Mercurial > repos > iuc > package_samtools_0_1_19

annotate tool_dependencies.xml @ 9:a0ab0fae27e5 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
author iuc
date Sat, 25 Jun 2016 17:21:12 -0400
parents 0e56e4dac6e7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
2 <tool_dependency>
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
3 <package name="samtools" version="0.1.19">
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
4 <install version="1.0">
8
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
5 <actions_group>
9
a0ab0fae27e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 8
diff changeset
6 <actions architecture="x86_64" os="linux">
a0ab0fae27e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 8
diff changeset
7 <action type="download_by_url" sha256sum="3cc457cd66e077b70887155435d8f563154371a61e7ac6714bc10b6aa19841bd" target_filename="samtools-0.1.19.tgz">https://depot.galaxyproject.org/software/samtools/samtools_0.1.19_linux_x64.tar.gz</action>
8
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
8 <action type="move_directory_files">
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
9 <source_directory>.</source_directory>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
10 <destination_directory>$INSTALL_DIR</destination_directory>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
11 </action>
9
a0ab0fae27e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 8
diff changeset
12 <action type="set_environment">
a0ab0fae27e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 8
diff changeset
13 <environment_variable name="BAM_INCLUDE" action="set_to">$INSTALL_DIR/include</environment_variable>
a0ab0fae27e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 8
diff changeset
14 </action>
8
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
15 </actions>
9
a0ab0fae27e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 8
diff changeset
16 <actions architecture="x86_64" os="darwin">
a0ab0fae27e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 8
diff changeset
17 <action type="download_by_url" sha256sum="01e0a2cb38b1bcd433461cef43ff6555755a30dfbe83cb9c0a24cb028b104ac7" target_filename="samtools-0.1.19.tgz">https://depot.galaxyproject.org/software/samtools/samtools_0.1.19_darwin_x64.tar.gz</action>
8
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
18 <action type="move_directory_files">
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
19 <source_directory>.</source_directory>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
20 <destination_directory>$INSTALL_DIR</destination_directory>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
21 </action>
9
a0ab0fae27e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 8
diff changeset
22 <action type="set_environment">
a0ab0fae27e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 8
diff changeset
23 <environment_variable name="BAM_INCLUDE" action="set_to">$INSTALL_DIR/include</environment_variable>
a0ab0fae27e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 8
diff changeset
24 </action>
8
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
25 </actions>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
26 <actions>
9
a0ab0fae27e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 8
diff changeset
27 <action type="download_by_url" sha256sum="d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4">https://depot.galaxyproject.org/software/samtools/samtools_0.1.19_src_all.tar.bz2</action>
8
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
28 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
29 <action type="shell_command">make</action>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
30 <action type="move_file">
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
31 <source>samtools</source>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
32 <destination>$INSTALL_DIR/bin</destination>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
33 </action>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
34 <action type="move_file">
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
35 <source>bcftools/bcftools</source>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
36 <destination>$INSTALL_DIR/bin</destination>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
37 </action>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
38 <action type="move_file">
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
39 <source>bcftools/vcfutils.pl</source>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
40 <destination>$INSTALL_DIR/bin</destination>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
41 </action>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
42 <action type="move_file">
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
43 <source>libbam.a</source>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
44 <destination>$INSTALL_DIR/lib</destination>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
45 </action>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
46 <action type="move_directory_files">
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
47 <source_directory>.</source_directory>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
48 <destination_directory>$INSTALL_DIR/include/bam</destination_directory>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
49 </action>
9
a0ab0fae27e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 8
diff changeset
50 <action type="set_environment">
a0ab0fae27e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 8
diff changeset
51 <environment_variable name="BAM_INCLUDE" action="set_to">$INSTALL_DIR/include/bam</environment_variable>
a0ab0fae27e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
parents: 8
diff changeset
52 </action>
8
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
53 </actions>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
54 <action type="set_environment">
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
55 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
56 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
57 <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
2
9f412e12b103 Uploaded
iuc
parents: 1
diff changeset
58 </action>
8
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
59 </actions_group>
0
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
60 </install>
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
61 <readme>
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
62 Program: samtools (Tools for alignments in the SAM format)
8
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
63 Version: 0.1.19-44428cd
0
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
64
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
65 Usage: samtools &lt;command&gt; [options]
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
66
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
67 Command: view SAM&lt;-&gt;BAM conversion
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
68 sort sort alignment file
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
69 mpileup multi-way pileup
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
70 depth compute the depth
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
71 faidx index/extract FASTA
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
72 tview text alignment viewer
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
73 index index alignment
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
74 idxstats BAM index stats (r595 or later)
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
75 fixmate fix mate information
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
76 flagstat simple stats
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
77 calmd recalculate MD/NM tags and '=' bases
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
78 merge merge sorted alignments
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
79 rmdup remove PCR duplicates
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
80 reheader replace BAM header
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
81 cat concatenate BAMs
8
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
82 bedcov read depth per BED region
0
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
83 targetcut cut fosmid regions (for fosmid pool only)
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
84 phase phase heterozygotes
8
0e56e4dac6e7 Uploaded
iuc
parents: 7
diff changeset
85 bamshuf shuffle and group alignments by name
0
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
86 </readme>
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
87 </package>
18ccfc4b9542 Uploaded
iuc
parents:
diff changeset
88 </tool_dependency>