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comparison tool_dependencies.xml @ 0:6eea04363026 draft

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author iuc
date Mon, 16 Mar 2015 12:39:24 -0400
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="samtools" version="1.2">
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-1.2-Linux-x86_64.tgz</action>
8 <action type="move_directory_files">
9 <source_directory>.</source_directory>
10 <destination_directory>$INSTALL_DIR</destination_directory>
11 </action>
12 </actions>
13 <actions>
14 <package name="ncurses" version="5.9">
15 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
16 </package>
17 <package name="zlib" version="1.2.8">
18 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
19 </package>
20 <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action>
21 <action type="set_environment_for_install">
22 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
23 <package name="ncurses" version="5.9" />
24 </repository>
25 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
26 <package name="zlib" version="1.2.8" />
27 </repository>
28 </action>
29 <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action>
30 <action type="shell_command">sed -i -e 's/-lcurses/-lncurses/' Makefile</action>
31 <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$NCURSES_LIB_PATH|g" Makefile</action>
32 <action type="shell_command">make</action>
33 <action type="move_file">
34 <source>samtools</source>
35 <destination>$INSTALL_DIR/bin</destination>
36 </action>
37 </actions>
38 <action type="set_environment">
39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
40 <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
41 </action>
42 </actions_group>
43 </install>
44 <readme>
45 Program: samtools (Tools for alignments in the SAM format)
46 Version: 1.2
47
48 Usage: samtools &lt;command&gt; [options]
49
50 Commands:
51 -- indexing
52 faidx index/extract FASTA
53 index index alignment
54 -- editing
55 calmd recalculate MD/NM tags and '=' bases
56 fixmate fix mate information
57 reheader replace BAM header
58 rmdup remove PCR duplicates
59 targetcut cut fosmid regions (for fosmid pool only)
60 -- file operations
61 bamshuf shuffle and group alignments by name
62 cat concatenate BAMs
63 merge merge sorted alignments
64 mpileup multi-way pileup
65 sort sort alignment file
66 split splits a file by read group
67 bam2fq converts a BAM to a FASTQ
68 -- stats
69 bedcov read depth per BED region
70 depth compute the depth
71 flagstat simple stats
72 idxstats BAM index stats
73 phase phase heterozygotes
74 stats generate stats (former bamcheck)
75 -- viewing
76 flags explain BAM flags
77 tview text alignment viewer
78 view SAM&lt;-&gt;BAM&lt;-&gt;CRAM conversion
79 </readme>
80 </package>
81 </tool_dependency>