Mercurial > repos > fgiacomoni > massbank_ws_searchspectrum

annotate README.md @ 0:023c380900ef draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Init repository with last massbank_ws_searchspectrum master version
author fgiacomoni
date Wed, 19 Apr 2017 11:31:58 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
1 MassBank spectrum searches - Search by pseudo-spectra on a High Quality Mass Spectral Database.
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
2 ===============================================================================================
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
3
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
4 [![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io) [![Build Status](https://travis-ci.org/workflow4metabolomics/wrapper-bank-massbank-spectrum_search.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/wrapper-bank-massbank-spectrum_search)
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
5
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
6 Our project
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
7 -----------
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
8 The [Workflow4Metabolomics](http://workflow4metabolomics.org), W4M in short, is a French infrastructure offering software tool processing, analyzing and annotating metabolomics data. It is based on the Galaxy platform.
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
9
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
10
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
11 MassBank spectrum searches - Search by pseudo-spectra on a High Quality Mass Spectral Database.
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
12 -----------------------------------------------------------------------------------------------
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
13
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
14 Tool using the MassBank API Spectrum Search.
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
15
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
16
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
17 Galaxy
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
18 ------
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
19 Galaxy is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
20
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
21 Homepage: [https://galaxyproject.org/](https://galaxyproject.org/)
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
22
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
23
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
24 Dependencies using Conda
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
25 ------------------------
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
26 [![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io)
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
27
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
28
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
29 [Conda](http://conda.pydata.org/) is package manager that among many other things can be used to manage Python packages.
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
30
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
31 ```
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
32 #To install miniconda2
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
33 #http://conda.pydata.org/miniconda.html
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
34 #To install the tool dependencies using conda:
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
35 conda install perl-lwp-simple perl-lwp-useragent perl-uri-url perl-soap-lite perl-list-moreutils perl-text-csv perl perl-html-template
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
36 #To set an environment:
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
37 conda create -n wrapper-bank-massbank-spectrum_search perl-soap-lite perl-list-moreutils perl-json perl-html-template`
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
38 #To activate the environment:
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
39 . activate wrapper-bank-massbank-spectrum_search
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
40 ```
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
41
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
42
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
43 Travis
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
44 ------
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
45 [![Build Status](https://travis-ci.org/workflow4metabolomics/wrapper-bank-massbank-spectrum_search.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/wrapper-bank-massbank-spectrum_search)
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
46
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
47 Test and Deploy with Confidence. Easily sync your GitHub projects with Travis CI and you'll be testing your code in minutes!
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
48
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
49 Historic contributors
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
50 ---------------------
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
51 - Franck Giacomoni @fgiacomoni - [French Metabolomics and Fluxomics Infrastructure (MetaboHUB)](http://www.metabohub.fr/en) - [La plateforme "Exploration du Métabolisme" (PFEM, Clermont-Ferrand)](http://www6.clermont.inra.fr/plateforme_exploration_metabolisme)
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
52 - Marion Landi - [LIFEGRID grant](http://www.lifegrid.fr/fr/home/le-pra-lifegrid.html) - [La plateforme "Exploration du Métabolisme" (PFEM, Clermont-Ferrand)](http://www6.clermont.inra.fr/plateforme_exploration_metabolisme)
023c380900ef Init repository with last massbank_ws_searchspectrum master version
fgiacomoni
parents:
diff changeset
53 - Yann Guitton @yguitton - [LABERCA - Laboratory of Food Contaminants and Residue Analysis](http://www.laberca.org/) - Ecole Nationale Vétérinaire, Agroalimentaire et de l'Alimentation Nantes-Atlantique - France