Mercurial > repos > iuc > package_hisat_2_0_3

annotate tool_dependencies.xml @ 0:dc03603edd43 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_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
author iuc
date Tue, 19 Apr 2016 17:44:15 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
2 <tool_dependency>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
3 <package name="hisat" version="2.0.3">
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
4 <install version="1.0">
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
5 <actions_group>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
6 <actions architecture="x86_64" os="linux">
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
7 <action type="download_by_url" sha256sum="4b32770619efcc6c14dcc9c39544cd4f7946cd286776b29965347f11f00e699d">https://depot.galaxyproject.org/software/hisat/hisat_2.0.3_linux_x64.zip</action>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
8 <action type="move_directory_files">
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
9 <source_directory>.</source_directory>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
11 </action>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
12 </actions>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
13 <actions architecture="x86_64" os="darwin">
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
14 <action type="download_by_url" sha256sum="e6bb2f06165085e6fd00408f6d1404d6875c9e58a9d3be7da966b6053789109e">https://depot.galaxyproject.org/software/hisat/hisat_2.0.3_darwin_x64.zip</action>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
15 <action type="move_directory_files">
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
16 <source_directory>.</source_directory>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
18 </action>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
19 </actions>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
20 <actions>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
21 <action type="download_by_url" sha256sum="b2f4aa59e000d98fc57455fd83ae69f0f50992477590ca35ce834510289d552d">https://depot.galaxyproject.org/software/hisat/hisat_2.0.3_src_all.zip</action>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
22 <action type="shell_command">make</action>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
23 <action type="move_directory_files">
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
24 <source_directory>.</source_directory>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
25 <destination_directory>$INSTALL_DIR/bin</destination_directory>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
26 </action>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
27 </actions>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
28 <action type="set_environment">
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
29 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
30 <environment_variable action="set_to" name="HISAT2_ROOT_DIR">$INSTALL_DIR</environment_variable>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
31 </action>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
32 </actions_group>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
33 </install>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
34 <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>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
35 </package>
dc03603edd43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_hisat_2_0_3/ commit 58bff9a70763ca43d9fed6c010b7de9044d48cf1
iuc
parents:
diff changeset
36 </tool_dependency>