Mercurial > repos > bgruening > antismash

comparison tool_dependencies.xml @ 16:e2df6fe8b447 draft

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Uploaded
author bgruening
date Fri, 11 Oct 2013 16:46:08 -0400
parents 9a099b9b6857
children 213d82f33fc2
comparison
equal deleted inserted replaced
15:9a099b9b6857 16:e2df6fe8b447
31 <destination_directory>$INSTALL_DIR</destination_directory> 31 <destination_directory>$INSTALL_DIR</destination_directory>
32 </action> 32 </action>
33 <action type="chmod"> 33 <action type="chmod">
34 <file mode="750">$INSTALL_DIR/run_antismash.py</file> 34 <file mode="750">$INSTALL_DIR/run_antismash.py</file>
35 </action> 35 </action>
36 <!-- AntiSmash has a prerequirement check that is not useful for us, because we
37 do not offer the option for genprediction and do not install glimmer and Co.
38 For that reason deactivate the check.
39 -->
40 <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/True/g' $INSTALL_DIR/run_antismash.py</action>
36 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action> 41 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
37 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action> 42 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
38 </actions> 43 </actions>
39 <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. --> 44 <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. -->
40 <actions architecture="i386" os="darwin"> 45 <actions architecture="i386" os="darwin">
44 <destination_directory>$INSTALL_DIR</destination_directory> 49 <destination_directory>$INSTALL_DIR</destination_directory>
45 </action> 50 </action>
46 <action type="chmod"> 51 <action type="chmod">
47 <file mode="750">$INSTALL_DIR/run_antismash.py</file> 52 <file mode="750">$INSTALL_DIR/run_antismash.py</file>
48 </action> 53 </action>
54 <!-- AntiSmash has a prerequirement check that is not useful for us, because we
55 do not offer the option for genprediction and do not install glimmer and Co.
56 For that reason deactivate the check.
57 -->
58 <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/True/g' $INSTALL_DIR/run_antismash.py</action>
49 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action> 59 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
50 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action> 60 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
51 </actions> 61 </actions>
52 <!-- Download the binaries for AntiSmash compatible with 64-bit Linux. --> 62 <!-- Download the binaries for AntiSmash compatible with 64-bit Linux. -->
53 <actions architecture="x86_64" os="linux"> 63 <actions architecture="x86_64" os="linux">
61 </action> 71 </action>
62 <!-- AntiSmash has a prerequirement check that is not useful for us, because we 72 <!-- AntiSmash has a prerequirement check that is not useful for us, because we
63 do not offer the option for genprediction and do not install glimmer and Co. 73 do not offer the option for genprediction and do not install glimmer and Co.
64 For that reason deactivate the check. 74 For that reason deactivate the check.
65 --> 75 -->
66 <action type="shell_command">sed -i s/check_prereqs(plugins, options) > 0/True/</action> 76 <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/True/g' $INSTALL_DIR/run_antismash.py</action>
67 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action> 77 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
68 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action> 78 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
69 </actions> 79 </actions>
70 <!-- Download the binaries for AntiSmash compatible with 32-bit Linux. --> 80 <!-- Download the binaries for AntiSmash compatible with 32-bit Linux. -->
71 <actions architecture="i386" os="linux"> 81 <actions architecture="i386" os="linux">
75 <destination_directory>$INSTALL_DIR</destination_directory> 85 <destination_directory>$INSTALL_DIR</destination_directory>
76 </action> 86 </action>
77 <action type="chmod"> 87 <action type="chmod">
78 <file mode="750">$INSTALL_DIR/run_antismash.py</file> 88 <file mode="750">$INSTALL_DIR/run_antismash.py</file>
79 </action> 89 </action>
90 <!-- AntiSmash has a prerequirement check that is not useful for us, because we
91 do not offer the option for genprediction and do not install glimmer and Co.
92 For that reason deactivate the check.
93 -->
94 <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/True/g' $INSTALL_DIR/run_antismash.py</action>
80 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action> 95 <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
81 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action> 96 <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
82 </actions> 97 </actions>
83 98
84 <actions> 99 <actions>