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Add PATH prepending.
author iuc
date Thu, 01 Oct 2015 11:08:19 -0400
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3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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1 <?xml version="1.0"?>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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2 <tool_dependency>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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3 <package name="hmmer3_1b1" version="3.1b1">
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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4 <install version="1.0">
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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5 <actions>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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6 <action type="download_by_url">ftp://selab.janelia.org/pub/software/hmmer3/3.1b1/hmmer-3.1b1.tar.gz</action>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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7 <action type="autoconf" />
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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8 <action type="change_directory">easel/miniapps/</action>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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9 <action type="make_install" />
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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10 <action type="set_environment">
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11 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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12 <environment_variable name="HMMER31_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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13 <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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14 <environment_variable name="CPLUS_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable>
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9b9efd1ae42b Add PATH prepending.
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15 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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16 </action>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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17 </actions>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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18 </install>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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19 <readme>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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20 HMMER is used for searching sequence databases for homologs of protein
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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21 sequences, and for making protein sequence alignments. It implements methods
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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22 using probabilistic models called profile hidden Markov models (profile HMMs).
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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23
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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24 Compared to BLAST, FASTA, and other sequence alignment and database search
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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25 tools based on older scoring methodology, HMMER aims to be significantly more
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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26 accurate and more able to detect remote homologs because of the strength of its
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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27 underlying mathematical models. In the past, this strength came at significant
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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28 computational expense, but in the new HMMER3 project, HMMER is now essentially
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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29 as fast as BLAST.
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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30
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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31 As part of this evolution in the HMMER software, we are committed to making the
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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32 software available to as many scientists as possible. Earlier releases of HMMER
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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33 were restricted to command line use. To make the software more accessible to
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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34 the wide scientific community, we now provide servers that allow sequence
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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35 searches to be performed interactively via the Web.
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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36
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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37 http://hmmer.janelia.org/
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38 </readme>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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39 </package>
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40 </tool_dependency>