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comparison README.txt @ 9:f3462128e87c

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Minor alterations to the galaxy interface with some better examples and error messages added.
author davidmurphy
date Mon, 30 Jan 2012 08:17:57 -0500
parents 5149eb3a89c2
children
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8:5149eb3a89c2 9:f3462128e87c
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2 CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence 2 CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence
3 logos from biological sequence alignments. It can be run from the command line as a standalone webserver or as a CGI webapp. 3 logos from biological sequence alignments. It can be run on the command line,
4 as a standalone webserver or as a CGI webapp.
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6 For help on the command line interface run 7 For help on the command line interface run
7 ./codonlogo --help 8 ./codonlogo --help
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17 An example file of probabilities is included, examplepriorfile.txt 18 An example file of probabilities is included, examplepriorfile.txt
18 It can be used with the following command. 19 It can be used with the following command.
19 20
20 ./codonlogo --prior ./examples/Escherichiacoli.txt < cap.fa > logo.eps 21 ./codonlogo --prior examplepriorfile.txt < cap.fa > logo.eps
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23 examplepriorfile contains the frequencies for codons in human CDS regions. 24 examplepriorfile contains the frequencies for codons in human CDS regions.
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26 KNOWN ISSUES: 27 There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault.
27 28 This is not believed to be a problem with CodonLogo.
28 There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault or prevent codonlogos from being generated in anything other than eps format. 29 This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 or earlier of ghostscript.
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30 This is believed to be an issue with ghostscript and a bug report has been submitted to the ghostscript mailing list.
31 This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 of ghostscript or earlier .
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35 For converting files to a suitable format the following sites can be used: 31 For converting files to a suitable format the following sites can be used:
36 32
37 http://genome.nci.nih.gov/tools/reformat.html 33 http://genome.nci.nih.gov/tools/reformat.html
38 http://www-bimas.cit.nih.gov/molbio/readseq/ 34 http://www-bimas.cit.nih.gov/molbio/readseq/