diff split_fasta.Rmd @ 2:38435c74e795 draft default tip

working version

--- a/split_fasta.Rmd	Mon Apr 09 13:32:55 2018 -0400
+++ b/split_fasta.Rmd	Mon Apr 09 14:20:42 2018 -0400
@@ -16,9 +16,9 @@
 
 # single-end.sh
 cat <<EOF >${X_d}/job-script.sh
-cd ${WORKING_DIR}/fasta_files && ${X_t}/split.pl \\
-  --input_file=${X_A} \\
-  --seqs_per_file=${X_B} \\  > ${X_d}/fasta_splitter-log.txt 2>&1
+cd ${WORKING_DIR}/fasta_files && \\
+  cp ${X_A} input.fasta && \\
+  ${X_t}/split.pl input.fasta ${X_B} > ${X_d}/fasta_splitter-log.txt 2>&1
 EOF
 ```
 
@@ -28,6 +28,12 @@
 sh ${X_d}/job-script.sh
 ```
 
+```{bash}
+# remove original input fasta
+rm ${WORKING_DIR}/fasta_files/input.fasta
+mv ${WORKING_DIR}/fasta_files/out ${X_d}/split-out.txt
+```
+
 ```{r, 'display output directory contents', results='asis', echo=FALSE}
 ## after the job is done, we list all files from the output directory.
 ## full relative path to the output directory needs to be displayed.