diff interproscan.Rmd @ 1:035457a30aea draft

update

--- a/interproscan.Rmd	Tue Apr 03 14:30:53 2018 -0400
+++ b/interproscan.Rmd	Tue Apr 03 15:02:39 2018 -0400
@@ -1,12 +1,6 @@
 ---
-title: 'HTML report title'
-output:
-    html_document:
-      number_sections: true
-      toc: true
-      theme: cosmo
-      highlight: tango
-      code_folding: hide
+title: 'InterProScan analysis'
+output: html_document
 ---
 
 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
@@ -17,7 +11,7 @@
 ```
 
 
-# Run InterProScan
+# InterProScan job script
 
 ```{bash echo=FALSE}
 #---- build job script ----
@@ -31,21 +25,22 @@
   --pathways ${X_F} \\
   --tempdir ${X_D}/temp_dir \\
   --output-dir ${X_D}/output_dir > /dev/null 2>&1
+  
 EOL
 
 # remove empty input lines
-grep -v 'None' |\
-  -v 'NO_ARGUMENT_NO' |\
-  sed s/NO_ARGUMENT_YES//g' > job-script.sh
+grep -v 'None' temp.sh |\
+  grep -v 'NO_ARGUMENT_NO' |\
+  sed 's/NO_ARGUMENT_YES//g' > job-script.sh
   
 # copy job-script.sh to OUTPUT_DIR
-cp job-script.sh ${OUTPUT_DIR}
+cp job-script.sh ${X_d}/job-script.sh
 ```
 
 ```{r echo=FALSE}
 # display job script
 job_script = paste0(opt$X_d, '/job-script.sh')
-tags$code(tags$pre(readChar(skewer_sh, file.info(job_script)$size )))
+tags$code(tags$pre(readChar(job_script, file.info(job_script)$size )))
 ```
 
 ```{bash echo=FALSE}
@@ -60,11 +55,11 @@
 
 cat('##All output files')
 cat('\n\n')
-all_files = list.files(path = Sys.getenv('REPORT_FILES_PATH'), 
+all_files = list.files(path = OUTPUT_DIR, 
                        full.names = TRUE, 
                        recursive = TRUE)
 
-for (f in sub(Sys.getenv('REPORT_FILES_PATH'), '.', all_files) ) {
+for (f in sub(OUTPUT_DIR, '.', all_files) ) {
   cat('* [', f, '](', f, ')\n')
 }
 cat('\n')