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Old 06-12-2013, 11:25 AM   #1
razzmataz
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Default building Torrent Suite v3.6

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!
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Old 06-19-2013, 03:56 PM   #2
jtackney
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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.
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Old 06-20-2013, 07:39 AM   #3
razzmataz
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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!
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Old 07-03-2013, 01:39 PM   #4
rbridenbecker
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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
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Old 08-14-2013, 11:45 PM   #5
ppsw
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Default 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/dis...allation+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,
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Old 08-15-2013, 06:55 PM   #6
rbridenbecker
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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
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Old 08-19-2013, 12:29 AM   #7
ppsw
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It almost worked. Three modules failed to build: gpu, Analysis and torrentR.

Do you know if it's necessary to build under sudo?
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Old 08-19-2013, 08:36 AM   #8
albert liu
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Question 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
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Old 08-20-2013, 04:29 PM   #9
rbridenbecker
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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.
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Old 08-20-2013, 04:37 PM   #10
lwhitmore
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Default Torrent Suite for Mac

Does anyone know if there is way to use torrent suite v3.6.2 on a mac ??
Thanks !
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Old 08-20-2013, 05:58 PM   #11
rbridenbecker
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Quote:
Originally Posted by lwhitmore View Post
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
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Old 08-21-2013, 08:08 AM   #12
albert liu
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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 ?

Last edited by albert liu; 08-21-2013 at 12:48 PM.
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Old 08-21-2013, 04:08 PM   #13
lwhitmore
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Default Torrent Suite for Mac

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

Thanks
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Old 08-22-2013, 09:31 AM   #14
IonTorrent
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Quote:
Originally Posted by lwhitmore View Post
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
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Old 12-08-2013, 11:45 PM   #15
Sacrolfur
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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.
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Old 12-09-2013, 08:59 AM   #16
albert liu
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Hi :
My solution for running a TS after failed to install on Ubuntu 12.04 and 10.04.
-- run the vm ( ts 4 and ts 3.6 directly downloaded from ion community ) .
First , I tested the vm on vm player ( free from vmware ).
Now I have both TS 4 and TS 3.6 on vmware station 10 on my Ubuntu 12.04 server.
Just an alternative. Hope this help.
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Old 12-09-2013, 09:37 AM   #17
Sacrolfur
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Quote:
Originally Posted by albert liu View Post
Hi :
My solution for running a TS after failed to install on Ubuntu 12.04 and 10.04.
-- run the vm ( ts 4 and ts 3.6 directly downloaded from ion community ) .
First , I tested the vm on vm player ( free from vmware ).
Now I have both TS 4 and TS 3.6 on vmware station 10 on my Ubuntu 12.04 server.
Just an alternative. Hope this help.
Thank you for the reply, Albert!
With vm I have a problem, too. I can't understand how to upload reads of Ion Torrent to the Torrent Server. On the site of ioncommunity I've read that raw data from sequencer will send to the server automatically. But I have only reads. So maybe you can tell me how to upload them to the VM and analyse?
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Old 12-10-2013, 06:32 AM   #18
albert liu
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Hi Sacrolfur :

-- Please note unless you are comfortable with ubuntu commands , you could mess up your TS server and your data.----

What do you want from the vm ?
1. reanalysed from previous run ( 1.wells Files )
2. from raw data (DAT )
What version of TS you are running now?
With the TS 4 you should be able to export and import reports using web interface.
This is the best way.
----------- Here is my experience and only for reference-------
I had tried both raw data and reports ( 1.wells ) on my vm.
due to some issues , I did not analyed from the raw data.
Again, Here is my situation and solution.
I need to reanalyse reports generated with 3.4 by 3.6.
Since I just updated my TS to 4.
I can only used the vm3.6 to do the job.
-- Please note unless you are comfortable with ubuntu command , you could mess up your TS server and your data.----

My host (Avatar)-ubuntu 12.04 server with NFS for data archive and storage.
My guest (ts3.6 vm )
ion torrent TS (G)-- connect to two NFS ( one is Avatar ) for reports storage.
1. download vm3.6 from ion community

2. run with vmware player /vmware workstation10
configure sharing_folder on both host and guest
guest(ts3.6vm) :
mkdir vmsharing
sudo mount -t vmhgfs .host:/ /home/ionadmin/vmsharing

3. copy iondb from your Torrent server to vm3.6
-- ssh into TS server with ionadmin and
pg_dump -C -h localhost -U ion iondb > iondb.sql

4. copy iondb.sql to vmsharing
5. Stop vm torrent server background processes
sudo /etc/init.d/ionCrawler stop
sudo /etc/init.d/ionJobServer stop
sudo /etc/init.d/ionPlugin stop
sudo /etc/init.d/celeryd stop

6. Switch users to postgres
sudo su postgres
7. restart postgres
/etc/init.d/postgresql-8.4 restart
8. dropdb iondb
9. Create a new db
psql <<- EOFdb
CREATE DATABASE iondb;
GRANT ALL PRIVILEGES ON DATABASE iondb to ion;
\q
EOFdb

10. copy the iondb
psql -U ion -d iondb -f iondb.sql
11. restart vm and check with webbroswer to verify the db is updated
12. update reference Hg19 , bed files and plugin
copy hg19 folder from gandlaf to vm and upload beds

13. rename /results/PGM_test to match your TS
mv PGM_test snnnnnn
14. copy reports to vm
cp -R /home/ionadmin/vmsharing/*SN2* /results/analysis/output/Home/
15. copy raw data to vm
cp -R /home/ionadmin/vmsharing/R* /results/snnnnnn
16. change the owner and group from ionadmin to www-data
sudo chown -R www-data:www-data *

--most information are from ion community --
some modification for copy iondb
hope this help.
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