view tool_dependencies.xml @ 13:657b651aa0c3 draft

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<?xml version="1.0"?>
<tool_dependency>

	<!--
	<package name="R" version="3.1.0">
		<repository name="package_r_3_1_0" owner="iuc" prior_installation_required="True" />
	</package>
	-->
	<package name="R" version="3.1.1">
		<repository changeset_revision="d9964efbfbe3" name="package_r_3_1_1" owner="fubar" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
	</package>

	<package name="qdnaseq" version="1.0.5">
		<install version="1.0">
			<actions>
				<action type="shell_command">echo "[DEBUG] Starting install actions"</action>
				<action type="setup_r_environment">
					
					<!--
					<repository name="package_r_3_1_0" owner="iuc">
						<package name="R" version="3.1.0" />
					</repository>
					-->

					<repository changeset_revision="d9964efbfbe3" name="package_r_3_1_1" owner="fubar" toolshed="https://testtoolshed.g2.bx.psu.edu">
						<package name="R" version="3.1.1" />
					</repository>
					
					<!--
					<action type="shell_command">Rscript -e "source(\"http://bioconductor.org/biocLite.R\"); biocLite(); biocLite(\"QDNAseq\"")"</action>
					-->
					
					<!--
					<package>http://path/to/R.methodsS3_1.6.1.tar.gz</package>
					<package>http://path/to/matrixStats_0.10.0.tar.gz</package>
					<package>http://path/to/R.oo_1.18.0.tar.gz</package>
					<package>http://path/to/R.utils_1.32.4.tar.gz</package>
					<package>http://path/to/BiocGenerics_0.10.0.tar.gz</package>
					<package>http://path/to/Biobase_2.24.0.tar.gz</package>
					<package>http://path/to/limma_3.20.5.tar.gz</package>
					<package>http://path/to/marray_1.42.0.tar.gz</package>
					<package>http://path/to/CGHbase_1.24.0.tar.gz</package>
					<package>http://path/to/impute_1.38.1.tar.gz</package>
					<package>http://path/to/DNAcopy_1.38.1.tar.gz</package>
					<package>http://path/to/snow_0.3-13.tar.gz</package>
					<package>http://path/to/snowfall_1.84-6.tar.gz</package>
					<package>http://path/to/CGHcall_2.26.0.tar.gz</package>
					<package>http://path/to/IRanges_1.22.9.tar.gz</package>
					<package>http://path/to/GenomeInfoDb_1.0.2.tar.gz</package>
					<package>http://path/to/XVector_0.4.0.tar.gz</package>
					<package>http://path/to/GenomicRanges_1.16.3.tar.gz</package>
					<package>http://path/to/zlibbioc_1.10.0.tar.gz</package>
					<package>http://path/to/Biostrings_2.32.0.tar.gz</package>
					<package>http://path/to/bitops_1.0-6.tar.gz</package>
					<package>http://path/to/Rsamtools_1.16.1.tar.gz</package>
					<package>http://path/to/QDNAseq_1.0.5.tar.gz</package>
					-->
					<!-- HERE all the packages hosted at bitbucket -->
					<!-- currently breaks at DNAcopy -->
					
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.methodsS3_1.6.1.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/matrixStats_0.10.0.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.oo_1.18.0.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/R.utils_1.32.4.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/BiocGenerics_0.10.0.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Biobase_2.24.0.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/limma_3.20.5.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/marray_1.42.0.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/CGHbase_1.24.0.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/impute_1.38.1.tar.gz</package>
					
					
					<!--
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/DNAcopy_1.38.1.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/snow_0.3-13.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/snowfall_1.84-6.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/CGHcall_2.26.0.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/IRanges_1.22.9.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/GenomeInfoDb_1.0.2.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/XVector_0.4.0.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/GenomicRanges_1.16.4.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/zlibbioc_1.10.0.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Biostrings_2.32.1.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/bitops_1.0-6.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/Rsamtools_1.16.1.tar.gz</package>
					<package>https://bitbucket.org/stef_van_lieshout/tmp/downloads/QDNAseq_1.0.5.tar.gz</package>
					-->

				</action>
				<action type="shell_command">echo "[DEBUG] ...done with install actions"</action>
			</actions>
		</install>
		<readme>
			Prepares R Bioconductor package "QDNAseq" and all of its dependencies.
		</readme>
	</package>
</tool_dependency>