Mercurial > repos > hammock > hammock

comparison tool_dependencies.xml @ 6:2277dd59b9f9 draft

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Uploaded
author hammock
date Wed, 01 Nov 2017 05:54:28 -0400
parents b7652b7c97bd
children 466c62f481d3
comparison
equal deleted inserted replaced
5:b7652b7c97bd 6:2277dd59b9f9
2 <tool_dependency> 2 <tool_dependency>
3 <package name="clustalomega" version="1.2.0"> 3 <package name="clustalomega" version="1.2.0">
4 <install version="1.0"> 4 <install version="1.0">
5 <actions_group> 5 <actions_group>
6 <actions architecture="x86_64" os="linux"> 6 <actions architecture="x86_64" os="linux">
7 <action type="download_by_url">http://www.clustal.org/omega/clustalo-1.2.0-Ubuntu-x86_64</action>
8 <action type="shell_command">chmod 755 clustalo-1.2.0-Ubuntu-x86_64</action>
9 <action type="move_file"> 7 <action type="move_file">
10 <source>clustalo-1.2.0-Ubuntu-x86_64</source> 8 <source>$REPOSITORY_INSTALL_DIR/external_tools/linux/clustalo-1.2.0-Ubuntu-x86_64</source>
11 <destination>$INSTALL_DIR</destination> 9 <destination>$INSTALL_DIR</destination>
12 </action> 10 </action>
13 <action type="shell_command">sed -i "s%#clustalOmegaCommand=%clustalOmegaCommand=$INSTALL_DIR/clustalo-1.2.0-Ubuntu-x86_64%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> 11 <action type="shell_command">sed -i "s%clustalOmegaCommand=clustalo%clustalOmegaCommand=$INSTALL_DIR/clustalo-1.2.0-Ubuntu-x86_64%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
14 </actions> 12 </actions>
15 <actions architecture="x86_64" os="darwin"> 13 <actions architecture="x86_64" os="darwin">
16 <action type="download_by_url">http://www.clustal.org/omega/clustal-omega-1.2.0-macosx</action>
17 <action type="shell_command">chmod 755 clustalo-1.2.0-Ubuntu-x86_64</action>
18 <action type="move_file"> 14 <action type="move_file">
19 <source>clustalo-1.2.0-Ubuntu-x86_64</source> 15 <source>$REPOSITORY_INSTALL_DIR/external_tools/darwin/clustal-omega-1.2.0-macosx</source>
20 <destination>$INSTALL_DIR</destination> 16 <destination>$INSTALL_DIR</destination>
21 </action> 17 </action>
22 <action type="shell_command">sed -i "s%#clustalOmegaCommand=%clustalOmegaCommand=$INSTALL_DIR/clustalo-1.2.0-Ubuntu-x86_64%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> 18 <action type="shell_command">sed -i "s%clustalOmegaCommand=clustalo%clustalOmegaCommand=$INSTALL_DIR/clustal-omega-1.2.0-macosx%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
23 </actions> 19 </actions>
24 </actions_group> 20 </actions_group>
25 </install> 21 </install>
26 </package> 22 </package>
27 23
28 <package name="hmmer" version="3.1b2"> 24 <package name="hmmer" version="3.1b2">
29 <install version="1.0"> 25 <install version="1.0">
30 <actions_group> 26 <actions_group>
31 <actions architecture="x86_64" os="linux"> 27 <actions architecture="x86_64" os="linux">
32 <action type="download_by_url">http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz</action>
33 <action type="move_file"> 28 <action type="move_file">
34 <source>binaries/hmmbuild</source> 29 <source>$REPOSITORY_INSTALL_DIR/external_tools/linux/hmmbuild</source>
35 <destination>$INSTALL_DIR</destination> 30 <destination>$INSTALL_DIR</destination>
36 </action> 31 </action>
37 <action type="move_file"> 32 <action type="move_file">
38 <source>binaries/hmmsearch</source> 33 <source>$REPOSITORY_INSTALL_DIR/external_tools/linux/hmmsearch</source>
39 <destination>$INSTALL_DIR</destination> 34 <destination>$INSTALL_DIR</destination>
40 </action> 35 </action>
41 <action type="shell_command">sed -i "s%#hmmbuildCommand=%hmmbuildCommand=$INSTALL_DIR/hmmbuild%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> 36 <action type="shell_command">sed -i "s%hmmbuildCommand=hmmbuild%hmmbuildCommand=$INSTALL_DIR/hmmbuild%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
42 <action type="shell_command">sed -i "s%#hmmsearchCommand=%hmmsearchCommand=$INSTALL_DIR/hmmsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> 37 <action type="shell_command">sed -i "s%hmmsearchCommand=hmmsearch%hmmsearchCommand=$INSTALL_DIR/hmmsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
43 </actions> 38 </actions>
44 <actions architecture="x86_64" os="darwin"> 39 <actions architecture="x86_64" os="darwin">
45 <action type="download_by_url">http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-macosx-intel.tar.gz</action>
46 <action type="move_file"> 40 <action type="move_file">
47 <source>binaries/hmmbuild</source> 41 <source>$REPOSITORY_INSTALL_DIR/external_tools/darwin/hmmbuild</source>
48 <destination>$INSTALL_DIR</destination> 42 <destination>$INSTALL_DIR</destination>
49 </action> 43 </action>
50 <action type="move_file"> 44 <action type="move_file">
51 <source>binaries/hmmsearch</source> 45 <source>$REPOSITORY_INSTALL_DIR/external_tools/darwin/hmmsearch</source>
52 <destination>$INSTALL_DIR</destination> 46 <destination>$INSTALL_DIR</destination>
53 </action> 47 </action>
54 <action type="shell_command">sed -i "s%#hmmbuildCommand=%hmmbuildCommand=$INSTALL_DIR/hmmbuild%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> 48 <action type="shell_command">sed -i "s%hmmbuildCommand=hmmbuild%hmmbuildCommand=$INSTALL_DIR/hmmbuild%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
55 <action type="shell_command">sed -i "s%#hmmsearchCommand=%hmmsearchCommand=$INSTALL_DIR/hmmsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> 49 <action type="shell_command">sed -i "s%hmmsearchCommand=hmmsearch%hmmsearchCommand=$INSTALL_DIR/hmmsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
56 </actions> 50 </actions>
57 </actions_group> 51 </actions_group>
58 </install> 52 </install>
59 </package> 53 </package>
60 54
61 <package name="hhsuite" version="2.0.16"> 55 <package name="hhsuite" version="2.0.16">
62 <install version="1.0"> 56 <install version="1.0">
63 <actions_group> 57 <actions_group>
64 <actions architecture="x86_64" os="linux"> 58 <actions architecture="x86_64" os="linux">
65 <action type="download_by_url">http://wwwuser.gwdg.de/~compbiol/data/hhsuite/releases/all/hhsuite-2.0.16-linux-x86_64.tar.gz</action>
66 <action type="move_file"> 59 <action type="move_file">
67 <source>bin/hhmake</source> 60 <source>$REPOSITORY_INSTALL_DIR/external_tools/linux/hhmake</source>
68 <destination>$INSTALL_DIR</destination> 61 <destination>$INSTALL_DIR</destination>
69 </action> 62 </action>
70 <action type="move_file"> 63 <action type="move_file">
71 <source>bin/hhsearch</source> 64 <source>$REPOSITORY_INSTALL_DIR/external_tools/linux/hhsearch</source>
72 <destination>$INSTALL_DIR</destination> 65 <destination>$INSTALL_DIR</destination>
73 </action> 66 </action>
74 <action type="move_file"> 67 <action type="move_file">
75 <source>lib</source> 68 <source>$REPOSITORY_INSTALL_DIR/external_tools/linux/lib</source>
76 <destination>$INSTALL_DIR</destination> 69 <destination>$INSTALL_DIR</destination>
77 </action> 70 </action>
78 <action type="shell_command">sed -i "s%#hhmakeCommand=%hhmakeCommand=$INSTALL_DIR/hhmake%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> 71 <action type="shell_command">sed -i "s%hhmakeCommand=hhmake%hhmakeCommand=$INSTALL_DIR/hhmake%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
79 <action type="shell_command">sed -i "s%#hhsearchCommand=%hhsearchCommand=$INSTALL_DIR/hhsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> 72 <action type="shell_command">sed -i "s%hhsearchCommand=hhsearch%hhsearchCommand=$INSTALL_DIR/hhsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
80 <action type="shell_command">sed -i "s%#reformatCommand=%reformatCommand=$INSTALL_DIR/lib/hh/scripts/reformat.pl%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> 73 <action type="shell_command">sed -i "s%reformatCommand=reformat.pl%reformatCommand=$INSTALL_DIR/lib/hh/scripts/reformat.pl%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
81 <action type="set_environment"> 74 <action type="set_environment">
82 <environment_variable name="HHLIB" action="set_to">$INSTALL_DIR/lib/hh</environment_variable> 75 <environment_variable name="HHLIB" action="set_to">$INSTALL_DIR/lib/hh</environment_variable>
83 </action> 76 </action>
84 </actions> 77 </actions>
85 <actions architecture="x86_64" os="darwin"> 78 <actions architecture="x86_64" os="darwin">
86 <action type="download_by_url">http://wwwuser.gwdg.de/~compbiol/data/hhsuite/releases/all/hhsuite-2.0.16-macosx.tar.gz</action>
87 <action type="move_file"> 79 <action type="move_file">
88 <source>bin/hhmake</source> 80 <source>$REPOSITORY_INSTALL_DIR/external_tools/darwin/hhmake</source>
89 <destination>$INSTALL_DIR</destination> 81 <destination>$INSTALL_DIR</destination>
90 </action> 82 </action>
91 <action type="move_file"> 83 <action type="move_file">
92 <source>bin/hhsearch</source> 84 <source>$REPOSITORY_INSTALL_DIR/external_tools/darwin/hhsearch</source>
93 <destination>$INSTALL_DIR</destination> 85 <destination>$INSTALL_DIR</destination>
94 </action> 86 </action>
95 <action type="move_file"> 87 <action type="move_file">
96 <source>lib</source> 88 <source>$REPOSITORY_INSTALL_DIR/external_tools/darwin/lib</source>
97 <destination>$INSTALL_DIR</destination> 89 <destination>$INSTALL_DIR</destination>
98 </action> 90 </action>
99 <action type="shell_command">sed -i "s%#hhmakeCommand=%hhmakeCommand=$INSTALL_DIR/hhmake%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> 91 <action type="shell_command">sed -i "s%hhmakeCommand=hhmake%hhmakeCommand=$INSTALL_DIR/hhmake%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
100 <action type="shell_command">sed -i "s%#hhsearchCommand=%hhsearchCommand=$INSTALL_DIR/hhsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> 92 <action type="shell_command">sed -i "s%hhsearchCommand=hhsearch%hhsearchCommand=$INSTALL_DIR/hhsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
101 <action type="shell_command">sed -i "s%#reformatCommand=%reformatCommand=$INSTALL_DIR/lib/hh/scripts/reformat.pl%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action> 93 <action type="shell_command">sed -i "s%reformatCommand=reformat.pl%reformatCommand=$INSTALL_DIR/lib/hh/scripts/reformat.pl%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
102 <action type="set_environment"> 94 <action type="set_environment">
103 <environment_variable name="HHLIB" action="set_to">$INSTALL_DIR/lib/hh</environment_variable> 95 <environment_variable name="HHLIB" action="set_to">$INSTALL_DIR/lib/hh</environment_variable>
104 </action> 96 </action>
105 </actions> 97 </actions>
106 </actions_group> 98 </actions_group>