Mercurial > repos > rnateam > mirdeep2_quantifier
comparison tool_dependencies.xml @ 0:2c039fc73f1f draft
Imported from capsule None
| author | rnateam |
|---|---|
| date | Tue, 27 Jan 2015 09:06:15 -0500 |
| parents | |
| children | 40dc77f3730c |
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| -1:000000000000 | 0:2c039fc73f1f |
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| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="perl" version="5.18.1"> | |
| 4 <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
| 5 </package> | |
| 6 <package name="bowtie" version="0.12.7"> | |
| 7 <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
| 8 </package> | |
| 9 <package name="vienna_rna" version="1.8.5"> | |
| 10 <repository changeset_revision="54e961ee33d4" name="package_vienna_rna_1_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
| 11 </package> | |
| 12 <package name="pdf_api2" version="2.023"> | |
| 13 <repository changeset_revision="b9b7fadfdb69" name="package_perl_pdf_api2_2_023" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
| 14 </package> | |
| 15 <package name="mirdeep2_quantifier" version="2.0"> | |
| 16 <install version="1.0"> | |
| 17 <actions> | |
| 18 <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-quantifier.tar.gz</action> | |
| 19 <action type="move_file"> | |
| 20 <source>quantifier.pl</source> | |
| 21 <destination>$INSTALL_DIR</destination> | |
| 22 </action> | |
| 23 <action type="move_file"> | |
| 24 <source>make_html2.pl</source> | |
| 25 <destination>$INSTALL_DIR</destination> | |
| 26 </action> | |
| 27 <action type="move_file"> | |
| 28 <source>convert_bowtie_output.pl</source> | |
| 29 <destination>$INSTALL_DIR</destination> | |
| 30 </action> | |
| 31 <action type="set_environment"> | |
| 32 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> | |
| 33 </action> | |
| 34 </actions> | |
| 35 </install> | |
| 36 <readme> | |
| 37 | |
| 38 The module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs. | |
| 39 First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too. | |
| 40 By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors. | |
| 41 The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined. | |
| 42 | |
| 43 </readme> | |
| 44 </package> | |
| 45 </tool_dependency> |