Mercurial > repos > iuc > package_bcftools_1_3

comparison tool_dependencies.xml @ 0:eb618a0f69a3 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
author iuc
date Mon, 21 Dec 2015 05:44:43 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:eb618a0f69a3
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="zlib" version="1.2.8">
4 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="bcftools" version="1.3">
7 <install version="1.0">
8 <actions_group>
9 <actions architecture="x86_64" os="linux">
10 <action sha256sum="e5c8ccdc2b5c0f09d7b467ab194cb78609bb8ec83b70949354b2794e403a904a" type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/bcftools/bcftools-1.3-Linux-x86_64.tar.gz</action>
11 <action type="move_directory_files">
12 <source_directory>.</source_directory>
13 <destination_directory>$INSTALL_DIR</destination_directory>
14 </action>
15 </actions>
16 <actions>
17 <action sha256sum="fc5332e49546d55120551b0d5fb690f79e4f2216b8492c7b53033cdaa4256a3d" type="download_by_url">https://github.com/samtools/bcftools/releases/download/1.3/bcftools-1.3.tar.bz2</action>
18 <action type="set_environment_for_install">
19 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
20 <package name="zlib" version="1.2.8" />
21 </repository>
22 </action>
23 <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action>
24 <action type="make_install" />
25 </actions>
26 <action type="set_environment">
27 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
28 <environment_variable action="set_to" name="BCFTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
29 </action>
30 </actions_group>
31 </install>
32 <readme>
33
34 Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
35 Version: 1.3 (using htslib 1.3)
36
37 Usage: bcftools [--version|--version-only] [--help] &lt;command&gt; &lt;argument&gt;
38
39 Commands:
40
41 -- Indexing
42 index index VCF/BCF files
43
44 -- VCF/BCF manipulation
45 annotate annotate and edit VCF/BCF files
46 concat concatenate VCF/BCF files from the same set of samples
47 convert convert VCF/BCF files to different formats and back
48 isec intersections of VCF/BCF files
49 merge merge VCF/BCF files files from non-overlapping sample sets
50 norm left-align and normalize indels
51 plugin user-defined plugins
52 query transform VCF/BCF into user-defined formats
53 reheader modify VCF/BCF header, change sample names
54 view VCF/BCF conversion, view, subset and filter VCF/BCF files
55
56 -- VCF/BCF analysis
57 call SNP/indel calling
58 consensus create consensus sequence by applying VCF variants
59 cnv HMM CNV calling
60 filter filter VCF/BCF files using fixed thresholds
61 gtcheck check sample concordance, detect sample swaps and contamination
62 roh identify runs of autozygosity (HMM)
63 stats produce VCF/BCF stats
64
65 Most commands accept VCF, bgzipped VCF, and BCF with the file type detected
66 automatically even when streaming from a pipe. Indexed VCF and BCF will work
67 in all situations. Un-indexed VCF and BCF and streams will work in most but
68 not all situations.
69
70
71 </readme>
72 </package>
73 </tool_dependency>