Mercurial > repos > iracooke > omssa

annotate README.rst @ 25:ea9ae5b25ce1 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/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:31:23 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
25
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
1 OMSSA
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
2 =====
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
3
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
4 Galaxy wrapper for the OMSSA tandem ms search tool
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
5
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
6 Requirements
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
7 ------------
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
8
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
9 This package uses protk_, omssa_ and blast_ which need to be present in order for the tool to work.
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
10
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
11 .. _protk: https://github.com/iracooke/protk
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
12 .. _omssa: http://www.ncbi.nlm.nih.gov/pubmed/15473683
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
13 .. _blast: https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
14
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
15
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
16 When installing this package, if you instruct galaxy to install dependencies it will automatically install blast_ but installation of protk_ and omssa_ may require additional steps (see below).
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
17
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
18 There are two ways you can satify these dependencies (choose one):
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
19
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
20 1. **Manual Install:** Details on how to install protk_ and omssa_ manually are available here_.
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
21
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
22 2. **Use Docker:** These tools are designed to run inside a docker_ container. If your galaxy supports `running tools within a docker container`__ you don't need to worry about dependencies. Simply install and things should just work. The docker container itself is versioned and new versions of this tool will automatically download an update to the container if needed.
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
23
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
24 .. _docker: https://www.docker.com/
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
25 .. _here: https://github.com/iracooke/protk/#galaxy-integration
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
26 .. _container: https://wiki.galaxyproject.org/Admin/Tools/Docker
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
27 __ container_
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
28
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
29
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
30 Further Info
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
31 ------------
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
32
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
33 The source code for this tool and other protk galaxy tools is on github_. Please visit the github page to contribute to the project or to `report an issue`__
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
34
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
35 .. _github: https://github.com/iracooke/protk-galaxytools
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
36 .. _issue: https://github.com/iracooke/protk-galaxytools/issues
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
37 __ issue_
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
38
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
39 Unfortunately the omssa_ search tool itself is `no longer actively developed`__ but it remains a useful tool. This wrapper uses the last released omssa_ binary.
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
40
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
41 .. _developed: http://pubchem.ncbi.nlm.nih.gov/omssa/
ea9ae5b25ce1 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
42 __ developed_