Mercurial > repos > iuc > package_bcftools_1_2
comparison tool_dependencies.xml @ 0:70a313a2366f draft default tip
planemo upload for repository https://github.com/davebx/tools-iuc/blob/master/packages/package_bcftools_1_2/tool_dependencies.xml commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
author | iuc |
---|---|
date | Tue, 19 May 2015 14:57:05 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:70a313a2366f |
---|---|
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="1.2"> | |
7 <install version="1.0"> | |
8 <actions_group> | |
9 <actions architecture="x86_64" os="linux"> | |
10 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/bcftools/bcftools-1.2-Linux-x86_64.tgz</action> | |
11 <action type="move_directory_files"> | |
12 <source_directory>.</source_directory> | |
13 <destination_directory>$INSTALL_DIR</destination_directory> | |
14 </action> | |
15 </actions> | |
16 <actions> | |
17 <action type="set_environment_for_install"> | |
18 <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | |
19 <package name="zlib" version="1.2.8" /> | |
20 </repository> | |
21 </action> | |
22 <action type="download_by_url">https://github.com/samtools/bcftools/releases/download/1.2/bcftools-1.2.tar.bz2</action> | |
23 <action type="shell_command">sed -i.bak 's#/usr/local#$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: 1.2 (using htslib 1.2.1) | |
36 | |
37 Usage: bcftools <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 filter filter VCF/BCF files using fixed thresholds | |
60 gtcheck check sample concordance, detect sample swaps and contamination | |
61 roh identify runs of autozygosity (HMM) | |
62 stats produce VCF/BCF stats | |
63 | |
64 Most commands accept VCF, bgzipped VCF, and BCF with the file type detected | |
65 automatically even when streaming from a pipe. Indexed VCF and BCF will work | |
66 in all situations. Un-indexed VCF and BCF and streams will work in most but | |
67 not all situations. | |
68 | |
69 </readme> | |
70 </package> | |
71 </tool_dependency> |