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comparison edge_pro.xml @ 3:ddcbf8732706 draft

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Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation.
author crs4
date Mon, 19 Jan 2015 12:48:51 -0500
parents bad8a51514dd
children d5464c9e1723
comparison
equal deleted inserted replaced
2:bad8a51514dd 3:ddcbf8732706
110 110
111 All 3 types of files (FASTA reference genome, PTT and RNT) must have the same order of chromosomes/plasmids (e.g. if chr1 is before chr2 in genome.fasta file, then chr1 must be before chr2 in ptt and rnt files as well). If there is no PTT or RNT file for one of chromosomes/plasmids, place this chromosome/plasmid at the end of the file. 111 All 3 types of files (FASTA reference genome, PTT and RNT) must have the same order of chromosomes/plasmids (e.g. if chr1 is before chr2 in genome.fasta file, then chr1 must be before chr2 in ptt and rnt files as well). If there is no PTT or RNT file for one of chromosomes/plasmids, place this chromosome/plasmid at the end of the file.
112 112
113 **License and citation** 113 **License and citation**
114 114
115 This Galaxy tool is Copyright © 2012-2013 `CRS4 Srl.`_ and is released under the `MIT license`_. 115 This Galaxy tool is Copyright © 2012-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
116 116
117 .. _CRS4 Srl.: http://www.crs4.it/ 117 .. _CRS4 Srl.: http://www.crs4.it/
118 .. _MIT license: http://opensource.org/licenses/MIT 118 .. _MIT license: http://opensource.org/licenses/MIT
119 119
120 If you use this tool in Galaxy, please cite |Cuccuru2013|_. 120 You can use this tool only if you agree to the license terms of: `EDGE-pro`_.
121
122 .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted
123 .. _Cuccuru2013: http://orione.crs4.it/
124
125 This tool uses `EDGE-pro`_, which is licensed separately. Please cite |Magoc2013|_.
126 121
127 .. _EDGE-pro: http://ccb.jhu.edu/software/EDGE-pro/ 122 .. _EDGE-pro: http://ccb.jhu.edu/software/EDGE-pro/
123
124 If you use this tool, please cite:
125
126 - |Cuccuru2014|_
127 - |Magoc2013|_.
128
129 .. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
130 .. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
128 .. |Magoc2013| replace:: Magoc, T., Wood, D., Salzberg, S. L. (2013) EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes. *Evol. Bioinform.* 2013:9, 127-136 131 .. |Magoc2013| replace:: Magoc, T., Wood, D., Salzberg, S. L. (2013) EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes. *Evol. Bioinform.* 2013:9, 127-136
129 .. _Magoc2013: http://www.la-press.com/edge-pro-estimated-degree-of-gene-expression-in-prokaryotic-genomes-article-a3586 132 .. _Magoc2013: http://www.la-press.com/edge-pro-estimated-degree-of-gene-expression-in-prokaryotic-genomes-article-a3586
130 </help> 133 </help>
131 </tool> 134 </tool>