Mercurial > repos > iuc > package_hmmer3_1b1

annotate tool_dependencies.xml @ 0:3c63f4328bef draft

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 4164b44c651bcbdac6637eccce61b2a802c9b569
author iuc
date Tue, 12 May 2015 15:04:12 -0400
parents
children 9b9efd1ae42b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
2 <tool_dependency>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
4 <install version="1.0">
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
5 <actions>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
7 <action type="autoconf" />
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
9 <action type="make_install" />
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
10 <action type="set_environment">
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
11 <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
12 <environment_variable name="HMMER31_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
13 <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
14 <environment_variable name="CPLUS_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
15 </action>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
16 </actions>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
17 </install>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
18 <readme>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
19 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
iuc
parents:
diff changeset
20 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
iuc
parents:
diff changeset
21 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
iuc
parents:
diff changeset
22
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
23 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
iuc
parents:
diff changeset
24 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
iuc
parents:
diff changeset
25 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
iuc
parents:
diff changeset
26 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
iuc
parents:
diff changeset
27 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
iuc
parents:
diff changeset
28 as fast as BLAST.
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
29
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
30 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
iuc
parents:
diff changeset
31 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
iuc
parents:
diff changeset
32 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
iuc
parents:
diff changeset
33 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
iuc
parents:
diff changeset
34 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
iuc
parents:
diff changeset
35
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
36 http://hmmer.janelia.org/
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
37
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
38 </readme>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
39 </package>
3c63f4328bef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_hmmer3_1b1 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
40 </tool_dependency>