March 13^th, 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:

4. Extract the file using the tar utility:

5. cd into the new extracted directory:

6. Run the installation script:

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!