Mercurial > repos > mvdbeek > test_sra

changeset 5:167041a5893b draft

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planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
author mvdbeek
date Fri, 14 Aug 2015 12:57:30 -0400
parents c01e4b9ccbc6
children a5ab0e9215c5
files tool_dependencies.xml
diffstat 1 files changed, 5 insertions(+), 16 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Aug 14 12:55:33 2015 -0400
+++ b/tool_dependencies.xml	Fri Aug 14 12:57:30 2015 -0400
@@ -6,25 +6,14 @@
         <action type="make_directory">src</action>
         <action type="make_directory">build</action>
         <action type="change_directory">src</action>
-        <action type="download_file">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
-        <action type="shell_command">
-            tar -xf ../2.5.2.tar.gz
-            rm 2.5.2.tar.gz
-            mv sra-tools-2.5.2 sra-tools
-        </action>
-        <action type="download_file">https://github.com/ncbi/ngs/archive/1.1.3.tar.gz</action>
+        <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
+        <action type="download_by_url">https://github.com/ncbi/ngs/archive/1.1.3.tar.gz</action>
+        <action type="download_by_url">https://github.com/ncbi/ncbi-vdb/archive/2.5.2.tar.gz</action>
+        <action type="change_directory">src</action>
         <action type="shell_command">
-            tar -xf ../1.1.3.tar.gz
-            rm 1.1.3.tar.gz
+            mv sra-tools-2.5.2 sra-tools
             mv ngs-1.1.3 ngs      
-        </action>
-        <action type="download_file">https://github.com/ncbi/ncbi-vdb/archive/2.5.2.tar.gz</action>
-        <action type="shell_command">
-            tar -xf ../2.5.2.tar.gz
-            rm 2.5.2.tar.gz
             mv  ncbi-vdb-2.5.2  ncbi-vdb      
-        </action>
-        <action type="shell_command">
             LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
             cd $INSTALL_DIR/src/ncbi-vdb
             ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build