Mercurial > repos > iuc > package_hmmer_3_1b1

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
author iuc
date Thu, 01 Oct 2015 11:13:06 -0400
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e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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1 <?xml version="1.0"?>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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2 <tool_dependency>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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3 <package name="hmmer" version="3.1b1">
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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4 <install version="1.0">
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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5 <actions>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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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>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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7 <action type="autoconf" />
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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8 <action type="change_directory">easel/miniapps/</action>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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9 <action type="make_install" />
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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10 <action type="set_environment">
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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11 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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12 <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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13 <environment_variable name="CPLUS_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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15 </action>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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16 </actions>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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17 </install>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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18 <readme>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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19 HMMER is used for searching sequence databases for homologs of protein
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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20 sequences, and for making protein sequence alignments. It implements methods
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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21 using probabilistic models called profile hidden Markov models (profile HMMs).
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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22
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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23 Compared to BLAST, FASTA, and other sequence alignment and database search
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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24 tools based on older scoring methodology, HMMER aims to be significantly more
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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25 accurate and more able to detect remote homologs because of the strength of its
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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26 underlying mathematical models. In the past, this strength came at significant
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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27 computational expense, but in the new HMMER3 project, HMMER is now essentially
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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28 as fast as BLAST.
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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29
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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30 As part of this evolution in the HMMER software, we are committed to making the
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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31 software available to as many scientists as possible. Earlier releases of HMMER
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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32 were restricted to command line use. To make the software more accessible to
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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33 the wide scientific community, we now provide servers that allow sequence
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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34 searches to be performed interactively via the Web.
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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35
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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36 http://hmmer.janelia.org/
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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37 </readme>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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38 </package>
e49dc46333e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer_3_1b1 commit 261c6a4ae771a24a27a23cd808a4ae6e5248939b
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39 </tool_dependency>