|
0
|
1 <?xml version="1.0"?>
|
|
|
2 <tool_dependency>
|
|
|
3 <package name="stringtie" version="0.97">
|
|
1
|
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/stringtie/dl/stringtie-0.97.Linux_x86_64.tar.gz</action>
|
|
0
|
8 <action type="move_file">
|
|
1
|
9 <source>stringtie</source>
|
|
0
|
10 <destination>$INSTALL_DIR/bin</destination>
|
|
|
11 </action>
|
|
|
12 </actions>
|
|
|
13 <actions architecture="x86_64" os="darwin">
|
|
1
|
14 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/stringtie/stringtie-0.97-Darwin-x86_64.tgz</action>
|
|
0
|
15 <action type="move_file">
|
|
1
|
16 <source>stringtie</source>
|
|
0
|
17 <destination>$INSTALL_DIR/bin</destination>
|
|
|
18 </action>
|
|
|
19 </actions>
|
|
1
|
20 <actions>
|
|
|
21 <package name="samtools" version="0.1.19">
|
|
|
22 <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="true" toolshed="https://testtoolshed.g2.bx.psu.edu" />
|
|
|
23 </package>
|
|
|
24 <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.tar.gz</action>
|
|
|
25 <action type="set_environment_for_install">
|
|
|
26 <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="true" toolshed="https://testtoolshed.g2.bx.psu.edu">
|
|
|
27 <package name="samtools" version="0.1.19" />
|
|
|
28 </repository>
|
|
|
29 </action>
|
|
|
30 <action type="shell_command">ln -s $SAMTOOLS_ROOT_DIR/src samtools</action>
|
|
|
31 <action type="shell_command">cp $SAMTOOLS_ROOT_DIR/lib/libbam.* samtools/</action>
|
|
|
32 <action type="shell_command">make</action>
|
|
|
33 <action type="move_file">
|
|
|
34 <source>stringtie</source>
|
|
|
35 <destination>$INSTALL_DIR/bin</destination>
|
|
|
36 </action>
|
|
|
37 </actions>
|
|
|
38 <action type="set_environment">
|
|
|
39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
|
|
|
40 </action>
|
|
|
41 </actions_group>
|
|
0
|
42 </install>
|
|
|
43 <readme>StringTie is a fast and highly efficient assembler of RNA-Seq
|
|
|
44 alignments into potential transcripts. It is primarily a genome-guided
|
|
|
45 transcriptome assembler, although it can borrow algorithmic techniques
|
|
|
46 from de novo genome assembly to help with transcript assembly. Its input
|
|
|
47 can include not only the spliced read alignments used by reference-based
|
|
|
48 assemblers, but also longer contigs that were assembled de novo from
|
|
|
49 unambiguous, non-branching parts of a transcript.</readme>
|
|
|
50 </package>
|
|
|
51 </tool_dependency>
|
