Mercurial > repos > rnateam > metilene

comparison tool_dependencies.xml @ 6:f9883968b113 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/metilene commit 090bc9bb5c775600f4727d8729a032b52e78bd05-dirty
author rnateam
date Thu, 17 Dec 2015 17:09:39 -0500
parents b6263bd3666f
children 9ad744d0804b
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5:b6263bd3666f 6:f9883968b113
10 <repository changeset_revision="e6f4a7398a47" name="package_bedtools_2_24" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="e6f4a7398a47" name="package_bedtools_2_24" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
11 </package> 11 </package>
12 <package name="gnu_coreutils" version="8.22"> 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" /> 13 <repository changeset_revision="1016a386a647" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
14 </package> 14 </package>
15 15 <package name="ggplot2" version="0.9.3">
16 <repository changeset_revision="ade406d47752" name="package_r_ggplot2_0_9_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
17 </package>
16 <package name="metilene" version="0.2-4"> 18 <package name="metilene" version="0.2-4">
17 <install version="1.0"> 19 <install version="1.0">
18 <actions> 20 <actions>
21 <action sha256sum="7430b4c2af4f43d389ad690dfe42c9ce7a63b2bff4ff0ac59afc0f1ec7e600f2" type="download_by_url">
22 https://depot.galaxyproject.org/software/metilene/metilene_0.2-4_src_all.tar.gz
23 </action>
24 <action type="shell_command">make</action>
25 <!-- move binary and scripts to installation bin directory -->
26 <action type="move_file">
27 <source>metilene</source>
28 <destination>$INSTALL_DIR/bin</destination>
29 </action>
30 <action type="move_file">
31 <source>metilene_input.pl</source>
32 <destination>$INSTALL_DIR/bin</destination>
33 </action>
34 <action type="move_file">
35 <source>metilene_output.pl</source>
36 <destination>$INSTALL_DIR/bin</destination>
37 </action>
38 <action type="move_file">
39 <source>metilene_output.R</source>
40 <destination>$INSTALL_DIR/bin</destination>
41 </action>
19 42
20 <action type="setup_r_environment"> 43 <action type="set_environment">
21 <repository changeset_revision="c6ebd3a51334" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> 44 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
22 <package name="R" version="3.2.1" /> 45 </action>
23 </repository>
24 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ggplot2_0.9.3.1.tar.gz</package>
25 </action>
26
27
28 <!-- don't use download_by_url, since archive name != directory name -->
29 <action type="download_file">http://www.bioinf.uni-leipzig.de/Software/metilene/metilene_v02-4.tar.gz</action>
30 <action type="shell_command">tar xfz metilene_v02-4.tar.gz</action>
31
32 <action type="change_directory">metilene_v0.2-4</action>
33
34 <action type="shell_command">make</action>
35
36 <!-- move binary and scripts to installation bin directory -->
37 <action type="move_file">
38 <source>metilene</source>
39 <destination>$INSTALL_DIR/bin</destination>
40 </action>
41 <action type="move_file">
42 <source>metilene_input.pl</source>
43 <destination>$INSTALL_DIR/bin</destination>
44 </action>
45 <action type="move_file">
46 <source>metilene_output.pl</source>
47 <destination>$INSTALL_DIR/bin</destination>
48 </action>
49 <action type="move_file">
50 <source>metilene_output.R</source>
51 <destination>$INSTALL_DIR/bin</destination>
52 </action>
53
54 <!-- include installation bin directory in path -->
55 <action type="set_environment">
56 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
57 <environment_variable action="set_to" name="METILENE_ROOT_PATH">$INSTALL_DIR</environment_variable>
58 </action>
59 </actions> 46 </actions>
60 </install> 47 </install>
61 <readme>Metilene is precompiled for Linux</readme> 48 <readme>Metilene is precompiled for Linux</readme>
62 </package> 49 </package>
63 </tool_dependency> 50 </tool_dependency>