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

working version

1:ecf34bd52987

# build job-script
mkdir -p ${WORKING_DIR}/fasta_files

# 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
EOF
```

```{bash, 'run jobs', echo=FALSE}
# run job script, always use absolute path. 
# we want to run all jobs within the working path.
sh ${X_d}/job-script.sh
```

```{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.

2:38435c74e795

# build job-script
mkdir -p ${WORKING_DIR}/fasta_files

# single-end.sh
cat <<EOF >${X_d}/job-script.sh
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
```

```{bash, 'run jobs', echo=FALSE}
# run job script, always use absolute path. 
# we want to run all jobs within the working path.
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.