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Merge pull request #71 from galaxyproject/adopt_devteams_samtools
adopt the rest of devteam's samtools
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| # repository published to https://toolshed.g2.bx.psu.edu/repos/iuc/package_samtools_0_1_16 | ||
| owner: iuc | ||
| name: package_samtools_0_1_16 |
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| <?xml version="1.0"?> | ||
| <tool_dependency> | ||
| <package name="samtools" version="0.1.16"> | ||
| <install version="1.0"> | ||
| <actions_group> | ||
| <actions os="linux" architecture="i386"> | ||
| <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.16-linux-i386.tgz</action> | ||
| <action type="move_directory_files"> | ||
| <source_directory>.</source_directory> | ||
| <destination_directory>$INSTALL_DIR</destination_directory> | ||
| </action> | ||
| </actions> | ||
| <actions os="linux" architecture="x86_64"> | ||
| <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.16-linux-x86_64.tgz</action> | ||
| <action type="move_directory_files"> | ||
| <source_directory>.</source_directory> | ||
| <destination_directory>$INSTALL_DIR</destination_directory> | ||
| </action> | ||
| </actions> | ||
| <actions os="darwin" architecture="i386"> | ||
| <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.16-Darwin-i386.tgz</action> | ||
| <action type="move_directory_files"> | ||
| <source_directory>.</source_directory> | ||
| <destination_directory>$INSTALL_DIR</destination_directory> | ||
| </action> | ||
| </actions> | ||
| <actions os="darwin" architecture="x86_64"> | ||
| <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.16-Darwin-x86_64.tgz</action> | ||
| <action type="move_directory_files"> | ||
| <source_directory>.</source_directory> | ||
| <destination_directory>$INSTALL_DIR</destination_directory> | ||
| </action> | ||
| </actions> | ||
| <actions> | ||
| <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.16.tar.bz2</action> | ||
| <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> | ||
| <action type="shell_command">make</action> | ||
| <action type="move_file"> | ||
| <source>samtools</source> | ||
| <destination>$INSTALL_DIR/bin</destination> | ||
| </action> | ||
| <action type="move_file"> | ||
| <source>libbam.a</source> | ||
| <destination>$INSTALL_DIR/lib</destination> | ||
| </action> | ||
| </actions> | ||
| <action type="set_environment"> | ||
| <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | ||
| <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable> | ||
| </action> | ||
| </actions_group> | ||
| </install> | ||
| <readme> | ||
| This is the last version of SAMTools to include the 'pileup' command. | ||
|
|
||
| Program: samtools (Tools for alignments in the SAM format) | ||
| Version: 0.1.16 (r963:234) | ||
|
|
||
| Usage: samtools <command> [options] | ||
|
|
||
| Command: view SAM<->BAM conversion | ||
| sort sort alignment file | ||
| pileup generate pileup output | ||
| mpileup multi-way pileup | ||
| depth compute the depth | ||
| faidx index/extract FASTA | ||
| tview text alignment viewer | ||
| index index alignment | ||
| idxstats BAM index stats (r595 or later) | ||
| fixmate fix mate information | ||
| glfview print GLFv3 file | ||
| flagstat simple stats | ||
| calmd recalculate MD/NM tags and '=' bases | ||
| merge merge sorted alignments | ||
| rmdup remove PCR duplicates | ||
| reheader replace BAM header | ||
| cat concatenate BAMs | ||
| targetcut cut fosmid regions (for fosmid pool only) | ||
| phase phase heterozygotes | ||
| </readme> | ||
| </package> | ||
| </tool_dependency> |
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| # repository published to https://toolshed.g2.bx.psu.edu/repos/iuc/package_samtools_0_1_18 | ||
| owner: iuc | ||
| name: package_samtools_0_1_18 |
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| <?xml version="1.0"?> | ||
| <tool_dependency> | ||
| <package name="samtools" version="0.1.18"> | ||
| <install version="1.0"> | ||
| <actions_group> | ||
| <actions os="linux" architecture="i386"> | ||
| <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz</action> | ||
| <action type="move_directory_files"> | ||
| <source_directory>.</source_directory> | ||
| <destination_directory>$INSTALL_DIR</destination_directory> | ||
| </action> | ||
| </actions> | ||
| <actions os="linux" architecture="x86_64"> | ||
| <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz</action> | ||
| <action type="move_directory_files"> | ||
| <source_directory>.</source_directory> | ||
| <destination_directory>$INSTALL_DIR</destination_directory> | ||
| </action> | ||
| </actions> | ||
| <actions os="darwin" architecture="i386"> | ||
| <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz</action> | ||
| <action type="move_directory_files"> | ||
| <source_directory>.</source_directory> | ||
| <destination_directory>$INSTALL_DIR</destination_directory> | ||
| </action> | ||
| </actions> | ||
| <actions os="darwin" architecture="x86_64"> | ||
| <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.18-Darwin-x86_64.tgz</action> | ||
| <action type="move_directory_files"> | ||
| <source_directory>.</source_directory> | ||
| <destination_directory>$INSTALL_DIR</destination_directory> | ||
| </action> | ||
| </actions> | ||
| <actions> | ||
| <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.18.tar.bz2</action> | ||
| <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> | ||
| <action type="shell_command">make</action> | ||
| <action type="move_file"> | ||
| <source>samtools</source> | ||
| <destination>$INSTALL_DIR/bin</destination> | ||
| </action> | ||
| <action type="move_file"> | ||
| <source>libbam.a</source> | ||
| <destination>$INSTALL_DIR/lib</destination> | ||
| </action> | ||
| <action type="move_directory_files"> | ||
| <source_directory>.</source_directory> | ||
| <destination_directory>$INSTALL_DIR/include/bam</destination_directory> | ||
| </action> | ||
| </actions> | ||
| <action type="set_environment"> | ||
| <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | ||
| <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable> | ||
| <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable> | ||
| </action> | ||
| </actions_group> | ||
| </install> | ||
| <readme> | ||
| Program: samtools (Tools for alignments in the SAM format) | ||
| Version: 0.1.18 (r982:295) | ||
|
|
||
| Usage: samtools <command> [options] | ||
|
|
||
| Command: view SAM<->BAM conversion | ||
| sort sort alignment file | ||
| mpileup multi-way pileup | ||
| depth compute the depth | ||
| faidx index/extract FASTA | ||
| tview text alignment viewer | ||
| index index alignment | ||
| idxstats BAM index stats (r595 or later) | ||
| fixmate fix mate information | ||
| flagstat simple stats | ||
| calmd recalculate MD/NM tags and '=' bases | ||
| merge merge sorted alignments | ||
| rmdup remove PCR duplicates | ||
| reheader replace BAM header | ||
| cat concatenate BAMs | ||
| targetcut cut fosmid regions (for fosmid pool only) | ||
| phase phase heterozygotes | ||
| </readme> | ||
| </package> | ||
| </tool_dependency> |