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Login to ls5 or stampede at TACCTACC. Execute commands to set up access to the multiqc binary:
lonestar5
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| language | bash |
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| title | lonestar5 setup for multiqc |
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module load python
export PATH="/work/projects/BioITeam/ls5/bin/multiqc-1.0:$PATH"
export PYTHONPATH="/work/projects/BioITeam/ls5/lib/python2.7/annab-packages:$PYTHONPATH"
# make sure it is working...
multiqc --help |
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| language | bash |
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| title | stampede setup for multiqc |
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module load python
export PATH="/work/projects/BioITeam/stampede/bin/multiqc-1.0:$PATH"
export PYTHONPATH="/work/projects/BioITeam/stampede/lib/python2.7/annab-packages:$PYTHONPATH"
# make sure it is working...
multiqc --help |
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mkdir -p $SCRATCH/byteclub/multiqc
cd $SCRATCH/byteclub/multiqc
ln -s -f /work/01063projects/abattenhBioITeam/projects/byteclub/multiqc/fastqc |
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To catch up, just stage Anna's pre-made files: | Code Block |
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| mkdir -p $SCRATCH/byteclub/multiqc/
cd $SCRATCH/byteclub/multiqc/
rsync -avrP --delete /work/01063projects/abattenhBioITeam/projects/byteclub/multiqc/0102_fastq/ . |
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After saving this file, remove the previous MultiQC outputs and re-run the program:
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cd $SCRATCH/byteclub/multiqc
rsync -avrP /work/01063projects/abattenhBioITeam/projects/byteclub/multiqc/bowtie2/ bowtie2/ |
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To catch up, just use Anna's pre-made files: | Code Block |
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| mkdir -p $SCRATCH/byteclub/multiqc/
cd $SCRATCH/byteclub/multiqc/
rsync -avrP --delete /work/01063projects/abattenhBioITeam/projects/byteclub/multiqc/03_bowtie/ . |
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To catch up, just use Anna's pre-made files: | Code Block |
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| mkdir -p $SCRATCH/byteclub/multiqc
cd $SCRATCH/byteclub/multiqc
rsync -avrP --delete /work/01063projects/abattenhBioITeam/projects/byteclub/multiqc/04_picard_fixed/ . |
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To catch up, just use Anna's pre-made files: | Code Block |
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| mkdir -p $SCRATCH/byteclub/multiqc
cd $SCRATCH/byteclub/multiqc
rsync -avrP --delete /work/01063projects/abattenhBioITeam/projects/byteclub/multiqc/05_section_order/ . |
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Next we edit the multiqc_config.yaml configuration file to add appropriate custom data sections:
x
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To catch up, just use Anna's pre-made files: | Code Block |
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| mkdir -p $SCRATCH/byteclub/multiqc
cd $SCRATCH/byteclub/multiqc
rsync -avrP --delete /work/projects/BioITeam/projects/byteclub/multiqc/06_custom_linegraph/ . |
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Then the usual...
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cd $SCRATCH/byteclub/multiqc; rm -rf mqc_report*; multiqc . |
Resulting in a report that includes our inset size distribution data the custom data section we configured: http://web.corral.tacc.utexas.edu/iyer/byteclub/multiqc/06_custom_linegraph.mqc_report.html, with a new section called Bowtie2 insert size.
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cd $SCRATCH/byteclub/multiqc
cp /work/01063projects/abattenhBioITeam/projects/byteclub/multiqc/07_custom_bargraph/for_multiqc/*mapq* for_multiqc/
cp /work/01063projects/abattenhBioITeam/projects/byteclub/multiqc/07_custom_bargraph/for_multiqc/*genomecov* for_multiqc/ |
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To catch up, just use Anna's pre-made files: | Code Block |
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| mkdir -p $SCRATCH/byteclub/multiqc
cd $SCRATCH/byteclub/multiqc
rsync -avrP --delete /work/01063projects/abattenhBioITeam/projects/byteclub/multiqc/07_custom_bargraph/ . |
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| Expand |
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To catch up, just use Anna's pre-made files: | Code Block |
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| mkdir -p $SCRATCH/byteclub/multiqc
cd $SCRATCH/byteclub/multiqc
rsync -avrP --delete /work/01063projects/abattenhBioITeam/projects/byteclub/multiqc/08_final/ . |
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