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comparison tool_dependencies.xml @ 10:9dc43bf7d1db draft

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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'230f018da2c0bc4eedc72e0f70eac0df1e85ebdb\n'-dirty
author nick
date Fri, 01 Jun 2018 17:55:23 -0400
parents fa563fa9b330
children
comparison
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9:fa563fa9b330 10:9dc43bf7d1db
7 <repository changeset_revision="c5908940967d" 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" />
8 </package> 8 </package>
9 <package name="networkx" version="1.10"> 9 <package name="networkx" version="1.10">
10 <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" />
11 </package> 11 </package>
12 <package name="dunovo" version="2.14"> 12 <package name="dunovo" version="2.15">
13 <install version="1.0"> 13 <install version="1.0">
14 <actions> 14 <actions>
15 <!-- download the main dunovo package files --> 15 <!-- download the main dunovo package files -->
16 <action sha256sum="e517a12794e7cac31b4ebcad99e6a6c0789027ace7d33f89d06ff2bc961515fc" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.14.tar.gz</action> 16 <action sha256sum="1cf02bcc37cc641a20bdf5e20c2b3b98d4dccd43b1182830cb1a9e7d173d1a78" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.15.tar.gz</action>
17 <!-- TODO: Store dunovo version number in variable instead of hardcoding it everywhere. --> 17 <!-- TODO: Store dunovo version number in variable instead of hardcoding it everywhere. -->
18 <!-- Move precheck.py and its dependencies into the main source directory. -->
19 <action type="move_file">
20 <source>utils/precheck.py</source>
21 <destination>$TMP_WORK_DIR/dunovo-2.14</destination>
22 </action>
23 <action type="move_file">
24 <source>utils/getreads.py</source>
25 <destination>$TMP_WORK_DIR/dunovo-2.14</destination>
26 </action>
27 <!-- install submodules --> 18 <!-- install submodules -->
28 <action type="shell_command">rmdir kalign utillib ET</action> 19 <action type="shell_command">rmdir kalign utillib ET</action>
29 <!-- download the utillib submodule --> 20 <!-- download the utillib submodule -->
30 <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action> 21 <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action>
31 <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action> 22 <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action>
32 <action type="shell_command">rm v0.1.0.tar.gz</action> 23 <action type="shell_command">rm v0.1.0.tar.gz</action>
33 <action rename_to="utillib" type="move_file"> 24 <action rename_to="utillib" type="move_file">
34 <source>utillib-0.1.0</source> 25 <source>utillib-0.1.0</source>
35 <destination>$TMP_WORK_DIR/dunovo-2.14</destination> 26 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
36 </action> 27 </action>
37 <!-- download the kalign submodule --> 28 <!-- download the kalign submodule -->
38 <action type="download_file">https://github.com/makrutenko/kalign-dunovo/archive/v0.2.0.tar.gz</action> 29 <action type="download_file">https://github.com/makovalab-psu/kalign-dunovo/archive/v0.2.0.tar.gz</action>
39 <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action> 30 <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action>
40 <action type="shell_command">rm v0.2.0.tar.gz</action> 31 <action type="shell_command">rm v0.2.0.tar.gz</action>
41 <action rename_to="kalign" type="move_file"> 32 <action rename_to="kalign" type="move_file">
42 <source>kalign-dunovo-0.2.0</source> 33 <source>kalign-dunovo-0.2.0</source>
43 <destination>$TMP_WORK_DIR/dunovo-2.14</destination> 34 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
44 </action> 35 </action>
45 <!-- download the ET submodule --> 36 <!-- download the ET submodule -->
46 <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action> 37 <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action>
47 <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action> 38 <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action>
48 <action type="shell_command">rm v0.2.2.tar.gz</action> 39 <action type="shell_command">rm v0.2.2.tar.gz</action>
49 <action rename_to="ET" type="move_file"> 40 <action rename_to="ET" type="move_file">
50 <source>ET-0.2.2</source> 41 <source>ET-0.2.2</source>
51 <destination>$TMP_WORK_DIR/dunovo-2.14</destination> 42 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
43 </action>
44 <!-- download the bfx submodule -->
45 <action type="download_file">https://github.com/NickSto/bfx/archive/v0.2.0.tar.gz</action>
46 <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action>
47 <action type="shell_command">rm v0.2.0.tar.gz</action>
48 <action rename_to="bfx" type="move_file">
49 <source>bfx-0.2.0</source>
50 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
51 </action>
52 <!-- Move some source files from subdirectories into the main source directory. -->
53 <action type="move_file">
54 <source>utils/precheck.py</source>
55 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
56 </action>
57 <action type="move_file">
58 <source>bfx/trimmer.py</source>
59 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
60 </action>
61 <action type="move_file">
62 <source>utils/getreads.py</source>
63 <destination>$TMP_WORK_DIR/dunovo-2.15</destination>
52 </action> 64 </action>
53 <!-- make and install --> 65 <!-- make and install -->
54 <action type="shell_command">make clean</action> 66 <action type="shell_command">make clean</action>
55 <action type="shell_command">make</action> 67 <action type="shell_command">make</action>
56 <action type="move_directory_files"> 68 <action type="move_directory_files">