Mercurial > repos > mingchen0919 > rmarkdown_mirdeep2
annotate mirdeep2.Rmd @ 1:75e53be98c51 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
author | mingchen0919 |
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date | Tue, 08 Aug 2017 13:23:44 -0400 |
parents | 963905bcb754 |
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rev | line source |
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963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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1 --- |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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2 title: 'Mirdeep2' |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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3 output: |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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4 html_document: |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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5 number_sections: true |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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6 toc: true |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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7 theme: cosmo |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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8 highlight: tango |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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9 --- |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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10 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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12 knitr::opts_chunk$set( |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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13 echo = ECHO |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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14 ) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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15 ``` |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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16 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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17 # Job command line |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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18 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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19 ```{r 'build PATH', echo=FALSE} |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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20 # set PATH environment. |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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21 PATH = system('pwd', intern = TRUE) %>% |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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22 (function(x) { |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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23 paste0('/home/galaxy/mirdeep2/bin:', x) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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24 }) %>% |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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25 (function(x) { |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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26 paste0('/home/galaxy/mirdeep2_patch:', x) |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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27 }) %>% |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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28 paste0(':$PATH') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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29 ``` |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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30 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
changeset
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31 ## Build job command line. |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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32 |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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33 ```{r 'build command line'} |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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34 # change directory to OUTPUT DIR |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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35 command_line = paste0('cd OUTPUT_DIR &&') %>% |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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36 # PATH and other environment variables |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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37 paste0('export PATH=', PATH, ' && ') %>% |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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38 (function(x) { |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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39 paste0(x, 'export PERL_MB_OPT="--install_base /home/galaxy/perl5" && |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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40 export PERL_MM_OPT="INSTALL_BASE=/home/galaxy/perl5" && |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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41 export PERL5LIB=/home/galaxy/mirdeep2/lib/perl5 && ') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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42 }) %>% |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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43 # link collapsed reads and reads mapping files |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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44 (function(x) { |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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45 paste0(x, 'ln -s COLLAPSED_READS reads_collapsed.fa && ') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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46 }) %>% |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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47 (function(x) { |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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48 paste0(x, 'ln -s READS_MAPPING reads_collapsed_vs_genome.arf && ') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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49 }) %>% |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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50 paste0(' miRDeep2.pl ') %>% |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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51 # collapsed reads |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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52 (function(x) { |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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53 paste0(x, ' reads_collapsed.fa ') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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54 }) %>% |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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55 # reference genome |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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56 (function(x) { |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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57 paste0(x, ' REFERENCE_GENOME ') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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58 }) %>% |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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59 # reads mapping |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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60 (function(x) { |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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61 paste0(x, ' reads_collapsed_vs_genome.arf ') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff
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62 }) %>% |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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63 # mature miRNA for this species |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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64 (function(x) { |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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65 if('SPECIES_MATURE_MIRNA' == 'None') { |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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66 paste0(x, tolower('SPECIES_MATURE_MIRNA'), ' ') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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67 } else { |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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68 paste0(x, ' SPECIES_MATURE_MIRNA ') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
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69 } |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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70 }) %>% |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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71 # mature miRNA from related species |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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72 (function(x) { |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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73 if('SPECIES_RELATED_MATURE_MIRNA' == 'None') { |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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74 paste0(x, tolower('SPECIES_RELATED_MATURE_MIRNA'), ' ') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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75 } else { |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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76 paste0(x, 'SPECIES_RELATED_MATURE_MIRNA ') |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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77 } |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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78 }) %>% |
963905bcb754
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
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79 # precursor sequences |
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80 (function(x) { |
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81 if('PRECURSOR_SEQUENCES' == 'None') { |
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82 paste0(x, tolower('PRECURSOR_SEQUENCES'), ' ') |
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83 } else { |
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84 paste0(x, 'PRECURSOR_SEQUENCES ') |
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85 } |
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86 }) %>% |
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87 # min read stack height |
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88 (function(x) { |
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89 ifelse('MIN_READ_STACK_HEIGHT' == 'TRUE', x, paste0(x, ' -a MIN_READ_STACK_HEIGHT ')) |
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90 }) %>% |
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91 # min score cutoff |
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92 (function(x) { |
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93 paste0(x, '-b MIN_SCORE_CUTOFF ') |
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94 }) %>% |
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95 # disable randfold analysis |
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96 (function(x) { |
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97 ifelse(RANDFOLD_ANALYSIS, paste0(x, '-c '), x) |
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98 }) %>% |
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99 # max precursors number |
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100 (function(x) { |
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101 paste0(x, ' -g MAX_PRECURSOR_NUMBER ') |
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102 }) %>% |
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103 # species |
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104 (function(x) { |
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105 ifelse('SPECIES' == 'all', x, paste0(x, ' -t SPECIES ')) |
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106 }) %>% |
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107 # switch |
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108 (function(x) { |
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109 ifelse(SWITCH, x, paste0(x, ' -P ')) |
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110 }) %>% |
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111 # write stdout to reprot.log |
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112 (function(x) { |
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113 paste0(x, ' >report.log 2>&1 ') |
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114 }) |
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115 |
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116 command_line |
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117 |
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118 ## run job |
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119 system(command_line) |
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120 ``` |
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121 |
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122 ## Results |
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123 |
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124 ```{r echo=TRUE} |
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125 system('cp OUTPUT_DIR/result*.html result.html') |
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126 system('cp OUTPUT_DIR/result*.csv result.csv') |
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127 system('cp OUTPUT_DIR/report.log report.log') |
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128 system('mv OUTPUT_DIR/pdfs_* OUTPUT_DIR/pdfs') |
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129 |
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130 ## check if OUTPUT DIR has results that we want. |
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131 system('ls OUTPUT_DIR', intern = TRUE) |
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132 ``` |
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133 |
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134 ### PDF files |
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135 |
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136 ```{r echo=TRUE} |
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137 pdf_report_list = list() |
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138 pdf_files = list.files('OUTPUT_DIR/pdfs', pattern = '.*pdf') |
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139 pdf_files |
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140 for (i in pdf_files) { |
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141 # note that the root directory is OUTPUT_DIR, all the file links should be a relative path to the root directory! |
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142 pdf_report_list[[i]] = tags$li(tags$a(href=paste0('pdfs/', i), i)) |
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143 } |
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144 tags$ul(pdf_report_list) |
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145 ``` |
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146 |