Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 70:6c5125c08e74 draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Wed, 21 May 2014 03:57:01 -0400 |
| parents | 74c06a2e4a69 |
| children | ea6e9c144fee |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 16 insertions(+), 9 deletions(-) [+] |
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--- a/tool_dependencies.xml Tue May 20 09:27:58 2014 -0400 +++ b/tool_dependencies.xml Wed May 21 03:57:01 2014 -0400 @@ -1,26 +1,33 @@ <?xml version="1.0"?> <tool_dependency> - <!--<package name="ncurses" version="5.9"> + <package name="ncurses" version="5.9"> <repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> - </package>--> + </package> <package name="samtools_parallel_mpileup" version="0.1.19"> <install version="1.0"> <actions> - <!--<action type="set_environment_for_install"> + <action type="set_environment_for_install"> <repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> <package name="ncurses" version="5.9" /> </repository> - </action>--> + </action> + + <action type="shell_command"> + svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup ; + + cd samtools-parallel-mpileup ; + cd $(ls |grep samtools-) ; - <action type="shell_command">svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup && cd samtools-parallel-mpileup</action> - <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> - <!-- <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action>--> - <action type="shell_command">cd samtools-parallel-mpileup && cd $(ls |grep samtools-) && make && cp samtools ../samtools-parallel-mpileup</action> + sed -i 's/-lcurses/-lncurses/' Makefile ; + sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile ; + + make ; + cp samtools ../samtools-parallel-mpileup</action> <action type="move_file"> - <source>samtools-parallel-mpileup</source> + <source>samtools-parallel-mpileup/samtools-parallel-mpileup</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="set_environment">