Mercurial > repos > mingchen0919 > rmarkdown_mirdeep2
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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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--- 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) ```