Mercurial > repos > bgruening > package_samtools_1_0

comparison tool_dependencies.xml @ 0:59273702eab9 draft default tip

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author bgruening
date Fri, 05 Sep 2014 09:58:06 -0400
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="ncurses" version="5.9">
4 <repository changeset_revision="c0735727b530" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="zlib" version="1.2.8">
7 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="samtools" version="0.1.19">
10 <install version="1.0">
11 <actions>
12 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/1.0/samtools-1.0.tar.bz2</action>
13 <action type="set_environment_for_install">
14 <repository changeset_revision="c0735727b530" name="package_ncurses_5_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
15 <package name="ncurses" version="5.9" />
16 </repository>
17 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
18 <package name="zlib" version="1.2.8" />
19 </repository>
20 </action>
21 <action type="shell_command">sed -i 's/-lcurses/-lncurses/' Makefile</action>
22 <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$NCURSES_LIB_PATH|g" Makefile</action>
23 <action type="shell_command">make</action>
24 <action type="move_file">
25 <source>samtools</source>
26 <destination>$INSTALL_DIR/bin</destination>
27 </action>
28 <action type="set_environment">
29 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
30 <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
31 </action>
32 </actions>
33 </install>
34 <readme>
35 Program: samtools (Tools for alignments in the SAM format)
36 Version: 1.0
37
38 Usage: samtools &lt;command&gt; [options]
39
40 Command: view SAM&lt;-&gt;BAM conversion
41 sort sort alignment file
42 mpileup multi-way pileup
43 depth compute the depth
44 faidx index/extract FASTA
45 tview text alignment viewer
46 index index alignment
47 idxstats BAM index stats (r595 or later)
48 fixmate fix mate information
49 flagstat simple stats
50 calmd recalculate MD/NM tags and '=' bases
51 merge merge sorted alignments
52 rmdup remove PCR duplicates
53 reheader replace BAM header
54 cat concatenate BAMs
55 targetcut cut fosmid regions (for fosmid pool only)
56 phase phase heterozygotes
57
58 Requirements: libncurses header files
59 </readme>
60 </package>
61 </tool_dependency>