Mercurial > repos > rnateam > mirdeep2_quantifier
diff tool_dependencies.xml @ 0:2c039fc73f1f draft
Imported from capsule None
author | rnateam |
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date | Tue, 27 Jan 2015 09:06:15 -0500 |
parents | |
children | 40dc77f3730c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jan 27 09:06:15 2015 -0500 @@ -0,0 +1,45 @@ +<?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> + <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" /> + </package> + <package name="vienna_rna" version="1.8.5"> + <repository changeset_revision="54e961ee33d4" name="package_vienna_rna_1_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="pdf_api2" version="2.023"> + <repository changeset_revision="b9b7fadfdb69" name="package_perl_pdf_api2_2_023" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="mirdeep2_quantifier" version="2.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-quantifier.tar.gz</action> + <action type="move_file"> + <source>quantifier.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>make_html2.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>convert_bowtie_output.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + +The module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs. +First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too. +By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors. +The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined. + + </readme> + </package> +</tool_dependency>