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comparison tool_dependencies.xml @ 0:bb194c224177 draft

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author iuc
date Sat, 06 Sep 2014 03:57:21 -0400
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="samtools" version="1.0">
4 <install version="1.0">
5 <actions_group>
6 <actions architecture="x86_64" os="linux">
7 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.0-Linux-x86_64.tgz</action>
8 <action type="move_directory_files">
9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR</destination_directory>
11 </action>
12 </actions>
13 <actions>
14 <package name="ncurses" version="5.9">
15 <repository changeset_revision="c0735727b530" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
16 </package>
17 <package name="zlib" version="1.2.8">
18 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
19 </package>
20 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/1.0/samtools-1.0.tar.bz2</action>
21 <action type="set_environment_for_install">
22 <repository changeset_revision="f6edc6908585" name="package_ncurses_5_9" owner="iuc" toolshed="https://gaius.bx.psu.edu">
23 <package name="ncurses" version="5.9" />
24 </repository>
25 <repository changeset_revision="b11233fcdc87" name="package_zlib_1_2_8" owner="iuc" toolshed="https://gaius.bx.psu.edu">
26 <package name="zlib" version="1.2.8" />
27 </repository>
28 </action>
29 <action type="shell_command">sed -i 's/-lcurses/-lncurses/' Makefile</action>
30 <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action>
31 <action type="shell_command">make</action>
32 <action type="move_file">
33 <source>samtools</source>
34 <destination>$INSTALL_DIR/bin</destination>
35 </action>
36 </actions>
37 <action type="set_environment">
38 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
39 <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
40 </action>
41 </actions_group>
42 </install>
43 <readme>
44 Program: samtools (Tools for alignments in the SAM format)
45 Version: 1.0 (using htslib 1.0)
46
47 Usage: samtools &lt;command&gt; [options]
48
49 Commands:
50 -- indexing
51 faidx index/extract FASTA
52 index index alignment
53 -- editing
54 calmd recalculate MD/NM tags and '=' bases
55 fixmate fix mate information
56 reheader replace BAM header
57 rmdup remove PCR duplicates
58 targetcut cut fosmid regions (for fosmid pool only)
59 -- file operations
60 bamshuf shuffle and group alignments by name
61 cat concatenate BAMs
62 merge merge sorted alignments
63 mpileup multi-way pileup
64 sort sort alignment file
65 split splits a file by read group
66 bam2fq converts a BAM to a FASTQ
67 -- stats
68 bedcov read depth per BED region
69 depth compute the depth
70 flagstat simple stats
71 idxstats BAM index stats
72 phase phase heterozygotes
73 stats generate stats (former bamcheck)
74 -- viewing
75 flags explain BAM flags
76 tview text alignment viewer
77 view SAM&lt;-&gt;BAM&lt;-&gt;CRAM conversion
78 </readme>
79 </package>
80 </tool_dependency>