Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
changeset 69:74c06a2e4a69 draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Tue, 20 May 2014 09:27:58 -0400 |
| parents | bc398d6bac85 |
| children | 6c5125c08e74 |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 8 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- a/tool_dependencies.xml Tue May 20 09:19:36 2014 -0400 +++ b/tool_dependencies.xml Tue May 20 09:27:58 2014 -0400 @@ -1,22 +1,23 @@ <?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>--> - <!-- Optimized samtools (for threaded mpileup) --> <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</action> - <action type="shell_command">sed -i '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$NCURSES_LIB_PATH|g" Makefile</action> + <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> + <!-- <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$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> <action type="move_file"> <source>samtools-parallel-mpileup</source>