Mercurial > repos > bgruening > package_samtools_1_0
changeset 0:59273702eab9 draft default tip
Uploaded
author | bgruening |
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date | Fri, 05 Sep 2014 09:58:06 -0400 |
parents | |
children | |
files | tool_dependencies.xml |
diffstat | 1 files changed, 61 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Sep 05 09:58:06 2014 -0400 @@ -0,0 +1,61 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ncurses" version="5.9"> + <repository changeset_revision="c0735727b530" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="zlib" version="1.2.8"> + <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="samtools" version="0.1.19"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/1.0/samtools-1.0.tar.bz2</action> + <action type="set_environment_for_install"> + <repository changeset_revision="c0735727b530" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="ncurses" version="5.9" /> + </repository> + <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="zlib" version="1.2.8" /> + </repository> + </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$NCURSES_LIB_PATH|g" Makefile</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> +Program: samtools (Tools for alignments in the SAM format) +Version: 1.0 + +Usage: samtools <command> [options] + +Command: view SAM<->BAM conversion + sort sort alignment file + mpileup multi-way pileup + depth compute the depth + faidx index/extract FASTA + tview text alignment viewer + index index alignment + idxstats BAM index stats (r595 or later) + fixmate fix mate information + flagstat simple stats + calmd recalculate MD/NM tags and '=' bases + merge merge sorted alignments + rmdup remove PCR duplicates + reheader replace BAM header + cat concatenate BAMs + targetcut cut fosmid regions (for fosmid pool only) + phase phase heterozygotes + +Requirements: libncurses header files + </readme> + </package> +</tool_dependency>