Mercurial > repos > mvdbeek > package_sra_toolkit_2_5_2

changeset 2:b7385e84a15b draft

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planemo upload commit 4abfa4aaee08afe2a3246420ce5d131e1c1d42d8
author mvdbeek
date Fri, 25 Sep 2015 11:31:58 -0400
parents 531f4eea4196
children 69288de0e2f4
files tool_dependencies.xml
diffstat 1 files changed, 5 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Sep 25 10:03:55 2015 -0400
+++ b/tool_dependencies.xml	Fri Sep 25 11:31:58 2015 -0400
@@ -9,25 +9,20 @@
     <package name="sra_toolkit" version="2.5.2">
         <install version="1.0">
             <actions>
+                <action target_filename="sra-tools-2.5.2.tar.gz" type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
                 <action type="set_environment_for_install">
                     <repository changeset_revision="96c348976275" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="ncbi_vdb" version="2.5.2" />
                     </repository>
-                    <repository changeset_revision="f530f97e76ea" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="b0e9867f0dfb" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="ngs_sdk" version="1.1.3" />
                     </repository>
                 </action>
-                <action target_filename="sra-tools-2.5.2.tar.gz" type="download_file">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
-                <action type="shell_command">tar -xf sra-tools-2.5.2.tar.gz</action>
-                <action type="change_directory">sra-tools-2.5.2</action>
-                <action type="shell_command">
-                    ./configure --prefix=$INSTALL_DIR -with-ngs-sdk-prefix=$NGS_SDK_DIR --with-ncbi-vdb-sources=$NCBI_VDB_DIR --with-ncbi-vdb-build=$NCBI_VDB_DIR --build=$INSTALL_DIR/build
-                    sed -i -e "109s/-static//" tools/copycat/Makefile
+                <action type="autoconf">
+                    --prefix=$INSTALL_DIR -with-ngs-sdk-prefix=$NGS_SDK_DIR --with-ncbi-vdb-sources=$NCBI_VDB_DIR --with-ncbi-vdb-build=$NCBI_VDB_DIR --build=$INSTALL_DIR/build
                 </action>
+                <action type="shell_command">sed -i -e "109s/-static//" tools/copycat/Makefile</action>
                 <action type="make_install" />
-                <action type="shell_command">
-                    $INSTALL_DIR/bin/vdb-config --restore-defaults
-                </action>
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                 </action>