Mercurial > repos > rnateam > metilene

comparison tool_dependencies.xml @ 3:f827043c2a97 draft

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planemo upload commit f14004d917b2be0c2f8678f14f069b1fd4ffa1a9-dirty
author rnateam
date Thu, 10 Dec 2015 12:22:34 -0500
parents 97b0c64b1067
children be094e3b86f5
comparison
equal deleted inserted replaced
2:91132980aecc 3:f827043c2a97
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="perl" version="5.18.1">
4 <repository changeset_revision="2590d4683481" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="R" version="3.2.1">
7 <repository changeset_revision="c6ebd3a51334" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="bedtools" version="2.24">
10 <repository changeset_revision="e6f4a7398a47" name="package_bedtools_2_24" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="gnu_coreutils" version="8.22">
13 <repository changeset_revision="1016a386a647" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
14 </package>
15
3 <package name="metilene" version="0.2-4"> 16 <package name="metilene" version="0.2-4">
4 <install version="1.0"> 17 <install version="1.0">
5 <actions> 18 <actions>
19
20 <action type="setup_r_environment">
21 <repository changeset_revision="c6ebd3a51334" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
22 <package name="R" version="3.2.1" />
23 </repository>
24 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ggplot2_0.9.3.1.tar.gz</package>
25 </action>
26
27
6 <!-- don't use download_by_url, since archive name != directory name --> 28 <!-- don't use download_by_url, since archive name != directory name -->
7 <action type="download_file"> 29 <action type="download_file">http://www.bioinf.uni-leipzig.de/Software/metilene/metilene_v02-4.tar.gz</action>
8 http://www.bioinf.uni-leipzig.de/Software/metilene/metilene_v02-4.tar.gz
9 </action>
10
11 <action type="shell_command">tar xfz metilene_v02-4.tar.gz</action> 30 <action type="shell_command">tar xfz metilene_v02-4.tar.gz</action>
12 31
13 <action type="change_directory">metilene_v0.2-4</action> 32 <action type="change_directory">metilene_v0.2-4</action>
14 33
15 <action type="shell_command">make</action> 34 <action type="shell_command">make</action>
28 <destination>$INSTALL_DIR/bin</destination> 47 <destination>$INSTALL_DIR/bin</destination>
29 </action> 48 </action>
30 49
31 <!-- include installation bin directory in path --> 50 <!-- include installation bin directory in path -->
32 <action type="set_environment"> 51 <action type="set_environment">
33 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 52 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
34 <environment_variable name="METILENE_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable> 53 <environment_variable action="set_to" name="METILENE_ROOT_PATH">$INSTALL_DIR</environment_variable>
35 </action> 54 </action>
36 </actions> 55 </actions>
37 </install> 56 </install>
38 <readme>Metilene is precompiled for Linux</readme> 57 <readme>Metilene is precompiled for Linux</readme>
39 </package> 58 </package>