JAVA in mac

[lupid]

Hi to all, I want to run trinity in the iMAC of my work, it has 10.7 Lion, and I had downloaded thousands of times java from the oracle page, but this is still the answer of trinity, please, help me

./runMe.sh #!/bin/bash -ve


if [ -e reads.right.fq.gz ] && [ ! -e reads.right.fq ]; then
    gunzip -c reads.right.fq.gz > reads.right.fq
fi

if [ -e reads.left.fq.gz ] && [ ! -e reads.left.fq ]; then
    gunzip -c reads.left.fq.gz > reads.left.fq
fi

if [ -e reads2.right.fq.gz ] && [ ! -e reads2.right.fq ]; then
    gunzip -c reads2.right.fq.gz > reads2.right.fq
fi

if [ -e reads2.left.fq.gz ] && [ ! -e reads2.left.fq ]; then
    gunzip -c reads2.left.fq.gz > reads2.left.fq
fi



#######################################################
##  Run Trinity to Generate Transcriptome Assemblies ##
#######################################################

../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz,reads2.left.fq.gz --right reads.right.fq.gz,reads2.right.fq.gz --SS_lib_type RF --CPU 4
Use of uninitialized value $java_version in pattern match (m//) at ../../Trinity line 818.



********************************************************************
** Warning, Trinity cannot determine which version of Java is being used.  Version 1.7 is required. 

Attempting to continue in 30 seconds
********************************************************************


Trinity version: v2.0.6
-currently using the latest production release of Trinity.

Error, cannot find 'java'.  Please be sure it is available within your ${PATH} setting and then try again. at ../../Trinity line 2193.

[Brian Bushnell]

What happens when you type "java --version"?

[GenoMax]

See if the answer in this thread helps: http://stackoverflow.com/questions/2...t-java-version

[lupid]

Ir say java comand not found

[GenoMax]

You don't have Java installed at all?

[lupid]

No, evento when I download the dmg, and follow the instructions

[GenoMax]

For 10.7.3 and above, Java 8 from Oracle is supposed to work. Are you at that patch level?

[lupid]

Lion 10.7.5, I download the java8_40

[GenoMax]

You do have admin rights to install software on this computer?

[lupid]

Yes I have

[GenoMax]

Do you get errors or what? Obviously you need to sort out the java problem first (tried to get Java 1.6 from apple?).

Before you go much further, what kind of assembly project do you have in mind? Trinity requires significant amount of RAM and if you are running an iMac (with 10.7) that may become a limiting factor.

[lupid]

This is what happend when I try to install JAVA and run ./runMe.sh in mac

https://www.dropbox.com/s/tsyzfh6nhq37mi5/Captura%20de%20pantalla%202015-04-14%2010.51.01.png?dl=0

I'm aware of the limiting factor of the ram, but I just need to run 8M fastq and do nothing more in this mac

[GenoMax]

Since you have now installed java (I think that is what the left half of the screenshot says) I will refer you back to posts #2 and 3. Tell us what happens when you try Brian's suggestion in #2 and then try to set the $java_version variable per #3.

[lupid]

java -version
-bash: java: command not found

[lupid]

I have installed Java from this dmg at least 10 times, and also from the version 7 and 6