PEAR is so.... impossible to use, could someone, or a PEAR author, please help?

[Lucy]

Dear Colleagues,

Illumina tech support suggested PEAR is a good program for assemble paired-end read. BUT as a lay biomedical lab scientist, I am having a hard time to figure out how to install PEAR on my Macbook Air and how to run it.

Step 1 misfortune = From PEAR page, I copied apt-get install build-essential autoconf automake lib tool,

but get error message from Mac terminal

-bash: apt-get: command not found

Step 2 misfortune  = I then copied 

mkdir $HOME/pear
git clone https://github.com/xflouris/PEAR.git
cd PEAR
./autogen.sh
./configure --prefix=$HOME/pear
make
make install

It seems installed, as I can see PEAR folder in application, and can open README file

Step 3 misfortune  = Following README, I typed cd pear, cd test, and seems entered the test folder. I then coped ./test.py to terminal, but got a long error message 

Traceback (most recent call last):

  File "./test.py", line 51, in <module>

    flag = unit_test(test[0], test[1], "temp", test[2])

  File "./test.py", line 9, in unit_test

    subprocess.call(["../src/pear", "-f", f, "-r", r, "-o", o, "-c", "0"], stdout=open(os.devnull, "w"), stderr=subprocess.STDOUT)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 524, in call

    return Popen(*popenargs, **kwargs).wait()

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 711, in __init__

    errread, errwrite)

  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1308, in _execute_child

    raise child_exception

OSError: [Errno 2] No such file or directory

Step 4 misfortune = I do not understand what this line in README means but copied  anyway ./pear -f forward_read.fastq -r reverse_read.fastq -o output_prefix, but terminal give another error message. 

-bash: ./pear: No such file or directory

Could someone please give me a tip on how to run PEAR in Macbook? The two Illunima reads file names are R1.fastq and R2.fastq, could someone give me a tip in lay-wordings which exact key to type to terminal to run PEAR? 

With many thanks!

[Jimmy O'Donnell]

Hi Lucy,

I'm not a PEAR developer, but I have recently dealt with installation on a new Apple computer. Installing PEAR using the above method requires certain other programs be installed, which themselves depend on others. An easier way to install PEAR is to use *another* set of programs called 'Homebrew'. To install homebrew, you need to have Apple's 'XCode/Developer Tools/Command Line Tools' installed (I'm not sure which is which and what the difference is, and some names have changed over the years).

This is all to say that the following commands should get you up and running.

1. Install command line tools. You should first connect to the internet, then open a Terminal window and copy and paste this command and hit enter:

xcode-select --install

2. Install homebrew. You should first connect to the internet, then open a Terminal window and copy and paste this command and hit enter:

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

3. Install PEAR using homebrew. You should first connect to the internet, then open a Terminal window and copy and paste this command and hit enter:

brew install homebrew/science/pear

I hope this helps.

Jimmy

[Lucy]

Thank you VERY MUCH for the answers to my post! 

I will give a try and will get back to you on how I go.

Have a great day!

Lucy

[Lucy]

Thank you Jimmy for the tip! It seemed working, and I get this back from terminal

......

==> Downloading https://homebrew.bintray.com/bottles-science/pear-0.9.6.maverick

######################################################################## 100.0%

==> Pouring pear-0.9.6.mavericks.bottle.tar.gz

🍺  /usr/local/Cellar/pear/0.9.6: 9 files, 744K

Lucy-MacBook-Air:~ Lucy$ 

Would you please kindly give me another foolproof tip on what to next? The 2 Illumina reads files I would like to assemble are named R1.fastq and R2.fastq, what do I type to terminal to run PEAR? 

Thank you for the valuable help

Lucy

On Thursday, October 1, 2015 at 4:51:05 AM UTC+10, Jimmy O'Donnell wrote:

[Jimmy O'Donnell]

Great; glad I could be of help. There are many, many ways in which a user might want to merge forward and reverse reads, and PEAR is very flexible in accommodating different needs. You can view all of the options by simply typing in your terminal window:

pear

And hitting enter. It should display all of the options available, and an explanation of each one. Thus, the most simple usage would be to open a terminal window, change directories ('cd') to the folder containing your reads, and type this:

pear -f R1.fastq -r R2.fastq -o pear_output

And your merged reads will be then called 'pear_output.assembled.fastq'. This will have used the default settings for all of the other (optional) arguments.

Hope this helps.

Jimmy

[Lucy]

Thank you Jimmy for the magic tips! 

It is working !!  I can see the output files and can open them in textedit. 

It is so helpful of you, thanks a lot!

GOOD LUCK with your own work.

Best wishes 

Lucy

[pley...@gmail.com]

Jimmy, thanks for your help.  I was having the same problems as Lucy, your tips did the trick!

On Sunday, September 27, 2015 at 12:27:08 AM UTC-7, Lucy wrote:

[Atanas Radkov]

Hi Jimmy,

I am having a lot of troubles installing PEAR. I tried using your method. Everything worked until the last step:

Warning: homebrew/science was deprecated. This tap is now empty as all its formulae were migrated.

==> Tapping homebrew/science

Cloning into '/usr/local/Homebrew/Library/Taps/homebrew/homebrew-science'...

remote: Counting objects: 9, done.

remote: Compressing objects: 100% (9/9), done.

remote: Total 9 (delta 0), reused 4 (delta 0), pack-reused 0

Unpacking objects: 100% (9/9), done.

Tapped 0 formulae (37 files, 30.4KB)

Error: No available formula with the name "homebrew/science/pear" 

==> Searching for a previously deleted formula (in the last month)...

Warning: homebrew/science is shallow clone. To get complete history run:

  git -C "$(brew --repo homebrew/science)" fetch --unshallow

Error: No previously deleted formula found.

==> Searching for similarly named formulae...

==> Searching local taps...

Error: No similarly named formulae found.

Can you suggest what to do here?

Thank you very much for your time and help.

Atanas

[Jimmy O'Donnell]

Hi Atanas,

From what I can find, it looks like the homebrew method of installing PEAR is no longer supported, but you could try to install from source.

Sorry I can't be of more help, but I have not been using PEAR. Hopefully one of the developers will weigh in.

Cheers

Jimmy