Mercurial > repos > iuc > package_trinity_2_0_6

comparison tool_dependencies.xml @ 0:0a09014ebc26 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
author iuc
date Fri, 20 Nov 2015 06:46:01 -0500
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children 442e500aae12
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-1:000000000000 0:0a09014ebc26
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="ncurses" version="5.9">
4 <repository changeset_revision="d5587dda75ff" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="zlib" version="1.2.8">
7 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="trinity" version="2.0.6">
10 <install version="1.0">
11 <actions>
12 <action sha256sum="e0c3ec885fdcfe3422ea492372518ddf5d1aed3daa187c69c4254516b0845de1" type="download_by_url">https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.6.tar.gz</action>
13 <action type="set_environment_for_install">
14 <repository changeset_revision="d5587dda75ff" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
15 <package name="ncurses" version="5.9" />
16 </repository>
17 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
18 <package name="zlib" version="1.2.8" />
19 </repository>
20 </action>
21 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' trinity-plugins/Makefile</action>
22 <action type="shell_command">sed -i.bak -e 's/-ltinfo//' trinity-plugins/Makefile</action> <!-- tinfo is included in ncurses lib-->
23 <action type="shell_command">sed -i.bak -e '/tar -zxvf ${RSEM_CODE}.tar.gz/a \\tsed -i.bak -e "s|-lz|-lz -L${ZLIB_ROOT_PATH}/lib|" ${RSEM_CODE}/Makefile ${RSEM_CODE}/sam/Makefile' trinity-plugins/Makefile</action> <!-- In case you have an obsolete zlib in /usr/lib -->
24 <action type="shell_command">make</action>
25 <action type="shell_command">make plugins</action>
26
27 <action type="move_file">
28 <source>Trinity</source>
29 <destination>$INSTALL_DIR</destination>
30 </action>
31 <action type="move_directory_files">
32 <source_directory>Analysis</source_directory>
33 <destination_directory>$INSTALL_DIR/Analysis</destination_directory>
34 </action>
35 <action type="move_directory_files">
36 <source_directory>Butterfly</source_directory>
37 <destination_directory>$INSTALL_DIR/Butterfly</destination_directory>
38 </action>
39 <action type="move_directory_files">
40 <source_directory>Chrysalis</source_directory>
41 <destination_directory>$INSTALL_DIR/Chrysalis</destination_directory>
42 </action>
43 <action type="move_directory_files">
44 <source_directory>Inchworm</source_directory>
45 <destination_directory>$INSTALL_DIR/Inchworm</destination_directory>
46 </action>
47 <action type="move_directory_files">
48 <source_directory>PerlLib</source_directory>
49 <destination_directory>$INSTALL_DIR/PerlLib</destination_directory>
50 </action>
51 <action type="move_directory_files">
52 <source_directory>trinity-plugins</source_directory>
53 <destination_directory>$INSTALL_DIR/trinity-plugins</destination_directory>
54 </action>
55 <action type="move_directory_files">
56 <source_directory>util</source_directory>
57 <destination_directory>$INSTALL_DIR/util</destination_directory>
58 </action>
59
60 <action type="shell_command">rm $INSTALL_DIR/trinity-plugins/*tar.gz</action>
61
62 <action type="set_environment">
63 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/</environment_variable>
64 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/util</environment_variable>
65 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/collectl/bin</environment_variable>
66 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/fastool</environment_variable>
67 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/jellyfish/bin</environment_variable>
68 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/parafly/bin</environment_variable>
69 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/transdecoder</environment_variable>
70 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/Trimmomatic</environment_variable>
71 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/slclust/bin</environment_variable>
72 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/GAL_0.2.1</environment_variable>
73 </action>
74 </actions>
75 </install>
76 </package>
77 </tool_dependency>