Mercurial > repos > iuc > package_hmmer_3_1b1
comparison tool_dependencies.xml @ 0:e49dc46333e2 draft
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 |
| parents | |
| children | ee143f73fee0 |
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| -1:000000000000 | 0:e49dc46333e2 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="hmmer" version="3.1b1"> | |
| 4 <install version="1.0"> | |
| 5 <actions> | |
| 6 <action type="download_by_url">ftp://selab.janelia.org/pub/software/hmmer3/3.1b1/hmmer-3.1b1.tar.gz</action> | |
| 7 <action type="autoconf" /> | |
| 8 <action type="change_directory">easel/miniapps/</action> | |
| 9 <action type="make_install" /> | |
| 10 <action type="set_environment"> | |
| 11 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable> | |
| 12 <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable> | |
| 13 <environment_variable name="CPLUS_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable> | |
| 14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
| 15 </action> | |
| 16 </actions> | |
| 17 </install> | |
| 18 <readme> | |
| 19 HMMER is used for searching sequence databases for homologs of protein | |
| 20 sequences, and for making protein sequence alignments. It implements methods | |
| 21 using probabilistic models called profile hidden Markov models (profile HMMs). | |
| 22 | |
| 23 Compared to BLAST, FASTA, and other sequence alignment and database search | |
| 24 tools based on older scoring methodology, HMMER aims to be significantly more | |
| 25 accurate and more able to detect remote homologs because of the strength of its | |
| 26 underlying mathematical models. In the past, this strength came at significant | |
| 27 computational expense, but in the new HMMER3 project, HMMER is now essentially | |
| 28 as fast as BLAST. | |
| 29 | |
| 30 As part of this evolution in the HMMER software, we are committed to making the | |
| 31 software available to as many scientists as possible. Earlier releases of HMMER | |
| 32 were restricted to command line use. To make the software more accessible to | |
| 33 the wide scientific community, we now provide servers that allow sequence | |
| 34 searches to be performed interactively via the Web. | |
| 35 | |
| 36 http://hmmer.janelia.org/ | |
| 37 </readme> | |
| 38 </package> | |
| 39 </tool_dependency> |