Mercurial > repos > iuc > package_sra_toolkit_2_5_2

diff tool_dependencies.xml @ 2:163cf5b7c14e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 1c0647ec605bc15e0a749833c37f2cf2c5bc69b4
author iuc
date Tue, 01 Mar 2016 03:06:46 -0500
parents 2255f3e3cbb3
children b1bf5fd340ca
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Dec 22 19:41:24 2015 -0500
+++ b/tool_dependencies.xml	Tue Mar 01 03:06:46 2016 -0500
@@ -1,7 +1,10 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="perl" version="5.18.1">
-        <repository changeset_revision="d5193a5f6203" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="318ccddfe301" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="libmagic" version="5.25">
+        <repository changeset_revision="c7b9857a1522" name="package_libmagic_5_25" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="ncbi_vdb" version="2.5.2">
         <repository changeset_revision="b0638a3ba7e6" name="package_ncbi_vdb_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
@@ -14,9 +17,12 @@
             <actions>
                 <action 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="d5193a5f6203" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="318ccddfe301" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="perl" version="5.18.1" />
                     </repository>
+                    <repository changeset_revision="c7b9857a1522" name="package_libmagic_5_25" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="libmagic" version="5.25" />
+                    </repository>
                     <repository changeset_revision="b0638a3ba7e6" name="package_ncbi_vdb_2_5_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="ncbi_vdb" version="2.5.2" />
                     </repository>
@@ -25,10 +31,7 @@
                     </repository>
                 </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=$INSTALL_DIR/build
-                </action>
-                <action type="shell_command">
-                    sed -i -e "109s/-static//" tools/copycat/Makefile
+                    ./configure --prefix=$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
                 </action>
                 <action type="make_install" />
                 <action type="set_environment">