• Rockhopperhome page

• Module Name: rockhopper (see the modules page for more information)
• Rockhopper is a multithreaded application (-p). Please match the number of allocated CPUs with the number of threads
• The $ROCKHOPPER_JAR variable is set to the path of the jar file
• Example files in $ROCKHOPPER_TEST_DATA

Allocate an interactive session and run the program. If using the GUI, make sure that you have a graphical connection to biowulf (NX or X11 forwarding though ssh). Sample session:

[user@biowulf]$ sinteractive --mem=5g --cpus-per-task=4 --gres=lscratch:20
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ module load rockhopper

[user@cn3144]$ # start up the GUI. Need to know the http proxy host for this.
[user@cn3144]$ # Note that the proxy may change from session to session
[user@cn3144]$ echo $http_proxy
http://dtn03-e0:3128
[user@cn3144]$ java -Dhttp.proxyHost=dtn03-e0 -Dhttp.proxyPort=3128 -jar $ROCKHOPPER_JAR

For more details on using the GUI, please see the Rockhopper manual. Now let's use the command line interface to do a reference based analysis of a small Mycoplasma genitalium data set:

[user@cn3144]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144]$ cp -r ${ROCKHOPPER_TEST_DATA:-none}/* .
[user@cn3144]$ tree
.
|-- [user    16M]  Example_Condition1.fastq
|-- [user    16M]  Example_Condition2.fastq
`-- [user   4.0K]  Mycoplasma_genitalium_G37
    |-- [user   575K]  NC_000908.fna
    |-- [user     46]  NC_000908.fna.fai
    |-- [user    10K]  NC_000908.genome
    |-- [user    59K]  NC_000908.gff
    |-- [user    37K]  NC_000908.ptt
    `-- [user   2.3K]  NC_000908.rnt

[user@cn3144]$ mkdir tmp
[user@cn3144]$ java -Xmx4000m -Djava.io.tmpdir=$PWD/tmp -cp $ROCKHOPPER_JAR Rockhopper \
    -g $PWD/Mycoplasma_genitalium_G37 \
    -p $SLURM_CPUS_PER_TASK \
    -L cond1,cond2 \
    -o $PWD/results \
    Example_Condition1.fastq Example_Condition1.fastq

Aligning sequencing reads from file:    Example_Condition1.fastq
Total reads:                    137473
Successfully aligned reads:     125676  91%     (Mycoplasma genitalium G37 chromosome)
        Aligning (sense) to protein-coding genes:       96%
        Aligning (antisense) to protein-coding genes:   0%
        Aligning (sense) to ribosomal RNAs:     0%
        Aligning (antisense) to ribosomal RNAs: 0%
        Aligning (sense) to transfer RNAs:      1%
[...snip...]

[user@cn3144]$ tree results
results/
|-- [user   4.0K]  genomeBrowserFiles
|   |-- [user   1.4M]  Example_Condition1_NC_000908_v1_m15_aT_d500_l33_fr_cF.minus.wig
|   |-- [user   1.5M]  Example_Condition1_NC_000908_v1_m15_aT_d500_l33_fr_cF.plus.wig
|   |-- [user   1.1M]  NC_000908_diffExpressedGenes.wig
|   |-- [user   1.1M]  NC_000908_ncRNAs.wig
|   |-- [user   1.3M]  NC_000908_operons.wig
|   `-- [user   1.1M]  NC_000908_UTRs.wig
|-- [user   4.0K]  intermediary
|   `-- [user   186K]  Example_Condition1_NC_000908_v1_m15_aT_d500_l33_fr_cF.gz
|-- [user   4.4K]  NC_000908_operons.txt
|-- [user    37K]  NC_000908_transcripts.txt
`-- [user   2.0K]  summary.txt

[user@cn3144]$ cp -r results /data/$USER

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

Create a batch input file (e.g. rockhopper.sh), which uses the input file 'rockhopper.in'. For example:

#!/bin/bash
wd=$PWD

module load rockhopper/2.0.3
cd /lscratch/$SLURM_JOB_ID
mkdir tmp

cp -r ${ROCKHOPPER_TEST_DATA:-none}/* .
java -Xmx4000m -Djava.io.tmpdir=$PWD/tmp -cp $ROCKHOPPER_JAR Rockhopper \
    -g $PWD/Mycoplasma_genitalium_G37 \
    -p $SLURM_CPUS_PER_TASK \
    -L cond1,cond2 \
    -o $PWD/results \
    Example_Condition1.fastq Example_Condition1.fastq
cp -r results $wd

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=5g rockhopper.sh