Mercurial > repos > eganrol > package_samtools_0_1_19
comparison tool_dependencies.xml @ 0:cfa5dcdccadf draft default tip
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| author | eganrol |
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| date | Thu, 11 Dec 2014 04:33:35 -0500 |
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| -1:000000000000 | 0:cfa5dcdccadf |
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| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="samtools" version="0.1.19"> | |
| 4 <install version="1.0"> | |
| 5 <actions_group> | |
| 6 <actions os="linux" architecture="x86_64"> | |
| 7 <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.19-Linux-x86_64.tgz</action> | |
| 8 <action type="move_directory_files"> | |
| 9 <source_directory>.</source_directory> | |
| 10 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 11 </action> | |
| 12 </actions> | |
| 13 <actions os="darwin" architecture="x86_64"> | |
| 14 <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.19-Darwin-x86_64.tgz</action> | |
| 15 <action type="move_directory_files"> | |
| 16 <source_directory>.</source_directory> | |
| 17 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 18 </action> | |
| 19 </actions> | |
| 20 <actions> | |
| 21 <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2</action> | |
| 22 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> | |
| 23 <action type="shell_command">make</action> | |
| 24 <action type="move_file"> | |
| 25 <source>samtools</source> | |
| 26 <destination>$INSTALL_DIR/bin</destination> | |
| 27 </action> | |
| 28 <action type="move_file"> | |
| 29 <source>libbam.a</source> | |
| 30 <destination>$INSTALL_DIR/lib</destination> | |
| 31 </action> | |
| 32 <action type="move_directory_files"> | |
| 33 <source_directory>.</source_directory> | |
| 34 <destination_directory>$INSTALL_DIR/include/bam</destination_directory> | |
| 35 </action> | |
| 36 </actions> | |
| 37 <action type="set_environment"> | |
| 38 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 39 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable> | |
| 40 <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable> | |
| 41 </action> | |
| 42 </actions_group> | |
| 43 </install> | |
| 44 <readme> | |
| 45 Program: samtools (Tools for alignments in the SAM format) | |
| 46 Version: 0.1.19-44428cd | |
| 47 | |
| 48 Usage: samtools <command> [options] | |
| 49 | |
| 50 Command: view SAM<->BAM conversion | |
| 51 sort sort alignment file | |
| 52 mpileup multi-way pileup | |
| 53 depth compute the depth | |
| 54 faidx index/extract FASTA | |
| 55 tview text alignment viewer | |
| 56 index index alignment | |
| 57 idxstats BAM index stats (r595 or later) | |
| 58 fixmate fix mate information | |
| 59 flagstat simple stats | |
| 60 calmd recalculate MD/NM tags and '=' bases | |
| 61 merge merge sorted alignments | |
| 62 rmdup remove PCR duplicates | |
| 63 reheader replace BAM header | |
| 64 cat concatenate BAMs | |
| 65 bedcov read depth per BED region | |
| 66 targetcut cut fosmid regions (for fosmid pool only) | |
| 67 phase phase heterozygotes | |
| 68 bamshuf shuffle and group alignments by name | |
| 69 </readme> | |
| 70 </package> | |
| 71 </tool_dependency> |