Mercurial > repos > mvdbeek > package_sra_toolkit_2_5_2

changeset 5:aabb60d93e4a draft

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planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
author mvdbeek
date Fri, 25 Sep 2015 13:18:52 -0400
parents 9b27d2331ce2
children 9a412e6be961
files tool_dependencies.xml
diffstat 1 files changed, 12 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Fri Sep 25 12:27:07 2015 -0400
+++ b/tool_dependencies.xml	Fri Sep 25 13:18:52 2015 -0400
@@ -4,25 +4,30 @@
         <repository changeset_revision="e053dbdb5302" name="package_ascp_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="ncbi_vdb" version="2.5.2">
-        <repository changeset_revision="a20af718e248" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="9e86738381d1" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <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="a20af718e248" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="9e86738381d1" 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="c9b972613908" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="a00c9a1db096" 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 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=$INSTALL_DIR/build
+                <action target_filename="sra-tools-2.5.2.tar.gz" type="download_file">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
+                <action type="shell_command">tar -xf sra-tools-2.5.2.tar.gz</action>
+                <action type="change_directory">sra-tools-2.5.2</action>
+                <action type="shell_command">
+                    ./configure --prefix=$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>
-                <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>