Mercurial > repos > iuc > package_bcftools_1_2
annotate tool_dependencies.xml @ 1:c1cd1b1ab6b2 draft default tip
planemo upload for repository https://github.com/davebx/tools-iuc/blob/master/packages/package_bcftools_1_2/ commit 97a064489364118d108b0dd2cfb4d9bc53080837
| author | iuc |
|---|---|
| date | Thu, 19 Nov 2015 12:58:34 -0500 |
| parents | cb6cd479c02e |
| children |
| rev | line source |
|---|---|
| 0 | 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="1.2"> | |
| 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>$INSTALL_DIR</destination_directory> | |
| 14 </action> | |
| 15 </actions> | |
| 16 <actions> | |
|
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c1cd1b1ab6b2
planemo upload for repository https://github.com/davebx/tools-iuc/blob/master/packages/package_bcftools_1_2/ commit 97a064489364118d108b0dd2cfb4d9bc53080837
iuc
parents:
0
diff
changeset
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17 <action type="download_by_url">https://github.com/samtools/bcftools/releases/download/1.2/bcftools-1.2.tar.bz2</action> |
| 0 | 18 <action type="set_environment_for_install"> |
| 19 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> | |
| 20 <package name="zlib" version="1.2.8" /> | |
| 21 </repository> | |
| 22 </action> | |
| 23 <action type="shell_command">sed -i.bak 's#/usr/local#$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: 1.2 (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> |