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| language | bash |
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| title | Click here for the solution |
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| collapse | true |
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cp -r /corral-repl/utexas/BioITeam/ngs_course $WORK/GVA2016 & # this will run the command in the background and hopefully not cause problems
# because the absolute path to both where the folder is, and where you want it to be are provided, this command can be executed anywhere.
# Absolute paths differ from relative paths in that they start with a / rather than a . or the name of a folder/file (which is assumed to have started with a .)
# This will likely take a few minutes, and produce messages such as:
# cp: cannot open `/corral-repl/utexas/BioITeam/ngs_course/IGV/.DS_Store' for reading: Permission denied |
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mkdir $WORK/tutorial_1
cp /corral-repl/utexas/BioITeam/ngs_course/lambda_mixed_pop/data/lambda_mixed_population.fastq $WORK/tutorial_1
cp /corral-repl/utexas/BioITeam/ngs_course/lambda_mixed_pop/data/lambda.gbk $WORK/tutorial_1
mkdir $WORK/tutorial_2
cp /corral-repl/utexas/BioITeam/ngs_course/ecoli_clones/data/* $WORK/tutorial_2 |
Now that we have all of the data that we want in our work directory, lets move the lambda phage data to scratch so we can begin using it. The following 2 files are in the lambda_mixed_pop/data directory inside of your newly created GVA2016 directory:
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mkdir $SCRATCH/BDIB_breseq_tutorial_11
# Try the following commands, if they do not work, skip them and try the next 2 commands
cp $WORK/GVA2016/lambda_mixed_pop/data/lambda_mixed_population.fastq $SCRATCH/BDIB_breseq_tutorial_1
cp $WORK/GVA2016/lambda_mixed_pop/data/lambda.gbk/data/lambda.gbk $SCRATCH/BDIB_breseq_tutorial_1
# IF the above 2 commands worked, do not try these commands. If the previous 2 failed, use this instead.
cp $WORK/tutorial_1/* $SCRATCH/BDIB_breseq_tutorial_1 |
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Now we'll try running breseq on some Escherichia coli genomes from an evolution experiment. These files are larger.
Data
The data files for this example are in the following path. Go ahead and copy them to a new folder in your $SCRATCH directory called .
Data
The data files for this example are in the following path. Go ahead and copy them to a new folder in your $SCRATCH directory called BDIB_breseq_tutorial_2:
| Code Block |
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| title | location of data files |
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$WORK/GVA2016/ecoli_clones/data
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| language | bash |
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| title | Click here for the solution |
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| collapse | true |
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mkdir $SCRATCH/BDIB_breseq_tutorial_2 |
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| title | location of data files |
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# Try this command first, if it does not work use the alternative command
cp $WORK/GVA2016/ecoli_clones/data
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| language | bash |
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| title | Click here for the solution |
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| collapse | true |
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mkdir/* $SCRATCH/BDIB_breseq_tutorial_2
# Use this command if the previous copy command does not work:
cp $WORK/GVA2016/ecoli_clones/datatutorial_2/* $SCRATCH/BDIB_breseq_tutorial_2
cd $SCRATCH/BDIB_breseq_tutorial_2 |
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