the default location for genome reference downloads from the snpEff.config: +data_dir = ~/snpEff/data/ +You can manually edit the installed snpEff.config and change the location, or you can create a symbolic link to the desired data location from ~/snpEff. + +The genome reference options used by the tools: + "SnpEff" snpEff.xml + "SnpEff Download" snpEff_download.xml +are taken from: tool-data/snpeffect_genomedb.loc + +There are 2 datamanagers to download and install prebuilt SnpEff Genome databases: + data_manager_snpeff_databases - generates a list of available SnpEff genome databases into the tool-data/snpeff_databases.loc + data_manager_snpeff_download - downloads a SnpEff genome database selected from: tool-data/snpeff_databases.loc and adds entries to snpeff_genomedb.loc,snpeff_regulationdb.loc,snpeff_annotations.loc + +SnpEff citation: +"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] + +SnpSift citation: +"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3, 2012.
--- a/snpEff_macros.xml Fri Nov 29 09:27:22 2013 -0500 +++ b/snpEff_macros.xml Fri Nov 29 09:29:05 2013 -0500 @@ -5,20 +5,6 @@ </requirements> </xml> <xml name="stdio"> - <conditional name="analysis_param_type"> - <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options"> - <option value="basic" selected="True">Basic</option> - <option value="advanced">Advanced</option> - </param> - <when value="basic"> - <!-- Do nothing here --> - </when> - <when value="advanced"> - <yield /> - </when> - </conditional> - </xml> - <xml name="reference_source_selector_param"> <stdio> <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> <exit_code range="1:" level="fatal" description="Error" />