| Previous changeset 0:d3a72e55deca (2013-09-18) Next changeset 2:565c0e690238 (2013-11-18) |
|
Commit message:
tool_data_table_conf.xml.sample fix |
|
modified:
tool-data/annovar.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml tools/annovar/annovar.xml |
|
added:
tool_data_table_conf.xml.sample~ tool_dependencies.xml~ |
| b |
| diff -r d3a72e55deca -r 7d9353127f8a tool-data/annovar.loc.sample --- a/tool-data/annovar.loc.sample Wed Sep 18 10:51:20 2013 -0400 +++ b/tool-data/annovar.loc.sample Tue Nov 05 07:16:32 2013 -0500 |
| b |
| @@ -1,5 +1,5 @@ #loc file for annovar tool - +# # <columns>value, dbkey, name, ANNOVAR_scripts, ANNOVAR_humandb</columns> hg18 hg18 build 36 (hg18) /path/to/annovarscripts /path/to/humandb |
| b |
| diff -r d3a72e55deca -r 7d9353127f8a tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Wed Sep 18 10:51:20 2013 -0400 +++ b/tool_data_table_conf.xml.sample Tue Nov 05 07:16:32 2013 -0500 |
| b |
| @@ -1,5 +1,7 @@ <!-- ANNOVAR files --> +<tables> <table name="annovar_loc" comment_char="#"> <columns>value, dbkey, name, ANNOVAR_scripts, ANNOVAR_humandb</columns> <file path="tool-data/annovar.loc" /> </table> +</tables> |
| b |
| diff -r d3a72e55deca -r 7d9353127f8a tool_data_table_conf.xml.sample~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample~ Tue Nov 05 07:16:32 2013 -0500 |
| b |
| @@ -0,0 +1,5 @@ +<!-- ANNOVAR files --> +<table name="annovar_loc" comment_char="#"> +<columns>value, dbkey, name, ANNOVAR_scripts, ANNOVAR_humandb</columns> +<file path="tool-data/annovar.loc" /> +</table> |
| b |
| diff -r d3a72e55deca -r 7d9353127f8a tool_dependencies.xml --- a/tool_dependencies.xml Wed Sep 18 10:51:20 2013 -0400 +++ b/tool_dependencies.xml Tue Nov 05 07:16:32 2013 -0500 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="cgatools17" version="1"> + <package name="cgatools" version="1.7"> <install version="1.0"> <actions> <action type="download_by_url">http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz</action> |
| b |
| diff -r d3a72e55deca -r 7d9353127f8a tool_dependencies.xml~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml~ Tue Nov 05 07:16:32 2013 -0500 |
| b |
| @@ -0,0 +1,23 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="cgatools17" version="1"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://sourceforge.net/projects/cgatools/files/1.7.1/cgatools-1.7.1.5-linux_binary-x86_64.tar.gz</action> + <action type="shell_command"> chmod a+x bin/cgatools</action> + <action type="move_file"> + <source>bin/cgatools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + Downloads and installs the cgatools binary. + </readme> + </package> +</tool_dependency> + |
| b |
| diff -r d3a72e55deca -r 7d9353127f8a tools/annovar/annovar.xml --- a/tools/annovar/annovar.xml Wed Sep 18 10:51:20 2013 -0400 +++ b/tools/annovar/annovar.xml Tue Nov 05 07:16:32 2013 -0500 |
| b |
| @@ -2,7 +2,7 @@ <description> Annotate a file using ANNOVAR </description> <requirements> - <requirement type="package" version="1">cgatools17</requirement> + <requirement type="package" version="1.7">cgatools</requirement> </requirements> <command interpreter="bash"> |