| Previous changeset 0:af18bb0baa92 (2015-01-27) Next changeset 2:ab8cd78709e1 (2016-11-23) |
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Commit message:
Uploaded |
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modified:
mapper.xml tool_dependencies.xml |
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| diff -r af18bb0baa92 -r 12fc62b7dc09 mapper.xml --- a/mapper.xml Tue Jan 27 09:06:06 2015 -0500 +++ b/mapper.xml Thu Feb 12 09:46:55 2015 -0500 |
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| @@ -73,7 +73,7 @@ #if $operation.refGenomeSource.genomeSource == "history" custom_bowtie_indices #else - $index + $operation.refGenomeSource.index #end if $operation.map_mismatch |
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| diff -r af18bb0baa92 -r 12fc62b7dc09 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jan 27 09:06:06 2015 -0500 +++ b/tool_dependencies.xml Thu Feb 12 09:46:55 2015 -0500 |
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| @@ -1,53 +1,53 @@ <?xml version="1.0"?> <tool_dependency> - <package name="perl" version="5.18.1"> - <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="perl" version="5.18.1"> + <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="bowtie" version="0.12.7"> - <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="mirdeep2_mapper" version="2.0"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-mapper.tar.gz</action> + <install version="1.0"> + <actions> + <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-mapper.tar.gz</action> <action type="move_file"> - <source>clip_adapters.pl</source> + <source>clip_adapters.pl</source> <destination>$INSTALL_DIR</destination> </action> <action type="move_file"> - <source>collapse_reads_md.pl</source> + <source>collapse_reads_md.pl</source> <destination>$INSTALL_DIR</destination> </action> <action type="move_file"> - <source>convert_bowtie_output.pl</source> + <source>convert_bowtie_output.pl</source> <destination>$INSTALL_DIR</destination> </action> <action type="move_file"> - <source>fastaparse.pl</source> + <source>fastaparse.pl</source> <destination>$INSTALL_DIR</destination> </action> <action type="move_file"> - <source>fastq2fasta.pl</source> + <source>fastq2fasta.pl</source> <destination>$INSTALL_DIR</destination> </action> <action type="move_file"> - <source>illumina_to_fasta.pl</source> + <source>illumina_to_fasta.pl</source> <destination>$INSTALL_DIR</destination> </action> <action type="move_file"> - <source>mapper.pl</source> + <source>mapper.pl</source> <destination>$INSTALL_DIR</destination> </action> <action type="move_file"> - <source>parse_mappings.pl</source> + <source>parse_mappings.pl</source> <destination>$INSTALL_DIR</destination> </action> <action type="move_file"> - <source>rna2dna.pl</source> + <source>rna2dna.pl</source> <destination>$INSTALL_DIR</destination> </action> <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> </action> </actions> </install> |