Mercurial > repos > yhoogstrate > package_samtools_parallel_mpileup_0_1_19_a
diff tool_dependencies.xml @ 0:7dd0c6a9be41 draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/samtools_parallel_mpileup_galaxy_wrapper commit ede01f67a8def5be7c88d5c31c2435b3946f1523-dirty
| author | yhoogstrate |
|---|---|
| date | Thu, 05 Nov 2015 07:48:42 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Nov 05 07:48:42 2015 -0500 @@ -0,0 +1,48 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ncurses" version="6.0"> + <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + + <package name="samtools_parallel_mpileup" version="0.1.19-a"> + <install version="1.0"> + <actions> + <action type="set_environment_for_install"> + <repository changeset_revision="c921f7ce9ca7" name="package_ncurses_6_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="ncurses" version="6.0" /> + </repository> + </action> + + <action type="shell_command"> + svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup ; + + cd samtools-parallel-mpileup ; + cd $(ls |grep samtools-) ; + + sed -i 's/-lcurses/-lncurses/' Makefile ; + sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$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/samtools-parallel-mpileup</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="prepend_to" name="PATH">$REPOSITORY_INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + Downloads and installs a modified version of samtools, able to paralellize the mpileup function. + + *Because of the parallelization, the output is not sorted on genomic location!!* + + If this is required for the tool that uses the mpileup as input, sort the mpileup file with: + + sort -k1,1V -k2,2g + </readme> + </package> +</tool_dependency>