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Old 04-13-2015, 02:58 PM   #1
lupid
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Default JAVA in mac

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

Code:
./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.
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Old 04-13-2015, 03:03 PM   #2
Brian Bushnell
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What happens when you type "java --version"?
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Old 04-13-2015, 03:05 PM   #3
GenoMax
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See if the answer in this thread helps: http://stackoverflow.com/questions/2...t-java-version
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Old 04-13-2015, 03:20 PM   #4
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Ir say java comand not found
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Old 04-13-2015, 03:39 PM   #5
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You don't have Java installed at all?
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Old 04-13-2015, 03:42 PM   #6
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No, evento when I download the dmg, and follow the instructions
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Old 04-14-2015, 04:46 AM   #7
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For 10.7.3 and above, Java 8 from Oracle is supposed to work. Are you at that patch level?

Last edited by GenoMax; 04-14-2015 at 04:48 AM.
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Old 04-14-2015, 04:54 AM   #8
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Lion 10.7.5, I download the java8_40
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Old 04-14-2015, 05:04 AM   #9
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You do have admin rights to install software on this computer?
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Old 04-14-2015, 05:25 AM   #10
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Yes I have
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Old 04-14-2015, 05:53 AM   #11
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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.
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Old 04-14-2015, 07:43 AM   #12
lupid
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This is what happend when I try to install JAVA and run ./runMe.sh in mac

https://www.dropbox.com/s/tsyzfh6nhq...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
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Old 04-14-2015, 07:52 AM   #13
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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 $java_version variable per #3.
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Old 04-14-2015, 08:10 AM   #14
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java -version
-bash: java: command not found
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Old 04-14-2015, 08:15 AM   #15
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I have installed Java from this dmg at least 10 times, and also from the version 7 and 6
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Old 04-14-2015, 08:29 AM   #16
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I do this
Quote:
sudo ln -nsf /Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents sudo ln -nsf /Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK
ln: /System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK: Not a directory
Admins-iMac-2:~ crg-user$ export JAVA_HOME="/Library/Java/JavaVirtualMachines/jdk1.7.0_51.jdk/Contents/Home"
Admins-iMac-2:~ crg-user$ java -version
-bash: java: command not found
Admins-iMac-2:~ crg-user$
and nothing, but it's weird for me at least because, this
Quote:
Admins-iMac-2:~ crg-user$ /usr/libexec/java_home -VMatching Java Virtual Machines (1): 1.7.0_75, x86_64: "Java SE 7" /Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents/Home

/Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents/Home
Admins-iMac-2:~ crg-user$

Last edited by lupid; 04-14-2015 at 08:32 AM.
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Old 04-14-2015, 11:01 AM   #17
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Any guess of what to do?
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Old 04-15-2015, 05:30 AM   #18
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What output does this command produce (I don't have a 10.7 machine handy to check but this works with newer OS X)?

Code:
$ mdfind "kMDItemDisplayName == java"
or if that does not work then what about this

Code:
$ /usr/libexec/java_home -V
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Old 04-15-2015, 08:38 AM   #19
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I get this, sorry for the delay.
Quote:
Admins-iMac-2:test_Trinity_Assembly crg-user$ mdfind "kMDItemDisplayName == java"
/Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents/Home/jre/bin/java
/Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents/Home/bin/java
/usr/local/bin/Contents/Home/jre/bin/java
/usr/local/bin/Contents/Home/bin/java
/usr/local/Cellar/app-engine-java-sdk/1.9.18/libexec/demos/shardedcounter/src/com/google/appengine/demos/shardedcounter/java
/Users/crg-user/Desktop/Tomas/R-2.12.1/share/java
/Library/Frameworks/R.framework/Versions/3.1/Resources/share/java
/System/Library/Frameworks/JavaVM.framework/Versions/A/Commands/java
/usr/share/java
/usr/share/file/magic/java
/usr/lib/java
Admins-iMac-2:test_Trinity_Assembly crg-user$ /usr/libexec/java_home -V
Matching Java Virtual Machines (1):
1.7.0_75, x86_64: "Java SE 7" /Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents/Home

/Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents/Home
Admins-iMac-2:test_Trinity_Assembly crg-user$
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Old 04-15-2015, 10:08 AM   #20
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It is odd that you still do not seem to have Java 8 installed though the screenshot yesterday seemed to indicate that.

Anyway, if you do this (based on the post I linked in #3):

Code:
$ export JAVA_HOME=`/usr/libexec/java_home -v 1.7.0_75`
Those are backtick symbols (not single quotes).

See if trinity works now.
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