SAMMate.app missing in SAMMate-2.7_mac download?

[Mengqing Xiang]

Hi,

I would very much like to try out SAMMate 2.7 on my Mac.  However, the SAMMate.app does not seem to exist in the folder following unzipping SAMMate-2.7_mac64.zip.  Could you please check whether it is included in the uploaded zip file?

Thanks for your help,

Meng Xiang

-- 
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
Mengqing Xiang, Ph.D., Professor
Center for Advanced Biotechnology and Medicine
UMDNJ-Robert Wood Johnson Medical School
679 Hoes Lane West
Piscataway, NJ 08854
Tel:  (732) 235-4491
Fax:  (732) 235-4466
Email:  xi...@cabm.rutgers.edu

[Dongxiao Zhu]

Hi Prof. Xiang, 

We will make .app available soon. You can launch SAMMate 2.7 by issuing the following command from a terminal on your Mac. For example, if you download SAMMate to your desktop, in your shell, please type "cd Desktop", then type "cd SAMMate-2.7", then copy and paste the following command.  

java -jar -XstartOnFirstThread -Xms256m -Xmx8192m SAMMate-2.7.jar

Please let me know if you have any questions. I will email you once the app is available.

Dongxiao

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From: "Mengqing Xiang" <mqx...@gmail.com>
To: asam...@googlegroups.com
Sent: Sunday, April 8, 2012 1:43:50 PM
Subject: SAMMate.app missing in SAMMate-2.7_mac download?

--
Dongxiao Zhu
Department of Computer Science
Wayne State University
5057 Woodward, Suite 14109.3
Detroit, MI 48202
http://www.cs.wayne.edu/dzhu/

[Meng]

Dear Dongxiao,

Thank you very much for your quick reply. I will give it a try and
look forward to your app. This seems to be an excellent app.

Best,
Meng

[Dongxiao Zhu]

Thank you. Will do it as soon as possible. Currently, we provide two algorithms for transcript quantification, one is RAEM (Deng et al 2011, Nuc. Acids Res.); another one is SASeq, currently under revision with Bioinformatics.

If you need any particular features, we will try to implement them.

Best,

Dongxiao

Dear Dongxiao,

Best,
Meng

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[Meng]

Hi Dongxiao,

I just did a test run using the command that you provided. It worked
well and I could get all the tasks done except for the R option. When
enabled, I got this error "The EdgeR cannot be successfully executed
due to no R exectuable file, no package 'edgeR' or no expressed
genes." I installed R and EdgeR from Bioconductor. I could start R in
terminal and got a reference list by entering: citation("edgeR"). The
path of Rscript was set to: /usr/bin/Rscript. I also tried: /Library/
Frameworks/R.framework/Resources/bin/Rscript. Nothing worked. I wonder
what I did wrong? Sorry that I am a novice on this. Any help would be
highly appreciated.

Thanks,
Meng

[Nan Deng]

Hi Prof. Meng,

    I tested on my Mac and it works. My setting is /usr/bin/Rscript 

    If it doesn't work on you machine, please first make sure that you installed edgeR from R. And then, when you use this function, please also choose sam/bam files for each group. The group tabs are next to the Work Space tab.

Thanks,

Nan

[Tin Chi Nguyen]

Dear Professor Xiang,

I checked SAMMate on Win64 and it worked. My setting was
C:\Program Files\R\R-2.14.2\bin\Rscript.exe

My friend tested on Mac64 and it worked for her. If you still have problems running it, please let us know

Thanks,
Tin Nguyen

----- Original Message -----
From: "Meng" <mqx...@gmail.com>
To: "asammate" <asam...@googlegroups.com>
Sent: Monday, April 9, 2012 8:15:03 PM
Subject: Re: SAMMate.app missing in SAMMate-2.7_mac download?

[Dongxiao Zhu]

Hi Prof. Xiang, 

Just so you know that we have released SAMMate 2.7.1 with both Mac and Window versions. The Mac version now has an .app for you to click and run. 

http://orleans.cs.wayne.edu/SASeq/ 

If you have GA II data, we recommend using RAEM option (based on read alignment, have no particular requirement for coverage), and if you have HiSeq data, we recommend SASeq (iterative, a coverage based method). 

Let us know any feedbacks, cheers!

Dongxiao Zhu

---

From: "Mengqing Xiang" <mqx...@gmail.com>
To: asam...@googlegroups.com
Sent: Sunday, April 8, 2012 1:43:50 PM

Subject: SAMMate.app missing in SAMMate-2.7_mac download?