---
title: "MOX-HISAT2-genome-align"
author: "Sarah Tanja"
date: "`r format(Sys.time(), '%d %B, %Y')`" 
editor: visual
format:
  gfm: default
  html:
    df-print: paged
    toc: true
    smooth-scroll: true
    link-external-icon: true
    link-external-newwindow: true
    code-fold: show
    code-tools: true
    code-copy: true
    highlight-style: arrow
    code-overflow: wrap
    theme:
      light: sandstone
      dark: vapor
---

# Use cloud computing?

## Connect to Hyak-Mox

![](images/mox-hyak.png)

-   In a unix `Terminal` type "`ssh stanja@mox.hyak.uw.edu`"

-   Enter UW NetID Password

-   Use Duo Mobile App to Push login approval

## Make a directory

Once logged into mox, navigate to `/gscratch/scrubbed/your-username`.

`cd /gscratch/scrubbed/stanja`

If the dir is not there you shoud create it. For every job you submit I recommend working within a directory.

`mkdir hisat`

## Generate a shell script

Create a shell script in your code directory named hisat-job.sh with contents:

```{r}
#!/bin/bash
## Job Name
#SBATCH --job-name=assign4
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=01-08:00:00
## Memory per node
#SBATCH --mem=100G
#SBATCH --mail-type=ALL
#SBATCH --mail-user=stanja@uw.edu
## Specify the working directory for this job
#SBATCH --chdir=/gscratch/scrubbed/stanja/assign_04

# for rsync
# run the following in the Rterminal, while connected to mox:
 rsync -avz assignments/code/04-* stanja@mox.hyak.uw.edu:/gscratch/scrubbed/stanja/assign_04

# for scp
# run the following in the Rterminal, while connected to mox:
# scp assignments/code/04-* stanja@mox.hyak.uw.edu:/gscratch/scrubbed/stanja/assign_04

# type the following to schedule the job
# sbatch 04-job-sh

# Then on mox, inside the assign_04 directory you will type”

# sbatch 04-job-sh to schedule the job.

# Once done you should have a couple of new files in the directory.

# You will want to check them to see if everything worked and then move the output back to your repo…

# rsync -avz stanja@mox.hyak.uw.edu:/gscratch/scrubbed/stanja/assign_04/ 

#run a python script you wrote!
module load intel-python3_2017

python 04-hello.py

# run blastx just to get manual
/gscratch/srlab/programs/ncbi-blast-2.10.1+/bin/blastx -help

#a few bash commands
pwd 

whoami

echo "yeah! I did it!!!!!!!!!!"

#this writes out  tofile
echo "yeah! I did it!!!!!!!!!!" > text.file
```

## rsync

run the following in the Rterminal, while connected to mox:

`rsync -avz code/hisat* stanja@mox.hyak.uw.edu:/gscratch/scrubbed/stanja/hisat`

## scp

run the following in the Rterminal, while connected to mox:

`scp assignments/code/04-* stanja@mox.hyak.uw.edu:/gscratch/scrubbed/stanja/assign_04`

```{r}
#!/bin/bash
## Hisat Test
#SBATCH --job-name=hisattest
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=01-08:00:00
## Memory per node
#SBATCH --mem=100G
#SBATCH --mail-type=ALL
#SBATCH --mail-user=stanja@uw.edu
## Specify the working directory for this job
#SBATCH --chdir=/gscratch/scrubbed/stanja/assign_04

# load modules needed
module load HISAT2/2.2.1-foss-2019b
module load SAMtools/1.9-foss-2018b

#unzip reference genome
#gunzip Montipora_capitata_HIv3.assembly.fasta.gz

# index the reference genome for Montipora capitata output index to working directory
hisat2-build -f /home/shared/8TB_HDD_02/sarahtanja/sarahtanja-coralRNA/data/Montipora_capitata_HIv3.assembly.fasta ./Mcapitata_ref_v3 # called the reference genome (scaffolds)
echo "Referece genome indexed. Starting alignment" $(date)

# This script exports alignments as bam files
# sorts the bam file because Stringtie takes a sorted file for input (--dta)
# removes the sam file because it is no longer needed
array=($(ls clean*)) # call the clean sequences - make an array to align
for i in ${array[@]}; do
        sample_name=`echo $i| awk -F [.] '{print $2}'`
	hisat2 -p 8 --dta -x Mcapitata_ref_v3 -U ${i} -S ${sample_name}.sam
        samtools sort -@ 8 -o ${sample_name}.bam ${sample_name}.sam
    		echo "${i} bam-ified!"
        rm ${sample_name}.sam
done
```