Mercurial > repos > bgruening > antismash

changeset 5:73d11f6a3cd7 draft

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Uploaded
author bgruening
date Fri, 04 Oct 2013 04:46:02 -0400
parents 9b91d26ee080
children acf3fd6c5c8e
files antismash.xml tool_dependencies.xml
diffstat 2 files changed, 26 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/antismash.xml	Fri Oct 04 04:27:10 2013 -0400
+++ b/antismash.xml	Fri Oct 04 04:46:02 2013 -0400
@@ -5,6 +5,8 @@
         <requirement type="package" version="2.3.2">hmmer</requirement>
         <requirement type="package" version="2.2.28">blast+</requirement>
         <requirement type="package" version="3.8.31">muscle</requirement>
+        <requirement type="package" version="1.62">biopython</requirement>
+        <requirement type="package" version="2.0.2">antismash_python_deps</requirement>
         <requirement type="package" version="2.0.2">antismash</requirement>
     </requirements>
     <command>
--- a/tool_dependencies.xml	Fri Oct 04 04:27:10 2013 -0400
+++ b/tool_dependencies.xml	Fri Oct 04 04:46:02 2013 -0400
@@ -1,16 +1,31 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="blast+" version="2.2.28">
-        <repository changeset_revision="d794cb2b0f45" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository name="package_blast_plus_2_2_28" owner="iuc" />
     </package>
     <package name="hmmer " version="2.3.2">
-        <repository changeset_revision="64510d86d77d" name="package_hmmer_2_3_2" owner="lionelguy" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository name="package_hmmer_2_3_2" owner="lionelguy" />
     </package>
     <package name="hmmer" version="3.0">
-        <repository changeset_revision="3bc37773c609" name="package_hmmer_3_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository name="package_hmmer_3_0" owner="jjohnson" />
     </package>
     <package name="muscle" version="3.8.31">
-        <repository changeset_revision="ce304c51f69b" name="package_muscle_3_8_31" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository name="package_muscle_3_8_31" owner="bgruening" />
+    </package>
+    <package name="biopython" version="1.62">
+        <repository name="package_biopython_1_62" owner="biopython" />
+    </package>
+    <package name="antismash_python_deps" version="2.0.2">
+        <install version="0.4">
+            <actions>
+                <action type="setup_virtualenv">helperlibs=0.1.2
+straight.plugin=1.4.0-post-1</action>
+            </actions>
+        </install>
+        </install>
+        <readme>
+            AntiSmash python dependencies.
+        </readme>
     </package>
     <package name="antismash" version="2.0.2">
         <install version="1.0">
@@ -27,7 +42,7 @@
                     </action>
                 </actions>
                 <!-- Download the binaries for AntiSmash compatible with 64-bit Linux. -->
-                <actions architecture="x86_64" os="linux">
+                <actions os="linux" architecture="x86_64">
                     <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.x86_64.tar.bz2</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
@@ -39,11 +54,11 @@
                     <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR/antismash/generic_modules/clusterblast</destination_directory>
+                        <destination_directory>$INSTALL_DIR/antismash-2.0.2/antismash/generic_modules/clusterblast</destination_directory>
                     </action>
                 </actions>
                 <!-- Download the binaries for AntiSmash compatible with 32-bit Linux. -->
-                <actions architecture="i386" os="linux">
+                <actions os="linux" architecture="i386">
                     <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.i686.tar.bz2</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
@@ -65,14 +80,9 @@
                     </action>
                 </actions>
 
-
-                <action type="setup_virtualenv">biopython=1.62
-helperlibs=0.1.2
-straight.plugin=1.4.0-post-1</action>
-
                 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
                 <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                 </action>
             </actions_group>
         </install>
@@ -81,3 +91,4 @@
         </readme>
     </package>
 </tool_dependency>
+