Mercurial > repos > iuc > package_stringtie_0_97

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author iuc
date Wed, 18 Feb 2015 11:36:26 -0500
parents 09b1ece7f3e9
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0:09b1ece7f3e9 1:0627e8e30873
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="samtools" version="0.1.19">
4 <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="stringtie" version="0.97"> 3 <package name="stringtie" version="0.97">
7 <install version="1.0"> 4 <install version="1.0">
8 <actions_group> 5 <actions_group>
9 <actions architecture="x86_64" os="linux"> 6 <actions architecture="x86_64" os="linux">
10 <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.Linux_x86_64.tar.gz</action> 7 <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.Linux_x86_64.tar.gz</action>
11 <action type="move_file"> 8 <action type="move_file">
12 <source>stringtie</source> 9 <source>stringtie</source>
13 <destination>$INSTALL_DIR/bin</destination> 10 <destination>$INSTALL_DIR/bin</destination>
14 </action> 11 </action>
15 </actions> 12 </actions>
16 <actions architecture="x86_64" os="darwin"> 13 <actions architecture="x86_64" os="darwin">
17 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/stringtie/stringtie-0.97-Darwin-x86_64.tgz</action> 14 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/stringtie/stringtie-0.97-Darwin-x86_64.tgz</action>
18 <action type="move_file"> 15 <action type="move_file">
19 <source>stringtie</source> 16 <source>stringtie</source>
20 <destination>$INSTALL_DIR/bin</destination> 17 <destination>$INSTALL_DIR/bin</destination>
21 </action> 18 </action>
22 </actions> 19 </actions>
23 <actions> 20 <actions>
24 <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.tar.gz</action> 21 <package name="samtools" version="0.1.19">
25 <action type="set_environment_for_install"> 22 <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="true" toolshed="https://testtoolshed.g2.bx.psu.edu" />
26 <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu"> 23 </package>
27 <package name="samtools" version="0.1.19" /> 24 <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.tar.gz</action>
28 </repository> 25 <action type="set_environment_for_install">
29 </action> 26 <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="true" toolshed="https://testtoolshed.g2.bx.psu.edu">
30 <action type="shell_command">ln -s $SAMTOOLS_ROOT_DIR/src samtools</action> 27 <package name="samtools" version="0.1.19" />
31 <action type="shell_command">cp $SAMTOOLS_ROOT_DIR/lib/libbam.* samtools/</action> 28 </repository>
32 <action type="shell_command">make</action> 29 </action>
33 <action type="move_file"> 30 <action type="shell_command">ln -s $SAMTOOLS_ROOT_DIR/src samtools</action>
34 <source>stringtie</source> 31 <action type="shell_command">cp $SAMTOOLS_ROOT_DIR/lib/libbam.* samtools/</action>
35 <destination>$INSTALL_DIR/bin</destination> 32 <action type="shell_command">make</action>
36 </action> 33 <action type="move_file">
37 </actions> 34 <source>stringtie</source>
38 <action type="set_environment"> 35 <destination>$INSTALL_DIR/bin</destination>
39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> 36 </action>
40 </action> 37 </actions>
41 </actions_group> 38 <action type="set_environment">
39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
40 </action>
41 </actions_group>
42 </install> 42 </install>
43 <readme>StringTie is a fast and highly efficient assembler of RNA-Seq 43 <readme>StringTie is a fast and highly efficient assembler of RNA-Seq
44 alignments into potential transcripts. It is primarily a genome-guided 44 alignments into potential transcripts. It is primarily a genome-guided
45 transcriptome assembler, although it can borrow algorithmic techniques 45 transcriptome assembler, although it can borrow algorithmic techniques
46 from de novo genome assembly to help with transcript assembly. Its input 46 from de novo genome assembly to help with transcript assembly. Its input