Mercurial > repos > iuc > package_bcftools_1_3
comparison tool_dependencies.xml @ 0:43a9aebf3adb draft default tip
planemo upload commit 71ac7e12419b8541746ebf8d4ba704cbbd603db1
author | iuc |
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date | Mon, 21 Dec 2015 06:02:52 -0500 |
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1 <?xml version="1.0"?> | |
2 <tool_dependency> | |
3 <package name="zlib" version="1.2.8"> | |
4 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.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>$INSTALL_DIR</destination_directory> | |
14 </action> | |
15 </actions> | |
16 <actions> | |
17 <action sha256sum="fc5332e49546d55120551b0d5fb690f79e4f2216b8492c7b53033cdaa4256a3d" type="download_by_url">https://github.com/samtools/bcftools/releases/download/1.3/bcftools-1.3.tar.bz2</action> | |
18 <action type="set_environment_for_install"> | |
19 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | |
20 <package name="zlib" version="1.2.8" /> | |
21 </repository> | |
22 </action> | |
23 <action type="shell_command">sed -i.bak 's#/usr/local#$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] <command> <argument> | |
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> |