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Implement type-aware repository realization.
The biggest upshot here is that not now in source repositories package (tool_dependency_definition) and suite (repository_suite_definition) directories can now have readmes. The shed upload code will just quietly discard these.
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name: package_1 | |||
owner: iuc | |||
description: package_1 description |
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Test Package 1 | |||
=============== | |||
|
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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] | |||
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|||
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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Test Suite 1 | |||
============ |
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<?xml version="1.0"?> | |||
<repositories description="A suite of Galaxy tools designed to work with version 1.2 of the SAMtools package."> | |||
<repository name="data_manager_sam_fasta_index_builder" owner="devteam" /> | |||
<repository name="bam_to_sam" owner="devteam" /> | |||
<repository name="sam_to_bam" owner="devteam" /> | |||
<repository name="samtools_bedcov" owner="devteam" /> | |||
<repository name="samtools_calmd" owner="devteam" /> | |||
<repository name="samtools_flagstat" owner="devteam" /> | |||
<repository name="samtools_idxstat" owner="devteam" /> | |||
<repository name="samtools_mpileup" owner="devteam" /> | |||
<repository name="samtools_phase" owner="devteam" /> | |||
<repository name="samtools_reheader" owner="devteam" /> | |||
<repository name="samtools_rmdup" owner="devteam" /> | |||
<repository name="samtools_slice_bam" owner="devteam" /> | |||
<repository name="samtools_sort" owner="devteam" /> | |||
<repository name="samtools_split" owner="devteam" /> | |||
<repository name="samtools_stats" owner="devteam" /> | |||
</repositories> |
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name: workflow_1 | |||
owner: iuc | |||
description: workflow_1 description |
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