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Old 08-14-2013, 07:22 AM   #1
jmwhitha
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Default Installing SEAS for Pathway Analysis of Differentially Expressed Genes

Hello SeqAnswers Community,

I am interested in using SEAS to do pathway analysis of my differentially expressed genes. I think I have installed all of the necessary dependencies, but I do not understand the following installation instruction (below). After extracting the files from seas-src-1.0.tar.gz, I couldn't find the "Seas.exe.config" or "appSettings" file in any of the extracted folders. So where is the file?

3. Change the app settings in Seas.exe.config (appSettings).

Example:
<appSettings>
<add key="FastaPath" value="data/fasta" />
<add key="AssocPath" value="data/assoc" />
<add key="RscriptPath" value="Rscript" />
<add key="GseaPath" value="thirdparty/R/GSEA.R" />
<add key="BlastPath" value="blastall" />
</appSettings>

Thank you and God bless,
Jason
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Old 08-14-2013, 07:27 AM   #2
GenoMax
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If you have installed the dependencies then you need to replace the dummy values shown in the above example with actual directory paths from your local system (e.g. replace blastall with /file_path_to/blastall).
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Old 08-14-2013, 07:36 AM   #3
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Good to hear from you GenoMax.

I imagine the dummy values you are talking about are in a Seas.exe.config file, but I don't see such a file. Is that what this #3 instruction is saying (e.g. go to the Seas.exe.config file and change the line that says <add key="BlastPath" value="blastall" /> to <add key="BlastPath" value="~/RNA_seq/bin/blastall" />)?

Thank you,
Jason
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Old 08-14-2013, 07:47 AM   #4
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I assume this is the package you are referring to: http://csbl.bmb.uga.edu/~xizeng/research/seas/

That seas.exe.config file is only in the windows binary tarball.

Edit: The file appears to be called "Console/app.config" in the linux install. That would be the one to edit.

Last edited by GenoMax; 08-14-2013 at 08:03 AM.
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Old 08-14-2013, 08:28 AM   #5
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GREAT!!! Thank you!!!
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Old 08-19-2013, 10:55 AM   #6
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Whoops, it looks like I do not have the correct MONO. I executed "yum install monodevelop" (using Fedora instead of Ubuntu right now) and that seemed to work, but when I tried to open the Console/app.config it gives me the warning:

There is no application installed for Mono application config files.
Do you want to search for an application to open this file?

Do you know what the correct install command is for the MONO? I also tried:
#Try "yum install mono" NOT RIGHT
#Try "yum -y install mono-*" NOT RIGHT
And did some searching online.

Thanks,
Jason
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Old 08-19-2013, 11:00 AM   #7
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Specifically, I need to get .NET 3.5 SP1 runtime environment (Mono 2.2 or above). Does this mean I need .NET 3.5 SP1 runtime environment and Mono 2.2 or above, or that Mono 2.2 or above is .NET 3.5 SP1 runtime environoment?

Thanks,
Jason
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Old 08-19-2013, 11:13 AM   #8
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http://www.mono-project.com/Mono_Installation says there is a way to install much newer versions than MONO 2.2 with "Fedora Core users: using yum" but I don't see it.
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Old 08-19-2013, 12:42 PM   #9
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Quote:
Originally Posted by jmwhitha View Post
http://www.mono-project.com/Mono_Installation says there is a way to install much newer versions than MONO 2.2 with "Fedora Core users: using yum" but I don't see it.
Not the yum way but there are some directions for installing mono on Fedora core here: http://forums.osgrid.org/viewtopic.php?f=14&t=4625
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Old 08-19-2013, 02:03 PM   #10
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So, I did the steps on http://forums.osgrid.org/viewtopic.php?f=14&t=4625.

When I got to this step:
edit the .bashrc file in your /home/<user> and insert and adjust the <user> to your home folder for your server
Code:
export PATH="/home/<user>/bin/mono/bin:$PATH"
export PKG_CONFIG_PATH="/home/<user>/bin/mono/lib/pkgconfig:$PKG_CONFIG_PATH"
export MANPATH="/home/<user>/bin/mono/share/man:$MANPATH"
export LD_LIBRARY_PATH="/home/<user>/bin/mono/lib:$LD_LIBRARY_PATH"
export MONO_THREADS_PER_CPU=75

I found that the .bashrc file was hidden. So I opened it in gedit and added the code putting in the correct <user>.

However, when I executed "mono-sgen --debug OpenSim.exe" the error below was returned.
Cannot open assembly 'OpenSim.exe': No such file or directory.


What am I doing wrong?

Thanks so much!
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Old 08-19-2013, 02:14 PM   #11
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As of now, I still can't open the app.config.
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Old 08-19-2013, 06:41 PM   #12
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I am going out on a limb here but here goes. You do not have "OpenSim" installed (http://opensimulator.org/wiki/Main_Page) which is why you are getting that error.

As for not being able to "open" app.config aren't you supposed to edit that file using an editor to adjust the file paths?
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Old 08-20-2013, 06:13 AM   #13
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Excellent! Yes, you were right. I did not have opensim, and I should have commanded gedit instead of double clicking to try and open the app.config file.

So, with the first time use of the opensim, it asks a bunch of questions about regions
http://opensimulator.org/wiki/Configuring_Regions
Where do I find this information to fill in?
Is it important that I configure the opensimulator if all I want to do is use SEAS?

Thanks again,
Jason
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Old 08-20-2013, 06:26 AM   #14
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OpenSim is only used as an example AFAIK. If it opens then that means mono is correctly installed. On to SEAS.
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Old 08-21-2013, 01:53 PM   #15
jmwhitha
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Default Running SEAS

So I tried to run each of the following commands and they all gave me the same error (line 1: $'\357\273\277mono': command not found)
./seas.sh
./seas.sh annotate
./seas.sh annotate --fastafile = ~/bin/CLJUmultifastaSample.txt --organism = 1538

What does that mean?
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Old 08-30-2013, 08:06 AM   #16
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Please help.
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Old 08-30-2013, 02:57 PM   #17
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Jason: Have you tried to contact SEAS developers to see if they can help? That looks like some sort of python script error.
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Old 08-30-2013, 04:21 PM   #18
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Thanks for the suggestion. I just sent them an email. I'll let everybody know what comes of it.
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Old 09-12-2013, 11:11 AM   #19
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Hello all,

Despite two emails, I have not received any answers. I will look around for some knowledgeable computer scientists to give me a hand.

Thanks again and God bless,
Jason
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