Mercurial > repos > pjbriggs > trimmomatic

annotate tool_dependencies.xml @ 6:141bba0e9a77 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.36.2 (adds support for compressed fastq inputs)
author pjbriggs
date Fri, 24 Feb 2017 05:12:32 -0500
parents f80107cdc406
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
1 <?xml version="1.0"?>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
2 <tool_dependency>
4
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 0
diff changeset
3 <package name="trimmomatic" version="0.36">
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
4 <install version="1.0">
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
5 <actions>
4
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 0
diff changeset
6 <action type="download_by_url">http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip</action>
5
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents: 4
diff changeset
7 <action type="move_file" rename_to="trimmomatic.jar">
4
14d05f2d511d Version that supports Trimmomatic 0.36.
pjbriggs
parents: 0
diff changeset
8 <source>trimmomatic-0.36.jar</source>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
9 <destination>$INSTALL_DIR</destination>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
10 </action>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
11 <action type="move_directory_files">
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
12 <source_directory>adapters</source_directory>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
13 <destination_directory>$INSTALL_DIR/adapters</destination_directory>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
14 </action>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
15 <action type="set_environment">
5
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents: 4
diff changeset
16 <environment_variable name="TRIMMOMATIC_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
17 </action>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
18 <action type="set_environment">
5
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents: 4
diff changeset
19 <environment_variable name="TRIMMOMATIC_ADAPTERS_PATH" action="set_to">$INSTALL_DIR/adapters</environment_variable>
0
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
20 </action>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
21 </actions>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
22 </install>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
23 <readme>Trimmomatic requires the Java Runtime Environment
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
24 </readme>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
25 </package>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
26 </tool_dependency>
3358c3d30143 Uploaded initial version.
pjbriggs
parents:
diff changeset
27