Mercurial > repos > mingchen0919 > rmarkdown_mirdeep2
diff mirdeep2.Rmd @ 0:963905bcb754 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 13:14:41 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mirdeep2.Rmd Tue Aug 08 13:14:41 2017 -0400 @@ -0,0 +1,146 @@ +--- +title: 'Mirdeep2' +output: + html_document: + number_sections: true + toc: true + theme: cosmo + highlight: tango +--- + +```{r setup, include=FALSE, warning=FALSE, message=FALSE} +knitr::opts_chunk$set( + echo = ECHO +) +``` + +# Job command line + +```{r 'build PATH', echo=FALSE} +# set PATH environment. +PATH = system('pwd', intern = TRUE) %>% + (function(x) { + paste0('/home/galaxy/mirdeep2/bin:', x) + }) %>% + (function(x) { + paste0('/home/galaxy/mirdeep2_patch:', x) + }) %>% + paste0(':$PATH') +``` + +## Build job command line. + +```{r 'build command line'} +# change directory to OUTPUT DIR +command_line = paste0('cd OUTPUT_DIR &&') %>% + # PATH and other environment variables + paste0('export PATH=', PATH, ' && ') %>% + (function(x) { + paste0(x, 'export PERL_MB_OPT="--install_base /home/galaxy/perl5" && + export PERL_MM_OPT="INSTALL_BASE=/home/galaxy/perl5" && + export PERL5LIB=/home/galaxy/mirdeep2/lib/perl5 && ') + }) %>% + # link collapsed reads and reads mapping files + (function(x) { + paste0(x, 'ln -s COLLAPSED_READS reads_collapsed.fa && ') + }) %>% + (function(x) { + paste0(x, 'ln -s READS_MAPPING reads_collapsed_vs_genome.arf && ') + }) %>% + paste0(' miRDeep2.pl ') %>% + # collapsed reads + (function(x) { + paste0(x, ' reads_collapsed.fa ') + }) %>% + # reference genome + (function(x) { + paste0(x, ' REFERENCE_GENOME ') + }) %>% + # reads mapping + (function(x) { + paste0(x, ' reads_collapsed_vs_genome.arf ') + }) %>% + # mature miRNA for this species + (function(x) { + if('SPECIES_MATURE_MIRNA' == 'None') { + paste0(x, tolower('SPECIES_MATURE_MIRNA'), ' ') + } else { + paste0(x, ' SPECIES_MATURE_MIRNA ') + } + }) %>% + # mature miRNA from related species + (function(x) { + if('SPECIES_RELATED_MATURE_MIRNA' == 'None') { + paste0(x, tolower('SPECIES_RELATED_MATURE_MIRNA'), ' ') + } else { + paste0(x, 'SPECIES_RELATED_MATURE_MIRNA ') + } + }) %>% + # precursor sequences + (function(x) { + if('PRECURSOR_SEQUENCES' == 'None') { + paste0(x, tolower('PRECURSOR_SEQUENCES'), ' ') + } else { + paste0(x, 'PRECURSOR_SEQUENCES ') + } + }) %>% + # min read stack height + (function(x) { + ifelse('MIN_READ_STACK_HEIGHT' == 'TRUE', x, paste0(x, ' -a MIN_READ_STACK_HEIGHT ')) + }) %>% + # min score cutoff + (function(x) { + paste0(x, '-b MIN_SCORE_CUTOFF ') + }) %>% + # disable randfold analysis + (function(x) { + ifelse(RANDFOLD_ANALYSIS, paste0(x, '-c '), x) + }) %>% + # max precursors number + (function(x) { + paste0(x, ' -g MAX_PRECURSOR_NUMBER ') + }) %>% + # species + (function(x) { + ifelse('SPECIES' == 'all', x, paste0(x, ' -t SPECIES ')) + }) %>% + # switch + (function(x) { + ifelse(SWITCH, x, paste0(x, ' -P ')) + }) %>% + # write stdout to reprot.log + (function(x) { + paste0(x, ' >report.log 2>&1 ') + }) + +command_line + +## run job +system(command_line) +``` + +## Results + +```{r echo=TRUE} +system('cp OUTPUT_DIR/result*.html result.html') +system('cp OUTPUT_DIR/result*.csv result.csv') +system('cp OUTPUT_DIR/report.log report.log') +system('mv OUTPUT_DIR/pdfs_* OUTPUT_DIR/pdfs') + +## check if OUTPUT DIR has results that we want. +system('ls OUTPUT_DIR', intern = TRUE) +``` + +### PDF files + +```{r echo=TRUE} +pdf_report_list = list() +pdf_files = list.files('OUTPUT_DIR/pdfs', pattern = '.*pdf') +pdf_files +for (i in pdf_files) { + # note that the root directory is OUTPUT_DIR, all the file links should be a relative path to the root directory! + pdf_report_list[[i]] = tags$li(tags$a(href=paste0('pdfs/', i), i)) +} +tags$ul(pdf_report_list) +``` +