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Old 07-21-2014, 12:01 PM   #1
samzorn1
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Location: Santa Clara

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Default Setting up Linux for SOAP de novo

Hey all,

I'm new to WGS and need some help getting my computer set up.

From a clean install of Ubuntu 14.04 x64, what packages are necessary

to install to be able to install and run SOAP de novo2?

Insofar I have gotten g++ from the build-essentials, but I haven't been able to

successfully install SOAP.

I have no idea what I am doing, so any advice would be awesome

Thanks,

Sam Zorn
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Old 07-21-2014, 01:06 PM   #2
Wallysb01
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Default

Are you trying to compile it from source and getting errors or are you just trying the provided binaries and they aren’t working?

If you’re trying to compile it, I’d suggest you try the binaries first.

Oh link: http://sourceforge.net/projects/soap...ovo2/bin/r240/
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Old 07-21-2014, 01:21 PM   #3
samzorn1
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I've been trying to compile it from source, I'll see if the binaries work out better


Thanks
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Old 07-21-2014, 03:05 PM   #4
dfornika
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There is a pre-compiled binary available for linux, so you likely don't need to compile the source code. Here is the download link for the binary distribution:

http://sourceforge.net/projects/soap...neric-r240.tgz

Code:
$ cd ~/Downloads
$ wget http://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2/bin/r240/SOAPdenovo2-bin-LINUX-generic-r240.tgz
$ tar -xvzf SOAPdenovo2-bin-LINUX-generic-r240.tgz
If you have admin (sudo) privileges and you want to install the program for all users on the machine, then I would do something like this:

Code:
$ sudo cp SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo* /usr/local/bin
If you don't have admin rights, then make bin directory in your home directory and run it from there:

Code:
$ mkdir ~/bin
$ cp SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo* ~/bin/
There are instructions for configuring the program in the file called 'MANUAL' inside the uncompressed SOAPdenovo2-bin-LINUX-generic-r240 directory.
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Old 09-09-2014, 09:41 AM   #5
kadiri.sreenu
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Hi,
As you explained above i have done till executable file copied into the bin folder.then i have tried to install by double click.but it is showing error like soapdenovo 63 is not availabloe or not fully up to date.

can any one plz help me to install the SOAPdenovo software in suse linux 10 version os.

please give me a detailed plan how to install by using precompile binary linux generic or using source code by command line options.
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Old 09-09-2014, 10:54 AM   #6
jpummil
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Default

Quote:
Originally Posted by kadiri.sreenu View Post
Hi,
As you explained above i have done till executable file copied into the bin folder.then i have tried to install by double click.but it is showing error like soapdenovo 63 is not availabloe or not fully up to date.

can any one plz help me to install the SOAPdenovo software in suse linux 10 version os.

please give me a detailed plan how to install by using precompile binary linux generic or using source code by command line options.
So, first...let's do away with this idea of "double clicking" anything. Essentially, if you do as dfornika mentions above...

cd Downloads

wget http://sourceforge.net/projects/soap...neric-r240.tgz

tar xvzf SOAPdenovo2-bin-LINUX-generic-r240.tgz

cd SOAPdenovo2-bin-LINUX-generic-r240/

./SOAPdenovo-63mer

Of course, there are configuration files that have to be created as well for the specific assembly you will be running...but this gets SOAPdenovo working at least...
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Old 09-09-2014, 07:56 PM   #7
kadiri.sreenu
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Default soap denovo

so as per your reply i need to create a configuration file to run the application weather 63mer or 120 soap assembly seperately..
i am new to this command line and as well for bioinformatics also.so plz send me a detailed plan how to create configuration file and run the soap software successfully.
waiting for ur kind guesture.
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Old 09-10-2014, 08:09 AM   #8
jpummil
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Kadiri,

I am not typically a SOAPdenovo user, but there are MANY good examples and tutorials on the internet. One example is a presentation by Mike Schatz found here: http://schatzlab.cshl.edu/teaching/2...20Tutorial.pdf

SOAPdenovo section starts on page 49 I believe...
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Old 09-11-2014, 08:36 PM   #9
kadiri.sreenu
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Default Allpath labs

Dear jpummil,

Thank you very for sending this presentation of all paths lab genome assembly which is very useful.but less information abt soapdernovo.it is ok i will search for soapdenovo.If u find please send sir.
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