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Download from hudsonalpha.org

Note

Required OS:

OS x or Linux. Windows users, please contact Maria Elena Hernandez-Gonzalez

Software:

wget / curl

Terminal emulator
  • Terminal (OS x)
  • Genome Terminal or Other Emulator (Linux)
Author:

This document was created by Saranga Wijeratne

Download

  1. Create a Samples.txt file with your sample links (the links are provided in the Excelsheet) as follows:

    #Content of the Samples.txt
    http://mysample.download.org/dl/d4/Meulia/myprojectnumber/data_150522/C6V7FANXX_s8_0_TruseqHTDual_D712-TruseqHTDual_D508_SL104628.fastq.gz
    http://mysample.download.org/dl/d4/Meulia/myprojectnumber/data_150522/C6V7FANXX_s3_0_TruseqHTDual_D703-TruseqHTDual_D501_SL104549.fastq.gz
    http://mysample.download.org/dl/d4/Meulia/myprojectnumber/data_150522/C6V7FANXX_s5_0_TruseqHTDual_D709-TruseqHTDual_D506_SL104602.fastq.gz
    http://mysample.download.org/dl/d4/Meulia/myprojectnumber/data_150522/C6V7FANXX_s8_0_TruseqHTDual_D705-TruseqHTDual_D501_SL104565.fastq.gz
    
  2. Use the Terminal and navigate to the location where Samples.txt is saved.

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    #If your Samples.txt is saved under ~/Downloads
    $ cd ~/Downloads
    
  3. On OS x, issue the following command to download your files:

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    $ for f in $(cat Samples.txt ); do curl --progress-bar -O $f; done
    
  4. On Linux, issue the following command to download your files,

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    $ for f in $(cat Samples.txt ); do wget -v $f; done
    

Check checksum

To detect errors which may have been introduced during the downloading, you have to run checksum on your downloaded files.

  1. Navigate to the location where you have downloaded your files.

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    #If your files are saved under ~/Downloads
    $ cd ~/Downloads
    
  2. Then, if you’re on OS x Terminal, type in the following command:

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    $ md5 *
    
    MD5 (C6V7FANXX_s3_0_TruseqHTDual_D703-TruseqHTDual_D501_SL104549.fastq.gz) = d41d8cd428f00b204e9800998ecf8427e
    MD5 (C6V7FANXX_s5_0_TruseqHTDual_D709-TruseqHTDual_D506_SL104602.fastq.gz) = d49d8cdf00j204e9800998ecf8427e
    MD5 (C6V7FANXX_s8_0_TruseqHTDual_D705-TruseqHTDual_D501_SL104565.fastq.gz) = d47d8cd98dfds0b204e9800998ecf8427e
    MD5 (C6V7FANXX_s8_0_TruseqHTDual_D712-TruseqHTDual_D508_SL104628.fastq.gz) = d42d8cd98f00bdfse9800998ecf8427e
    

    If you’re on Linux terminal, type in the following commmand:

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    $ md5sum *
    
    d41d8cd428f00b204e9800998ecf8427e   C6V7FANXX_s3_0_TruseqHTDual_D703-TruseqHTDual_D501_SL104549.fastq.gz
    d49d8cdf00j204e9800998ecf8427ed56   C6V7FANXX_s5_0_TruseqHTDual_D709-TruseqHTDual_D506_SL104602.fastq.gz
    d47d8cd98dfds0b204e9800998ecf8427e  C6V7FANXX_s8_0_TruseqHTDual_D705-TruseqHTDual_D501_SL104565.fastq.gz
    d47d8cd98dfds0b204e9800998ecf8427e  C6V7FANXX_s8_0_TruseqHTDual_D712-TruseqHTDual_D508_SL104628.fastq.gz
    

Tip

Match these checksum values with the values provided in the Excelsheet. For any samples with mismatching checksum, you have to re-download the samples.