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comparison tool_dependencies.xml @ 8:658eefb99fd7 draft

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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'7d364d2b3f4fd9a7787165a883efa122b326d4c2\n'-dirty
author nick
date Fri, 12 Jan 2018 19:18:41 -0500
parents e7b88ffb8294
children fa563fa9b330
comparison
equal deleted inserted replaced
7:e7b88ffb8294 8:658eefb99fd7
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="bowtie2" version="2.2.5"> 3 <package name="bowtie" version="1.1.2">
4 <repository changeset_revision="30bd7eaeddbf" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="samtools" version="0.1.18">
7 <repository changeset_revision="1409782220c9" name="package_samtools_0_1_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package> 5 </package>
9 <package name="mafft" version="7.221"> 6 <package name="mafft" version="7.221">
10 <repository changeset_revision="15974dd17515" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="c5908940967d" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
11 </package> 8 </package>
12 <package name="networkx" version="1.10"> 9 <package name="networkx" version="1.10">
13 <repository changeset_revision="e761775277c1" name="package_networkx_1_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="e761775277c1" name="package_networkx_1_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
14 </package> 11 </package>
15 <package name="dunovo" version="2.0.9"> 12 <package name="dunovo" version="2.0.12">
16 <install version="1.0"> 13 <install version="1.0">
17 <actions> 14 <actions>
18 <action sha256sum="6f5295b8eae0e161ee3bd28829ca140657743c695624ffc7f467f13eab2c547c" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.9.tar.gz</action> 15 <!-- download the main dunovo package files -->
16 <action sha256sum="6973f163dabf82d236982534d88b5d11573a5aa0982bf9d6236be635fb9b4e11" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.12.tar.gz</action>
17 <!-- TODO: Store dunovo version number in variable instead of hardcoding it everywhere. -->
18 <action type="shell_command">rmdir kalign utillib ET</action>
19 <!-- download the utillib submodule -->
20 <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action>
21 <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action>
22 <action type="shell_command">rm v0.1.0.tar.gz</action>
23 <action rename_to="utillib" type="move_file">
24 <source>utillib-0.1.0</source>
25 <destination>$TMP_WORK_DIR/dunovo-2.0.12</destination>
26 </action>
27 <!-- download the kalign submodule -->
28 <action type="download_file">https://github.com/makrutenko/kalign-dunovo/archive/v0.2.0.tar.gz</action>
29 <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action>
30 <action type="shell_command">rm v0.2.0.tar.gz</action>
31 <action rename_to="kalign" type="move_file">
32 <source>kalign-dunovo-0.2.0</source>
33 <destination>$TMP_WORK_DIR/dunovo-2.0.12</destination>
34 </action>
35 <!-- download the ET submodule -->
36 <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action>
37 <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action>
38 <action type="shell_command">rm v0.2.2.tar.gz</action>
39 <action rename_to="ET" type="move_file">
40 <source>ET-0.2.2</source>
41 <destination>$TMP_WORK_DIR/dunovo-2.0.12</destination>
42 </action>
43 <!-- make and install -->
44 <action type="shell_command">make clean</action>
19 <action type="shell_command">make</action> 45 <action type="shell_command">make</action>
20 <action type="move_directory_files"> 46 <action type="move_directory_files">
21 <source_directory>.</source_directory> 47 <source_directory>.</source_directory>
22 <destination_directory>$INSTALL_DIR</destination_directory> 48 <destination_directory>$INSTALL_DIR</destination_directory>
23 </action> 49 </action>
24 <action type="set_environment"> 50 <action type="set_environment">
25 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> 51 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
26 </action> 52 </action>
27 <!-- Note: This does not install the submodules.
28 Functionality they provide will not be available. -->
29 </actions> 53 </actions>
30 </install> 54 </install>
31 </package> 55 </package>
32 </tool_dependency> 56 </tool_dependency>