building Torrent Suite v3.6

[razzmataz]

Has anyone had any success in building any of the Torrent Suite tools from the github checkout? I've been pulling my hair out from trying to figure out what external dependencies are missing (freebayes, vcflib, samtools code from/for TMAP) or working around missing patch files. It appears that I may be using the wrong version of freebayes (I'm pulling that straight from github), but I'm not entirely sure.

Thanks in advance for any help!

[jtackney]

I just have experience on compiling the tmap aligner on RedHat Enterprise 5 (old , I know) and whatever the latest version of Ubuntu is. In both cases, I agree, the missing dependencies is annoying. I know what does help with the samtools error is that after you git tmap you *need* to do their submodule initiatilization as per their instructions or else it won't compile.

git clone git://github.com/iontorrent/TMAP.git
cd TMAP
git submodule init
git submodule update

Have you gotten tmap installed or is there another particular error you've run into? I haven't messed with their variant caller except on the actual torrent server.

[razzmataz]

I've had pretty good success with building tmap - it's just some of the other pieces that are giving me a bit of stress, primarily stuff under the Analysis directory in the source checkout.

Thanks again!

[rbridenbecker]

Torrent Suite 3.6.2 source code was posted.

There were indeed some modules missing from "external" in the 3.6 posting, so I apologize for the frustration. Please try it again with the 3.6.2 source code.

Also, please cross-post support issues on http://ioncommunity.lifetechnologies.com if you aren't already. We have more folks monitoring and responding there. --rob

[ppsw]

Trying to build Torrent Suite 3.6.2

I am trying to build TS 3.6.2 at the moment on Ubuntu 12.04.

I have built and install lapack++ but I am still unable to build Torrent Suite successfully.

The instructions in BUILD.txt refers this page for further instructions

https://iontorrent.jira.com/wiki/display/TS/HOWTO+-+TorrentR+Server+Installation+Steps

However, I am unable to access this page, and not sure how to sign up for an account to view the page.

Also, do I need to build TMAP separately or is it part of Torrent Suite?

Many thanks,

[rbridenbecker]

Hi, we don't support 12.04, it may be possible to get it to work, but I don't know what issues you will run into.

The instructions in that jira link are obsolete, the torrentR build script handles that automatically now.

Try building packages in this order since there are module dependencies
MODULES="gpu Analysis torrentR" ./buildTools/build.sh

TMAP source code is now under the Analysis package, and it gets compiled when you build Analysis. But an independent binary is still created that you can call from the command line.

On the ioncommunity site, I believe we still provide a VMWare image of an Ubuntu 10.04 OS with Torrent Suite pre-installed. Maybe try using that as a 10.04 build environment before you try to tackle it in 12.04 --rob

[ppsw]

It almost worked. Three modules failed to build: gpu, Analysis and torrentR.

Do you know if it's necessary to build under sudo?

[albert liu]

TS3.6.2 failed on 10.04

same failed result from TS 3.6.2. on a vm with 10.04.4 for me
build of module failed ( gpu, analysis and Torrent R).

I also failed to install the TS on 12.04.
I Knew that it is not supported but just want to give it a try.

Would like to know if anyone sucessfully install TS too.
Best

[rbridenbecker]

Should not be necessary to build as sudo.

Here is what I did
- downloaded the 3.6.2 TS VM from ioncommunity
- installed the 10.04 pkgs listed here https://github.com/iontorrent/TS/blo...ools/BUILD.txt
- downloaded the current 3.6.2 source code from Github
and had no problems building all the packages.

[lwhitmore]

Torrent Suite for Mac

Does anyone know if there is way to use torrent suite v3.6.2 on a mac ??
Thanks !

[rbridenbecker]

Does anyone know if there is way to use torrent suite v3.6.2 on a mac ??
Thanks !

I use VMWare Fusion on my MacBookPro

[albert liu]

thanks rbridenbecker.
First to clearify, my vm is ubuntu 10.04.4 ( not vm directly from ion ).
I had tried installation without sudo which gave one more failed module of torrentR.
And yes, I did follow the build.txt.
any suggestion ?

[lwhitmore]

Torrent Suite for Mac

Does anyone know if there are instructions regarding how to use Torrent suite modules such as the analysis module

Thanks

[IonTorrent]

Does anyone know if there are instructions regarding how to use Torrent suite modules such as the analysis module

Thanks

Hi there,

If you are an Ion Torrent customer, the documentation for Torrent Suite may be found linked within Torrent Browser. For others, or for offline access, the relevant documents are also location on Ion Community. For example, the current Torrent Suite v3.6.2 documents may be found at:

http://ioncommunity.lifetechnologies.com/docs/DOC-3343

[Sacrolfur]

I can't build Torrent Suite on Ubuntu 13.04. I've downloaded its zip from github (https://github.com/iontorrent/TS), then I've installed all of the following packages:

apt-get install \
build-essential \
git-core \
cmake \
liblapack-dev \
liblapack3gf \
libblas-dev \
libblas3gf \
libatlas-base-dev \
gfortran \
zlib1g-dev \
libgsl0-dev \
libbz2-dev \
libcurl4-openssl-dev \
libncurses5-dev \
libboost-serialization-dev \
libfftw3-dev \
libhdf5-dev

And here I've already got a question: do I need to install lapack++. If I do, how can I do it? Because instructions which I can obtain from https://help.ubuntu.com/community/Lapack%2B%2B are not detailed enough.

I get the following errors while building TS:
CMake Error at /home/****/Downloads/TS-master/external/CMake/ExternalProject.cmake:585 (add_custom_command):
add_custom_command given APPEND option with output - several such errors for different modules

and

CMake Error at /home/******/Downloads/TS-master/external/CMake/ExternalProject.cmake:194 (define_property):
define_property given invalid argument "ExternalProject module.".
Thank you.