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Code Block
languagebash
titleNote the need to add the suffix _fix to "samtools_tutorial" in final 4 copy steps if used the single file execution
mkdir BDIB_IGV_export
cp -i NC_012967.1.gbk.gff BDIB_IGV_export  # copy the new file you just converted to the export directory
cp -i $SCRATCH/BDIB_bowtie2_mapping/NC_012967.1.fasta BDIB_IGV_export
cp -i $SCRATCH/BDIB_samtools_tutorial/NC_012967.1.fasta.fai BDIB_IGV_export
cp -i $SCRATCH/BDIB_samtools_tutorial/SRR030257.vcf BDIB_IGV_export
cp -i $SCRATCH/BDIB_samtools_tutorial/SRR030257.sorted.bam BDIB_IGV_export/bowtie2.sorted.bam
cp -i $SCRATCH/BDIB_samtools_tutorial/SRR030257.sorted.bam.bai BDIB_IGV_export/bowtiebowtie2.sorted.bam.bai
tar -czvf BDIB_IGV_export.tar.gz BDIB_IGV_export

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Expand
titleAnother refresher on how to copy files back from lonestar

In the terminal connected to Lonestar, figure out the complete path to the IGV directory.

Code Block
pwd

Open a new terminal window on your Desktop. Fill in the parts in brackets <> in this command:

Code Block
scp -r <username>@ls5.tacc.utexas.edu:<full_path_to_IGV>/BDIB_IGV_export.tar.gz .
# enter your password 
tar -xvzf BDIB_IGV_export.tar.gz

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  1. Expand
    titleLocally on the classroom machines booted in Mac OSX

    Click here to download and install the mac application version. Save it to your desktop, then extract the zip file and launch the application.

  2. Expand
    titleLocally on the classroom machines booted in Linux

    This downloads the IGV executable and tells the command line to launch it (via the java command).

    Code Block
    wget http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.32.zip unzip IGV_2.3.32.zip cd IGV_2.3.32 java -Xmx2g -jar igv.jar
  3. Expand
    titleIn a Web browser

    Navigate a web browser to this page:http://www.broadinstitute.org/software/igv/download. You will need to register your email address to use this option, but in years of registration I have never noticed any emails from them. Go ahead and click on the "Launch with 2 GB" option. This will download a "Java Web Start" file that you can launch by locating it on your Desktop and double-clicking.

    Warning
    titleMac warning

    This will not work on recent Mac OS updates without severely modifying security permissions as administrator (which you can not do on a classroom computer). Recommended to use Mac directions above during the class.

  4. Expand
    titleLocally on a Mac or Windows computer

    Click here to download version 2.3.53 of IGV or visit https://www.broadinstitute.org/software/igv/download to download the latest binary version. After unzipping, you should be able to click on igv.bat for Windows or igv.command on MacOSX to lauch IGV. If this is not working, you might need to try the web start.

    Warning
    titleMac warning

    This will not work on recent Mac OS updates without severely modifying security permissions as administrator. Recommended to use Mac directions above.

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