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.pyIn 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! |
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