Mercurial > repos > mvdbeek > test_sra

changeset 10:472f8a7e13b3 draft

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planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
author mvdbeek
date Fri, 14 Aug 2015 13:30:47 -0400
parents 9c04607bbb08
children 833f4feaee33
files tool_dependencies.xml
diffstat 1 files changed, 5 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Aug 14 13:23:46 2015 -0400
+++ b/tool_dependencies.xml	Fri Aug 14 13:30:47 2015 -0400
@@ -13,25 +13,16 @@
             make
             make install
         </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="change_directory">../src</action>
         <action type="shell_command">
-            ls
-            mv sra-tools-2.5.2 sra-tools
-            mv ngs-1.1.3 ngs      
-            mv  ncbi-vdb-2.5.2  ncbi-vdb      
             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
             make
             make install
-            cd $INSTALL_DIR/src/ngs/ngs-sdk
-            ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
-            make
-            make install
-            cd $INSTALL_DIR/src/sra-tools
-            ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build --with-ncbi-vdb-build=$INSTALL_DIR/build --with-ncbi-vdb-sources=$INSTALL_DIR/src/ncbi-vdb --with-ngs-sdk-prefix=$INSTALL_DIR
+        </action>
+        <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
+        <action type="shell_command">
+            ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build --with-ncbi-vdb-build=$INSTALL_DIR/build 
             sed -i -e "109s/-static//" tools/copycat/Makefile
             make
             make install
@@ -39,6 +30,7 @@
             ./vdb-config -s "/repository/user/main/public/cache-enabled=false"
             ./vdb-config -s "/repository/user/main/public/root=$INSTALL_DIR"
         </action>
+<!--        <action type="change_directory">../src</action> -->
         <action type="set_environment">
             <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
         </action>