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Code Block
languagebash
cd
cp /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/tacc/bashrc.corengs.stampede2  .bashrc
chmod 600 .bashrc

# or, using your symlink
cd
cp ~/CoreNGS/tacc/bashrc.corengs.stampede2  .bashrc
chmod 600 .bashrc

Source it to make it active (if this doesn't work, log off then log back in):

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Code Block
languagebash
export ALLOCATION=UT-2015-05-18
export BI=/corral-repl/utexas/BioITeam
export BIWORK=/workwork2/projects/BioITeam
export CORENGS=$BIWORK/projects/courses/Core_NGS_Tools

 exportexport PATH=.:$HOME/local/bin:$PATH
# For cutadapt support:
export PYTHONPATH=$BIWORK/ls5/lib/python2.7/site-packages:$PYTHONPATH
# For MultiQC support:
export PYTHONPATH=$BIWORK/ls5/lib/python2.7/annab-packages:$PYTHONPATH

Turn on coloring by file type in the shell:

Code Block
languagebash
export LS_OPTIONS='-N --color=auto -T 0'

# For better colors using a whitedark background terminal, un-comment this line:
export LS_COLORS=$LS_COLORS:'di=1;33:fi=01:ln=01;36:'

# For better colors using a white background terminal:
export LS_COLORS=$LS_COLORS:'di=1;34:fi=01:ln=01;36:'

# May or may not be needed
export LS_OPTIONS='-N --color=auto -T 0

TACC intro

Anchor
Catchup_cmds
Catchup_cmds
Commands files

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Code Block
languagebash
mkdir -p $SCRATCH/core_ngs/slurm/simple
cd $SCRATCH/core_ngs/slurm/simple
cp $CORENGS/tacc/simple.cmds .

Wayness commands

Code Block
languagebash
mkdir -p $SCRATCH/core_ngs/slurm/wayness
cd $SCRATCH/core_ngs/slurm/wayness
cp $CORENGS/tacc/wayness.cmds .

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Code Block
languagebash
titleStart an idev session
idev -p normal -m 180120 -N 1 -n 2468 -A UT-2015-05-18 --reservation=CCBBBIO_DATA_week_1
Tip

You can tell you're in a idev session because the hostname command will return a compute node name (e.g. nid00438. c401-041.stampede2.tacc.utexas.edu) instead of a login node name (e.g. login5. login2.stampede2.tacc.utexas.edu).

The n idev session will terminate when the requested time has expired, or you use the exit command.

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Code Block
languagebash
# Area for "original" sequencing data
mkdir -p $WORK$WORK2/archive/original/2018_05.core_ngs
cd $WORK$WORK2/archive/original/2018_05.core_ngs
wget http://web.corral.tacc.utexas.edu/BioITeam/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz
wget http://web.corral.tacc.utexas.edu/BioITeam/yeast_stuff/Sample_Yeast_L005_R2.cat.fastq.gz

# Create a $SCRATCH area for FASTQ prep and link the yeast data there
mkdir -p $SCRATCH/core_ngs/fastq_prep
cd $SCRATCH/core_ngs/fastq_prep
ln -s -f $WORK/archive/original/2018_05.core_ngs/Sample_Yeast_L005_R1.cat.fastq.gz
ln -s -f $WORK/archive/original/2018_05.core_ngs/Sample_Yeast_L005_R2.cat.fastq.gz

# Copy over a small FASTQ file
cd $SCRATCH/core_ngs/fastq_prep
cp $CORENGS/misc/small.fq .

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Code Block
languagebash
mkdir -p $SCRATCH/core_ngs/multiqc/fqc.atacseq
cd $SCRATCH/core_ngs/multiqc/fqc.atacseq
cp $CORENGS/multiqc/fqc.atacseq/*.html .

Anchor
Catchup_cutadapt
Catchup_cutadapt
FASTQ files for cutadapt

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Code Block
languagebash
# Pre-built references
mkdir -p $SCRATCH/core_ngs/references
rsync -avrP $CORENGS/references/ $SCRATCH/core_ngs/references/

# FASTQ (to align)
mkdir -p $SCRATCH/core_ngs/alignment/fastq
cp $CORENGS/alignment/*fastq.gz $SCRATCH/core_ngs/alignment/fastq/

# Alignment directory
mkdir -p $SCRATCH/core_ngs/alignment/yeast_bwa
cd $SCRATCH/core_ngs/alignment/yeast_bwa
ln -s -f ../fastq
ln -s -f ../../references/bwa/sacCer3

module load biocontainers  # takes a while
module load bwa
module load samtools

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Code Block
languagebash
mkdir -p $SCRATCH/core_ngs/alignment/yeast_bwa
cd $SCRATCH/core_ngs/alignment/yeast_bwa
cp $CORENGS/catchup/yeast_bwa/yeast_pairedend.bam .

module load biocontainers  # takes a while
module load samtools

# If the sorted, indexed BAM is needed:
cp $CORENGS/catchup/yeast_bwa/yeast_pairedend.sort* .

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Code Block
languagebash
titleSetup for samtools exercises
mkdir -p $SCRATCH/core_ngs/samtools
cd $SCRATCH/core_ngs/samtools
cp $CORENGS/catchup/for_samtools/* .

module load biocontainers  # takes a while
module load samtools