Mercurial > repos > iuc > package_stacks_1_40

annotate tool_dependencies.xml @ 3:51d4ab2c4dcf draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
author iuc
date Sat, 25 Jun 2016 17:24:08 -0400
parents 95cffefc0dfe
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5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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1 <?xml version="1.0"?>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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2 <tool_dependency>
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3 <package name="samtools" version="0.1.19">
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51d4ab2c4dcf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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4 <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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5 </package>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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6 <package name="stacks" version="1.40">
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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7 <install version="1.0">
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8 <actions>
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9 <action sha256sum="bf2304ba4ec44991db327ea77eb0f8c58de6d665162abf72470f5cd9dfb71493" type="download_by_url">https://depot.galaxyproject.org/software/stacks/stacks_1.40_src_all.tar.gz</action>
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95cffefc0dfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit 6b38bb0f0d7e65b01680a4b56bf8a996c445e58f
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95cffefc0dfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit 6b38bb0f0d7e65b01680a4b56bf8a996c445e58f
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11 <action type="set_environment_for_install">
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51d4ab2c4dcf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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12 <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
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95cffefc0dfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit 6b38bb0f0d7e65b01680a4b56bf8a996c445e58f
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13 <package name="samtools" version="0.1.19" />
95cffefc0dfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit 6b38bb0f0d7e65b01680a4b56bf8a996c445e58f
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14 </repository>
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15 </action>
95cffefc0dfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit 6b38bb0f0d7e65b01680a4b56bf8a996c445e58f
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16
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17 <action type="shell_command">./configure --prefix=$INSTALL_DIR --enable-bam --with-bam-include-path=${BAM_INCLUDE} --with-bam-lib-path=${BAM_LIB_PATH}</action>
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5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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18 <action type="shell_command">make</action>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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19 <action type="shell_command">make install</action>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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20 <!-- create env.sh -->
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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21 <action type="set_environment">
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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22 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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23 <environment_variable action="set_to" name="STACKS_ROOT_DIR">$INSTALL_DIR/</environment_variable>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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24 </action>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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25 </actions>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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26 </install>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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27 <readme>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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28 This package installs STACKS from the sources available. Based on Cyril Monjeuad version
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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29 </readme>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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30 </package>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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31 </tool_dependency>