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1 ---
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1
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2 title: 'InterProScan analysis'
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3 output: html_document
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4 ---
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5
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6 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
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7 knitr::opts_chunk$set(
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8 echo = TRUE,
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9 error = TRUE
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10 )
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11 ```
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12
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13
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14 # InterProScan job script
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15
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16 ```{bash echo=FALSE}
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2
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17 # create two directorys: tempdir and output-dir
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18 mkdir -p ${X_d}/temp_dir
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19 mkdir -p ${X_d}/output_dir
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20
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21 #---- build job script ----
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22 cat >temp.sh <<EOL
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23 /opt/main/InterProScan/5.28-67.0/interproscan.sh \\
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24 -i ${X_A} \\
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25 -f ${X_B} \\
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26 --disable-precalc ${X_C} \\
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27 --iprlookup ${X_D} \\
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28 --goterms ${X_E} \\
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29 --pathways ${X_F} \\
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30 --tempdir ${X_d}/temp_dir \\
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31 --output-dir ${X_d}/output_dir > ${X_d}/interproscan.log.txt 2>&1
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32
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33 EOL
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34
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35 # remove empty input lines
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36 grep -v 'None' temp.sh |\
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37 grep -v 'NO_ARGUMENT_NO' |\
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38 sed 's/NO_ARGUMENT_YES//g' > job-script.sh
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39
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40 # copy job-script.sh to OUTPUT_DIR
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41 cp job-script.sh ${X_d}/job-script.sh
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42 ```
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43
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44 ```{r echo=FALSE}
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45 # display job script
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46 job_script = paste0(opt$X_d, '/job-script.sh')
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47 tags$code(tags$pre(readChar(job_script, file.info(job_script)$size )))
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48 ```
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49
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50 ```{bash echo=FALSE}
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51 #run job-script.sh
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52 sh job-script.sh
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53 ```
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54
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55
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56 ```{r, 'display output directory contents', results='asis', echo=FALSE}
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57 ## after the job is done, we list all files from the output directory.
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58 ## full relative path to the output directory needs to be displayed.
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59
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60 cat('##All output files')
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61 cat('\n\n')
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62 all_files = list.files(path = OUTPUT_DIR,
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63 full.names = TRUE,
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64 recursive = TRUE)
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65
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66 for (f in sub(OUTPUT_DIR, '.', all_files) ) {
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67 cat('* [', f, '](', f, ')\n')
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68 }
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69 cat('\n')
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70 ``` |
