---
title: HW2 - Introduction to Biocluster and Linux
linkTitle: "HW2: Linux & HPC"
description: >
type: docs
weight: 302
---

## Topic: Linux Basics

1. Log into your user account on the HPCC cluster, and from there into a compute node with `srun`.

   ```sh
   srun --x11 --partition=short --mem=2gb --cpus-per-task 4 --ntasks 1 --time 1:00:00 --pty bash -l
   ```

2. Download code from this page
    ```sh
    wget https://cluster.hpcc.ucr.edu/~tgirke/Linux.sh --no-check-certificate 
    ```

3. Download Halobacterium proteome and inspect it
    ```sh
    wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/archaea/Halobacterium_salinarum/all_assembly_versions/GCA_004799605.1_ASM479960v1/GCA_004799605.1_ASM479960v1_protein.faa.gz
    gunzip GCA_004799605.1_ASM479960v1_protein.faa.gz
    mv GCA_004799605.1_ASM479960v1_protein.faa halobacterium.faa
    less halobacterium.faa # press q to quit
    ```

4. How many protein sequences are stored in the downloaded file?
    ```sh
    grep '>' halobacterium.faa | wc
    grep '^>' halobacterium.faa --count
    ```

5. How many proteins contain the pattern `WxHxxH` or `WxHxxHH`?
    ```sh
    egrep 'W.H..H{1,2}' halobacterium.faa --count
    ```

6. Use `less` to find IDs for pattern matches or use `awk`
    ```sh
    awk --posix -v RS='>' '/W.H..(H){1,2}/ { print ">" $0;}' halobacterium.faa | less
    awk --posix -v RS='>' '/W.H..(H){1,2}/ { print ">" $0;}' halobacterium.faa | grep '^>' | cut -c 2- | cut -f 1 -d\ > myIDs
    ```

7. Create a BLASTable database with `formatdb`
    ```sh
    module load ncbi-blast/2.2.31+
    makeblastdb -in halobacterium.faa -out halobacterium.faa -dbtype prot -hash_index -parse_seqids
    ```

8. Query BLASTable database by IDs stored in a file (_e.g._ `myIDs`)
    ```sh
    blastdbcmd -db halobacterium.faa -dbtype prot -entry_batch myIDs -get_dups -out myseq.fasta
    ```

9. Run BLAST search for sequences stored in `myseq.fasta`
    ```sh
    blastp -query myseq.fasta -db halobacterium.faa -outfmt 0 -evalue 1e-6 -out blastp.out
    blastp -query myseq.fasta -db halobacterium.faa -outfmt 6 -evalue 1e-6 -out blastp.tab
    ```

10. Return system time and host name 
    ```sh
    date
    hostname
    ```

Additional exercise material in [Linux Manual](https://hpcc.ucr.edu/manuals_linux-basics_shell.html)

## Homework assignment

Perform above analysis on the protein sequences from [E. coli](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/008/865/GCA_000008865.2_ASM886v2/GCA_000008865.2_ASM886v2_protein.faa.gz). A right click on the link will allow you to copy the URL so that it can be used together with `wget`. 
Record result from final BLAST command (with `outfmt 6`) in text file named `myresult.txt`.

## Homework submission

Upload result file (`myresult.txt`) to your private course GitHub repository under `Homework/HW2/HW2.txt`.

## Due date

Most homeworks will be due one week after they are assigned. This one is due on Thu, April 11th at 6:00 PM.

## Homework solution

To be posted.