Mercurial > repos > iuc > package_hmmer3_1b1

annotate tool_dependencies.xml @ 0:517f2c49e8e7 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
author iuc
date Tue, 12 May 2015 14:59:42 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
2 <tool_dependency>
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
3 <package name="hmmer3_1b1" version="3.1b1">
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
4 <install version="1.0">
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
5 <actions>
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
6 <action type="download_by_url">ftp://selab.janelia.org/pub/software/hmmer3/3.1b1/hmmer-3.1b1.tar.gz</action>
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
7 <action type="autoconf" />
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
8 <action type="change_directory">easel/miniapps/</action>
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
9 <action type="make_install" />
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
10 <action type="set_environment">
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
11 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
12 <environment_variable name="HMMER31_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
13 <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable>
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
14 <environment_variable name="CPLUS_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable>
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
15 </action>
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
16 </actions>
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
17 </install>
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
18 <readme>
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
19 HMMER is used for searching sequence databases for homologs of protein
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
20 sequences, and for making protein sequence alignments. It implements methods
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
21 using probabilistic models called profile hidden Markov models (profile HMMs).
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
22
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
23 Compared to BLAST, FASTA, and other sequence alignment and database search
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
24 tools based on older scoring methodology, HMMER aims to be significantly more
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
25 accurate and more able to detect remote homologs because of the strength of its
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
26 underlying mathematical models. In the past, this strength came at significant
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
27 computational expense, but in the new HMMER3 project, HMMER is now essentially
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
28 as fast as BLAST.
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
29
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
30 As part of this evolution in the HMMER software, we are committed to making the
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
31 software available to as many scientists as possible. Earlier releases of HMMER
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
32 were restricted to command line use. To make the software more accessible to
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
33 the wide scientific community, we now provide servers that allow sequence
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
34 searches to be performed interactively via the Web.
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
35
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
36 http://hmmer.janelia.org/
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
37
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
38 </readme>
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
39 </package>
517f2c49e8e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 649ac868f2e7d79f354882cb75bf5d1055b30907
iuc
parents:
diff changeset
40 </tool_dependency>