|
0
|
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 <command> [options]
|
|
|
39
|
|
|
40 Command: view SAM<->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>
|
