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adopt the rest of devteam's samtools #71

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Mar 16, 2015
Merged

adopt the rest of devteam's samtools #71

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3 changes: 3 additions & 0 deletions packages/package_samtools_0_1_16/.shed.yml
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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
82 changes: 82 additions & 0 deletions packages/package_samtools_0_1_16/tool_dependencies.xml
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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 &lt;command&gt; [options]

Command: view SAM&lt;-&gt;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>
3 changes: 3 additions & 0 deletions packages/package_samtools_0_1_18/.shed.yml
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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
83 changes: 83 additions & 0 deletions packages/package_samtools_0_1_18/tool_dependencies.xml
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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 &lt;command&gt; [options]

Command: view SAM&lt;-&gt;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>