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Update split_libraries_fastq.py in MacQIIME 1.4.0

March 13th, 2012

There is an update to split_libraries_fastq.py to allow it to handle some of the new FASTQ file formats out there. It's amazing how many different formats there are for a FASTQ file!  If you'd like to update to the newest version of split_libraries_fastq.py in MacQIIME 1.4.0 (or 1.4.0a), you can follow the instructions below. The installation package that you run will replace the following files:

/macqiime/lib/python2.7/site-packages/qiime/split_libraries_fastq.py
/macqiime/lib/python2.7/site-packages/qiime/split_libraries_fastq.pyc
/macqiime/QIIME/bin/split_libraries_fastq.py
/macqiime/QIIME/tests/test_split_libraries_fastq.py

and it will create the following new library:

/macqiime/lib/python2.7/site-packages/qiime/quality.py
/macqiime/lib/python2.7/site-packages/qiime/quality.pyc

Instructions: How to update split_libraries_fastq.py

In order to follow these instructions, you need to be logged in as a user with administrative privileges (a sudoer).

1
. Download this archive file into your Downloads folder (do not decompress with Archive Utility): fix_split_libraries_fastq.tgz

2. Open the Terminal.app

3. cd into the folder into which you downloaded the file.  E.g., if you put it in the Downloads folder:
cd ~/Downloads

4. Extract the file using the tar utility:
tar -xvf fix_split_libraries_fastq.tgz

5. cd into the new extracted directory:
cd fix_split_libraries_fastq

6. Run the installation script:
./fix_split_libraries_fastq.s

You will be asked for a password; this is your administrative (sudo) password for your user account. It is needed to copy files into the /macqiime/ subfolders, which are root-owned.

That should do it!  Please let me know if this causes any problems. Thanks!

ċ
fix_split_libraries_fastq.tgz
(14k)
Jeff Werner,
Mar 13, 2012, 11:16 AM
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