There doesn't seem to be a lot of resources troubleshooting this error for Trinity.  Because we are running it on a Mac OSX and Trinity is compiled only for Linux, there is no real support from the Trinity side of things. It may be possible that we are missing libc++abi. This is not a minor undertaking and takes about 24 hours to download, configure, build, and compile. Despite this terrifying error message:

Mac users, remember to be careful when replacing the system's libc++. Your system will not be able to boot without a funcioning libc++.

I will carry onwards.

http://clang.llvm.org/get_started.html

svn co http://llvm.org/svn/llvm-project/llvm/trunk llvm

cd llvm/tools

svn co http://llvm.org/svn/llvm-project/cfe/trunk clang

cd ../..

cd llvm/tools/clang/tools

svn co http://llvm.org/svn/llvm-project/clang-tools-extra/trunk extra

cd ../../../..

cd llvm/projects

svn co http://llvm.org/svn/llvm-project/compiler-rt/trunk compiler-rt

cd ../..

mkdir build

cd build

../llvm/configure

make #this took several hours; make sure to screen

#check to see if it worked

clang --help

http://libcxx.llvm.org

http://libcxxabi.llvm.org

#now install the other libraries

brew update

brew install cmake #you will need this later

cd

cd llvm/projects

svn co http://llvm.org/svn/llvm-project/libcxxabi/trunk libcxxabi

svn co http://llvm.org/svn/llvm-project/libcxx/trunk libcxx

cd .. #now you are in the llvm directory

mkdir build && cd build

cmake ..

make cxx

make #this also takes several hours

Okay done. Let's hope I didn't break break the computer and let's see if this actually did anything.

Fail.

succeeded(0), failed(58736)   99.9949% completed.    libc++abi.dylib: terminating with uncaught exception of type std::length_error: vector::_M_fill_insert

succeeded(0), failed(58737)   99.9966% completed.    libc++abi.dylib: terminating with uncaught exception of type std::length_error: vector::_M_fill_insert

succeeded(0), failed(58738)   99.9983% completed.    libc++abi.dylib: terminating with uncaught exception of type std::length_error: vector::_M_fill_insert

succeeded(0), failed(58739)   100% completed.

We are sorry, commands in file: [failed_quantify_graph_commands.6513.txt] failed.  :-(

Error, cmd: /usr/local/Cellar/trinity/r20131110/trinity-plugins/parafly/bin/ParaFly -c /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/to_assemble/DR_004_Arjam_MOE/trinity_output//chrysalis/quantifyGraph_commands -CPU 4 -failed_cmds failed_quantify_graph_commands.6513.txt -v -shuffle  died with ret 256 at /usr/local/bin/Trinity.pl line 1793.

This is to be continued. At least they put a frowny face in the error message. 

Here is a blog that gives excellent Trinity instructions:
https://cartwrightlab.wikispaces.com/RNAseq+Assembly+in+Trinity

#for paired end reads, combine each side of pairs into one file

cat pair.DR004_Artibeus_Jamaicensis_MOE_ACAGTG_L001_R1* >> Arjam_MOE_R1.fq

cat pair.DR004_Artibeus_Jamaicensis_MOE_ACAGTG_L001_R2* >> Arjam_MOE_R2.fq

#run a trimming script

python ~/Scripts/q-trim.py Arjam_MOE_R1.fq Arjam_MOE_R1_trim.fq

#woops I run into this error:

importerror no module named screed

#it looks like I need the "screed" module for this; looks like I also need to update "setup tools"

#first install pip

sudo python get-pip.py

pip install ipython #not sure what this did

#still missing the screed module

sudo pip install setuptools --upgrade

sudo pip install git+https://github.com/ged-lab/screed.git

#okay seems to be working now

#trimmed with the default setting in which a minimum Qscore = 5

#minimum length = 30; lets see how this works

python ~/Scripts/q-trim.py Arjam_MOE_R1.fq Arjam_MOE_R1_trim.fq

python ~/Scripts/q-trim.py Arjam_MOE_R2.fq Arjam_MOE_R2_trim.fq

#now i need to assemble paired reads--extracting only the pairs using both.py

python ~/Scripts/both.py Arjam_MOE_R1_trim.fq Arjam_MOE_R2_trim.fq

#this creates two files ...R1_trim.fq.both and R2_trim.fq.both

#this script took about one hour to run

#finally time to run trinity!

Trinity.pl --seqType fq --left Arjam_MOE_R1_trim.fq.both --right Arjam_MOE_R2_trim.fq.both --CPU 4 --JM 20G --output trinity_output/

Everything is up and running now. Stay tuned.

Okay we have FINALLY updated our operating system.

Apparently Mavericks already has commandline tools installed so it is not necessary to install again. However, there are some issues if you install Homebrew and the gcc compiler not being linked. So starting from scratch, here is what do do.

#install homebrew

ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"

#check to see your comp is ready to brew

brew doctor

#i had several errors/warnings (errors indicated in orange)

/usr/bin comes before /usr/local/bin

export PATH='/usr/local/bin:$PATH' >> ~/.bash_profile

/usr/local/lib/gcc is not writable.

sudo chown -R laurelyohe /usr/local

brew install homebrew/science/bowtie

brew install apple-gcc42

brew install samtools

brew install trinity

Okay, everything seems good to go. Now I am unzipping the transcriptome output from trimmomatic. 

#installing bamm

brew tap macroevolution/bamm
brew install bamm

#it worked

Because I did such a horrid job taking comprehensible notes while in London, I am going to be more efficient this time around with transcriptome assembly.

We have our illumina RNA-seq reads back (yay!).

To download the reads from UArizona, you have to download this horridly complicated program called irods (http://uagc.arl.arizona.edu/resources/user-guide). After much struggle, the easiest way to get things installed and compiled is the "non-fancy" way. HOWEVER, you MUST download the most recent version of iRods (as of right now 3.3.1)

Navigate to your iRODs folder. Things in blue are what you type. Things in pink are what you would change differently based on your computer.

 export PATH=$PATH:$HOME/iRODS/clients/icommands/bin

 iinit #this will prompt you for a bunch of information

Enter the host name (DNS) of the server to connect to:  mozart.arl.arizona.edu

Enter the port number:  1247

Enter your irods user name:  <your login name from UAGC/BCF>

Enter your irods zone:  BCFZone

Enter your current iRODS password:  <your password from UAGC/BCF>

 

#now your session should start

ils #lists all of the folders in your iRODS account

icd 14140709_SN885_0197_Lane1SideA_Project_Davalos_RNA #change directory

iget -r 140709_SN885_0197_Lane1SideA_Project_Davalos_RNA /Volumes/Spare/ 

#iget -r copies the folder you want to whatever directory you want

Okay now all of the data should be on your computer.

Now I need to install Trinity:

#install homebrew if you do not already have it

ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"

#now install programs necessary for trinity to run on your mac

brew install homebrew/science/bowtie

brew install git

#to allow for new installation of compiler

brew tap homebrew/dupes

brew install apple-gcc42

#okay guess I can't do that because it requires an operating system higher than Mac OSX Lion...

Yes, you read that correctly. Our operating system is still pre-lion. Seems like I will have to wait until our operating system is figured out.

Once we figure this out though, remember this link: http://sourceforge.net/p/trinityrnaseq/mailman/message/31892980/

It allows for trinity to be installed on Mac (even though it is compiled for Linux).

This is from awhile ago--I found it in my drafts, but I just wanted to reopen this can of worms.
selecting priors:

1) select random node on the tree:
#randomly sample a node from a randomly trimmed tree
random.node<-sample(tree.trim$edge[1,], 1)
> random.node
[1] 75

2) open up mesquite and simulate random character in Brownian motion on the tree and look at before and after rates on node 75 in Mesquite using these instructions:
https://nunn.rc.fas.harvard.edu/groups/pica/revisions/7b932/24/
https://nunn.rc.fas.harvard.edu/groups/pica/wiki/f4cc5/43_Squared_Change_Parsimony.html

Take the rate at node 75 for sig1 1 prior: -0.86245
Pick random branch within this clade for sig2 prior (Pellorneum_pyrrogenys):1.1092
Alpha: random uniform distribution runif(1)
rand.shift = 0.05 --used what Revell, et al uses
use ngen=100,000
sample:100