Mercurial > repos > peterjc > rxlr_venn_workflow

comparison README.rst @ 8:2dfe8b788fb6 draft

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Uploaded v0.0.1h, attempt to show image in README file
author peterjc
date Mon, 19 Aug 2013 13:22:30 -0400
parents 51aeb3d4799d
children d893133128d8
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7:51aeb3d4799d 8:2dfe8b788fb6
13 13
14 http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz 14 http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz
15 15
16 You can upload this directly into Galaxy via this URL. Galaxy will handle 16 You can upload this directly into Galaxy via this URL. Galaxy will handle
17 removing the gzip compression to give you the FASTA protein file which 17 removing the gzip compression to give you the FASTA protein file which
18 has 19,805 protein sequences. Of these, only 79 sequences pass all three 18 has 19,805 protein sequences. The expected results:
19 of the RXLR prediction tools. 19
20 * 89 RXLRs using Whisson et al. (2007)
21 * 124 RXLRs using Win et al. (2007)
22 * 162 RXLRs using Bhattacharjee et al. (006)
23
24 Of these, only 79 sequences pass all three of the RXLR prediction tools,
25 while 19643 have no RXLR matches at all.
26
27 .. image:: Phyca11_example_output.png
28 :height: 400px
29 :width: 400px
30 :alt: RXLR Venn diagram using Phytophthora capsici (Phyca11)
20 31
21 32
22 Citation 33 Citation
23 ======== 34 ========
24 35
84 95
85 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow 96 https://github.com/peterjc/picobio/tree/master/galaxy_workflows/rxlr_venn_workflow
86 97
87 To prepare the tar-ball for uploading to the Tool Shed, I use this: 98 To prepare the tar-ball for uploading to the Tool Shed, I use this:
88 99
89 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga 100 $ tar -cf rxlr_venn_workflow.tar.gz README.rst repository_dependencies.xml rxlr_venn_workflow.ga Phyca11_example_output.png
90 101
91 Check this, 102 Check this,
92 103
93 $ tar -tzf rxlr_venn_workflow.tar.gz 104 $ tar -tzf rxlr_venn_workflow.tar.gz
94 README.rst 105 README.rst
95 repository_dependencies.xml 106 repository_dependencies.xml
96 rxlr_venn_workflow.ga 107 rxlr_venn_workflow.ga
108 Phyca11_example_output.png