Mercurial > repos > devteam > package_hisat_2_0

comparison tool_dependencies.xml @ 0:ee153209837a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0/ commit c00b9d5d57ec8b352afdf3bde9d238bd59a5e6be
author devteam
date Wed, 16 Sep 2015 13:38:39 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:ee153209837a
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="hisat" version="2.0">
4 <install version="1.0">
5 <actions_group>
6 <actions architecture="x86_64" os="linux">
7 <action type="download_by_url">http://ccb.jhu.edu/software/hisat2/downloads/hisat2-2.0.0-beta-Linux_x86_64.zip</action>
8 <action type="move_directory_files">
9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
11 </action>
12 </actions>
13 <actions architecture="x86_64" os="darwin">
14 <action type="download_by_url">http://ccb.jhu.edu/software/hisat2/downloads/hisat2-2.0.0-beta-OSX_x86_64.zip</action>
15 <action type="move_directory_files">
16 <source_directory>.</source_directory>
17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
18 </action>
19 </actions>
20 <actions>
21 <action type="download_by_url">http://ccb.jhu.edu/software/hisat2/downloads/hisat2-2.0.0-beta-source.zip</action>
22 <action type="shell_command">make</action>
23 <action type="move_directory_files">
24 <source_directory>.</source_directory>
25 <destination_directory>$INSTALL_DIR/bin</destination_directory>
26 </action>
27 </actions>
28 <action type="set_environment">
29 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
30 </action>
31 </actions_group>
32 </install>
33 <readme>HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents the general population, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).</readme>
34 </package>
35 </tool_dependency>