Mercurial > repos > iuc > package_samtools_1_0

comparison tool_dependencies.xml @ 0:063e42aeeba8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
author iuc
date Tue, 19 May 2015 15:02:01 -0400
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children 2d1ce13600b5
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-1:000000000000 0:063e42aeeba8
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="ncurses" version="5.9">
4 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="zlib" version="1.2.8">
7 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="samtools" version="1.0">
10 <install version="1.0">
11 <actions_group>
12 <actions architecture="x86_64" os="linux">
13 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.0-Linux-x86_64.tgz</action>
14 <action type="move_directory_files">
15 <source_directory>.</source_directory>
16 <destination_directory>$INSTALL_DIR</destination_directory>
17 </action>
18 </actions>
19 <actions>
20 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/1.0/samtools-1.0.tar.bz2</action>
21 <action type="set_environment_for_install">
22 <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
23 <package name="ncurses" version="5.9" />
24 </repository>
25 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
26 <package name="zlib" version="1.2.8" />
27 </repository>
28 </action>
29 <action type="shell_command">sed -i -e 's/-lcurses/-lncurses/' Makefile</action>
30 <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$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>