aurora_bdss_sra: rmarkdown_report.Rmd annotate

annotate rmarkdown_report.Rmd @ 10:4b73dbd97a0e draft default tip

planemo upload for repository https://github.com/feltus/BDSS

author	mingchen0919
date	Tue, 12 Jun 2018 12:30:21 -0400
parents	39831b70aabb
children

rev	line source
0 759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	1 ---
9 39831b70aabb planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 8 diff changeset	2 title: 'BDSS download from SRA'
0 759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	3 output:
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	4 html_document:
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	5 highlight: pygments
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	6 ---
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	7
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	8 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	9 knitr::opts_chunk$set(error = TRUE, echo = FALSE)
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	10 ```
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	11
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	12 ```{css echo=FALSE}
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	13 # code chunks scrollable
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	14 pre code, pre, code {
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	15 white-space: pre !important;
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	16 overflow-x: scroll !important;
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	17 word-break: keep-all !important;
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	18 word-wrap: initial !important;
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	19 }
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	20 ```
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	21
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	22
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	23 ```{r, echo=FALSE}
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	24 # to make the css theme to work, <link></link> tags cannot be added directly
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	25 # as <script></script> tags as below.
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	26 # it has to be added using a code chunk with the htmltool functions!!!
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	27 css_link = tags$link()
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	28 css_link$attribs = list(rel="stylesheet", href="vakata-jstree-3.3.5/dist/themes/default/style.min.css")
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	29 css_link
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	30 ```
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	31
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	32 ```{r, eval=FALSE, echo=FALSE}
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	33 # this code chunk is purely for adding comments
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	34 # below is to add jQuery and jstree javascripts
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	35 ```
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	36 <script src="https://code.jquery.com/jquery-3.3.1.min.js"></script>
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	37 <script src="vakata-jstree-3.3.5/dist/jstree.min.js"></script>
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	38
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	39 ---
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	40 # javascript code below is to build the file tree interface
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	41 # see this for how to implement opening hyperlink: https://stackoverflow.com/questions/18611317/how-to-get-i-get-leaf-nodes-in-jstree-to-open-their-hyperlink-when-clicked-when
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	42 ---
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	43 <script>
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	44 $(function () {
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	45 // create an instance when the DOM is ready
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	46 $('#jstree').jstree().bind("select_node.jstree", function (e, data) {
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	47 window.open( data.node.a_attr.href, data.node.a_attr.target )
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	48 });
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	49 });
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	50 </script>
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	51
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	52 ---
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	53 # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	54 ---
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	55
9 39831b70aabb planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 8 diff changeset	56 # Job script
0 759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	57
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	58 ```{r echo=FALSE}
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	59 # create two directories to store downloaded data
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	60 se_dir = paste0(Sys.getenv('JOB_WORKING_DIR'), '/se_read_files_dir')
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	61 pe_dir = paste0(Sys.getenv('JOB_WORKING_DIR'), '/pe_read_files_dir')
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	62 ```
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	63
1 bd236d81187b planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 0 diff changeset	64 ```{r 'download and extract reads', echo=-1}
bd236d81187b planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 0 diff changeset	65 Sys.setenv(PATH=paste0('/main/sites/galaxy/galaxy/tools/_conda/bin:', Sys.getenv('PATH')))
bd236d81187b planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 0 diff changeset	66
0 759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	67 # download and extract reads (single end)
3 cf17a4199861 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 1 diff changeset	68 sra_ids_se = strsplit(gsub(',', ' ', opt$X_s), ' ')[[1]]
0 759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	69 sra_ids_se = sra_ids_se[sra_ids_se != '']
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	70 # loop through SRA accessions to download and extract reads.
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	71 for(id in sra_ids_se) {
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	72 # build URL from SRA id
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	73 url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	74 substr(id, 1, 3), '/',
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	75 substr(id, 1, 6), '/', id, '/', id, '.sra')
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	76 # download sra file with bdss
4 c062782a7534 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 3 diff changeset	77 bdss_command = paste0('bdss transfer -u ', url, '>> ${REPORT_FILES_PATH}/log.txt 2>&1')
0 759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	78 command_stdout = system(bdss_command, intern = TRUE)
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	79 # convert .sra to .fastq/.fasta
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	80 if(opt$X_f == 'fasta') {
5 a1dfadeb3b59 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 4 diff changeset	81 command = paste0('fastq-dump --fasta -O ', se_dir, ' ', id, '.sra')
0 759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	82 } else {
5 a1dfadeb3b59 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 4 diff changeset	83 command = paste0('fastq-dump -O ', se_dir, ' ', id, '.sra')
0 759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	84 }
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	85 command_stdout = system(command, intern = TRUE)
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	86 write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/fastq-dump.log.txt'), append = TRUE)
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	87 }
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	88
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	89 # download and extract reads (paired end)
3 cf17a4199861 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 1 diff changeset	90 sra_ids_pe = strsplit(gsub(',', ' ', opt$X_p), ' ')[[1]]
0 759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	91 sra_ids_pe = sra_ids_pe[sra_ids_pe != '']
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	92 # loop through SRA accessions to download and extract reads.
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	93 for(id in sra_ids_pe) {
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	94 # build URL from SRA id
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	95 url = paste0('ftp://ftp.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/',
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	96 substr(id, 1, 3), '/',
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	97 substr(id, 1, 6), '/', id, '/', id, '.sra')
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	98 # download sra file with bdss
4 c062782a7534 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 3 diff changeset	99 bdss_command = paste0('bdss transfer -u ', url, '>> ${REPORT_FILES_PATH}/log.txt 2>&1')
0 759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	100 command_stdout = system(bdss_command, intern = TRUE)
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	101 # convert .sra to .fastq/.fasta
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	102 if(opt$X_f == 'fasta') {
6 9dabaecf12ff planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 5 diff changeset	103 command = paste0('fastq-dump --fasta --split-files -O ', pe_dir, ' ', id, '.sra')
0 759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	104 } else {
6 9dabaecf12ff planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 5 diff changeset	105 command = paste0('fastq-dump --split-files -O ', pe_dir, ' ', id, '.sra')
0 759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	106 }
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	107 command_stdout = system(command, intern = TRUE)
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	108 write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/fastq-dump.log.txt'), append = TRUE)
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	109 }
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	110
10 4b73dbd97a0e planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 9 diff changeset	111 ```
4b73dbd97a0e planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 9 diff changeset	112
4b73dbd97a0e planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 9 diff changeset	113 ```{r echo=FALSE}
0 759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	114 # rename files for paired end reads
5 a1dfadeb3b59 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 4 diff changeset	115 old_files = list.files(path = pe_dir, full.names = TRUE)
0 759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	116 new_files = gsub('_1', '_forward', old_files)
759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	117 new_files = gsub('_2', '_reverse', new_files)
10 4b73dbd97a0e planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 9 diff changeset	118 res = file.rename(old_files, new_files)
0 759232961286 planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: diff changeset	119 ```
10 4b73dbd97a0e planemo upload for repository https://github.com/feltus/BDSS mingchen0919 parents: 9 diff changeset	120

Mercurial > repos > mingchen0919 > aurora_bdss_sra

annotate rmarkdown_report.Rmd @ 10:4b73dbd97a0e draft default tip