Mercurial > repos > nick > dunovo

changeset 23:04a9c9e8c8c3 draft

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planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fd1625359a101d8a6b0b8d97028cc8be509398f2\n'-dirty
author nick
date Fri, 05 Jan 2018 03:12:52 -0500
parents e875e5572808
children 4f1eb9bd336d
files tool_dependencies.xml
diffstat 1 files changed, 10 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Jan 05 00:50:23 2018 -0500
+++ b/tool_dependencies.xml	Fri Jan 05 03:12:52 2018 -0500
@@ -19,22 +19,22 @@
         <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action>
         <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action>
         <action type="shell_command">rm v0.1.0.tar.gz</action>
-        <action type="shell_command">ls -lFhAb &gt; /home/me/tmp/galaxy/install.root1.log</action>
-        <action type="shell_command">ls -lFhAb utillib-0.1.0 &gt; /home/me/tmp/galaxy/install.utillib1.log</action>
+        <action type="shell_command">ls -lFhAb &gt; /home/me/tmp/galaxy/install.ls1.log</action>
+        <action type="shell_command">ls -lFhAb utillib-0.1.0 &gt; /home/me/tmp/galaxy/install.ls2.log</action>
+        <action type="shell_command">echo DEBUG $TMP_WORK_DIR</action>
         <action rename_to="utillib" type="move_file">
           <source>utillib-0.1.0</source>
-          <destination>.</destination>
+          <destination>$TMP_WORK_DIR</destination>
         </action>
-        <action type="shell_command">ls -lFhAb &gt; /home/me/tmp/galaxy/install.root2.log</action>
-        <action type="shell_command">ls -lFhAb utillib-0.1.0 &gt; /home/me/tmp/galaxy/install.utillib2.log</action>
-        <action type="shell_command">ls -lFhAb utillib &gt; /home/me/tmp/galaxy/install.utillib3.log</action>
+        <action type="shell_command">ls -lFhAb &gt; /home/me/tmp/galaxy/install.ls3.log</action>
+        <action type="shell_command">ls -lFhAb utillib &gt; /home/me/tmp/galaxy/install.ls4.log</action>
         <!-- download the kalign submodule -->
         <action type="download_file">https://github.com/makrutenko/kalign-dunovo/archive/v0.2.0.tar.gz</action>
         <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action>
         <action type="shell_command">rm v0.2.0.tar.gz</action>
         <action rename_to="kalign" type="move_file">
           <source>kalign-dunovo-0.2.0</source>
-          <destination>.</destination>
+          <destination>$TMP_WORK_DIR</destination>
         </action>
         <!-- download the ET submodule -->
         <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action>
@@ -42,17 +42,17 @@
         <action type="shell_command">rm v0.2.2.tar.gz</action>
         <action rename_to="ET" type="move_file">
           <source>ET-0.2.2</source>
-          <destination>.</destination>
+          <destination>$TMP_WORK_DIR</destination>
         </action>
         <!-- make and install -->
         <action type="shell_command">make clean</action>
         <action type="shell_command">make</action>
-        <action type="shell_command">ls -lFhAb &gt; /home/me/tmp/galaxy/install.root4.log</action>
+        <action type="shell_command">ls -lFhAb &gt; /home/me/tmp/galaxy/install.ls5.log</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>
           <destination_directory>$INSTALL_DIR</destination_directory>
         </action>
-        <action type="shell_command">ls -lFhAb $INSTALL_DIR &gt; /home/me/tmp/galaxy/install.install_dir1.log</action>
+        <action type="shell_command">ls -lFhAb $INSTALL_DIR &gt; /home/me/tmp/galaxy/install.ls6.log</action>
         <action type="set_environment">
           <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
         </action>