Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam
view tool_dependencies.xml @ 86:c1424388f08b draft
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 1477c39d48b290394b7247b9c7b1e4a62a85f2de-dirty
author | yhoogstrate |
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date | Thu, 05 Nov 2015 03:45:02 -0500 |
parents | ddbaf017720a |
children | a92c2ae342c4 |
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<?xml version="1.0"?> <tool_dependency> <package name="ncurses" version="6.0"> <repository changeset_revision="7fae9c4b2d10" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.19"> <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="samtools_parallel_mpileup_0_1_19a" version="0.1.19a"> <install version="1.0"> <actions> <action type="set_environment_for_install"> <repository changeset_revision="387c0609c0b7" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="ncurses" version="5.9" /> </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. </readme> </package> <package name="varscan" version="2.3.6"> <repository changeset_revision="f82940004c84" name="varscan_version_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>