Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

annotate bdss_client.Rmd @ 10:b7171118a078 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
author mingchen0919
date Wed, 11 Oct 2017 13:31:47 -0400
parents efb1938c3020
children bfc6133f3a2b
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efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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1 ---
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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2 title: 'Download with BDSS client'
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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3 output:
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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4 html_document:
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5 number_sections: true
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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6 toc: true
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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7 theme: cosmo
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8 highlight: tango
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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9 ---
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11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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12 knitr::opts_chunk$set(
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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13 echo = ECHO
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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14 )
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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15 ```
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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17 # Command line arguments
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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19 ```{r 'command line arguments'}
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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20 str(opt)
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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21 ```
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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23 # BDSS configuration file
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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25 First, we create a bdss configuration file `bdss.cfg` in the current directory.
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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27 ```{r}
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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28 system('echo "[metadata_repository]" > bdss.cfg')
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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29 system('echo url=http://bdss.bioinfo.wsu.edu/ >> bdss.cfg')
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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30 ```
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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32 # Download and extract reads
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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34 ```{r 'download and extract reads'}
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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35 # create a directory to store read files
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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36 dir.create('read_files_directory')
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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37 # download and extract reads
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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38 urls = strsplit(gsub(',', ' ', 'URLS'), ' ')[[1]]
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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39 urls = urls[urls != '']
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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40 # loop through SRA accessions to download and extract reads.
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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41 for(url in urls) {
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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42 bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url)
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43 system(bdss_command, intern = TRUE)
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44 }
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45 move_files_command = 'find . -type f -print0 | xargs -0 mv -t ./read_files_directory'
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46 system(move_files_command, intern = TRUE)
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47 ```
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49 * `fastq-dump` command
efb1938c3020 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
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50 ```{r}
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51 print(command)
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52 ```
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54 * `command line stdout`
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56 ```{r}
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57 system(command = command, intern = TRUE)
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58 ```
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