Mercurial > repos > iracooke > spectrast

annotate README.rst @ 12:f6fd2798879a 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/tree/master/spectrast commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:41:43 -0400
parents e6fada5ebec4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
1 SpectraST
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
2 =========
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
3
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
4 Galaxy wrappers for SpectraST
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
5
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
6 These wrappers are experimental. The plan is to divide SpectraST into 3 tools, create, filter and search, each with its own wrapper
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
7
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
8 Requirements
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
9 ------------
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
10
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
11 This package uses protk_ and the trans_proteomic_pipeline_ which need to be present in order for the tool to work.
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
12
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
13 .. _protk: https://github.com/iracooke/protk
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
14 .. _trans_proteomic_pipeline: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
15
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
16 There are two ways you can satify these dependencies (choose one):
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
17
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
18 1. **Manual Install:** Details on how to install protk_ and the trans_proteomic_pipeline_ manually are available here_.
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
19
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
20 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.
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
21
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
22 .. _docker: https://www.docker.com/
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
23 .. _here: https://github.com/iracooke/protk/#galaxy-integration
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
24 .. _container: https://wiki.galaxyproject.org/Admin/Tools/Docker
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
25 __ container_
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
26
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
27
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
28 Further Info
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
29 ------------
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
30
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
31 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`__
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
32
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
33 .. _github: https://github.com/iracooke/protk-galaxytools
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
34 .. _issue: https://github.com/iracooke/protk-galaxytools/issues
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
35 __ issue_
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
36
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
37 Please visit the SpectraST_ website for details of the SpectraST tool itself
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
38
e6fada5ebec4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/spectrast commit ab3789a6bc1491ab98f43d30dfddcca4f41b8334
iracooke
parents:
diff changeset
39 .. _SpectraST: http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST