Installing tranSMART

[ajpat...@wccnet.edu]

I discovered a couple of gotchas while installing tranSMART using the instructions:  https://wiki.transmartfoundation.org/display/transmartwiki/Install+the+current+official+release#Installthecurrentofficialrelease-all-in-oneAll-in-oneInstallScript,plusData-Loading

To start, things will go a little more smoothly if you remember to have a JDK installed and $JAVA_HOME set before executing the script...

transmart@server:~$ echo $JAVA_HOME
/usr/lib/jvm/java-7-openjdk-amd64

Then execution was halted while executing /home/transmart/transmart/transmart-data/R/other_pkg.R

Error in download.file(url = "http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.10.0.tar.gz"
,  :
  cannot open URL 'http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.10.0.tar.gz'
In addition: Warning message:
In download.file(url = "http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.10.0.tar.gz",  :
  cannot open: HTTP status was '404 Not Found'
Execution halted

The problem is that the resource isn't present, hence the HTTP status code.

One way to approach this problem is to find where the script that is requesting the nonexistent resource is located and change the URL:

grep -rn '/home/transmart/' -e 'QDNAseq_1.10.0.tar.gz'

Or, you can chase it down through the scripts.

It is located in /home/transmart/transmart/transmart-data/R/other_pkg.R

I used Google to find this: https://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.12.0.tar.gz

I don't know if it's OK to do this or not, but I just swapped out the relevant pieces of the URLs in the script file and it seems to work.


Another issue I ran into was this: Expected grails version 2.3.11 exactly; currently ; needs to be upgraded.

After chasing it down, I discovered that the script is just trying to execute grails and grails is not in the path.

 sudo find / -name 'grails'

export GRAILS_HOME=/path/to/grails 
export PATH=$PATH:$GRAILS_HOME/bin

(Source: https://stackoverflow.com/questions/7413061/setting-environment-variables)

That got it working.


The script failed during the setup of postgres due to a locale setting in my environment: 

locale-gen it_IT.utf8

And, finally, ~/Scripts/install-ubuntu/checks/checkWeb.sh can't see that the page loaded correctly because it's grepping for the wrong string.  I changed it to:

probe=$(curl -L $transmartUrl | grep "title" | grep "Transmart")

Looks good:
transmart@server:~/Scripts/install-ubuntu/checks$ ./checkAll.sh 2>&1 2>&1 | tee ~/checks.log
-------------------------------------
|  Checking for basic command-line tools; if any of the following does not exist,
|  then recheck the instructions for installing the missing items
-------------------------------------
git ok
make ok
java ok
ant ok
mvn ok
tar ok
rsync ok
php ok
g++ ok
gfortran ok
psql ok
groovy ok
grails ok
-------------------------------------
|  Checking for incompatible version of basic command-line tools;
|  If any problems are reported, then recheck the instructions,
|  and install or re-installing the missing items
-------------------------------------
The java version, 1.7.0_151, is good!
The php version, 5.5.9-1, is good!
The psql version, 9.3.18, is good!
The groovy version, 2.4.5, is good!
The grails version, 2.3.11, is good!
-------------------------------------
|  Checking for required files and folders from basic set up
-------------------------------------
|  ALL Required files and folders from basic set up are present
-------------------------------------
-------------------------------------
|  Checking for tomcat install and modifications to tomcat configuration

[Ward Weistra - The Hyve]

Thank you very much for your careful feedback! And also thanks to the two recent commenters on the page: https://wiki.transmartfoundation.org/display/transmartwiki/Install+the+current+official+release?focusedCommentId=13467724#comment-13467724.

Peter Rice will look at these suggestions soon and incorporate them in the instructions.

Best regards,
Ward

[karsten...@outlook.com]

Thank's for the feedback, that was helpful.

 

Originally, I planned to install transmart on Centos 7 but the provided installation scripts didn't work as I had imagined for that platform. In the end I followed the instructions and installed transmart on Ubuntu 14.04. That worked much better, but there are still a few additional issues that can be encountered:

 

1) After a reboot neither RServe nor SOLR startet automatically

2) The installation of R fails and manual intervention is required

                cran_pkg.R - By choosing a different cran mirror installation of the packages succeded

                other_pkg.R - I couldn't find a suitable mirror for the required packages (manual installation from source might be necessary?).

               

                The downloaded default version of R 3.2.x is outdated --> required packages are not available. Is it possible to replace this version with something up to date or are there any concequences to be expected?

 

How is the software distribution process to be handled in the future? The current approach with the install scripts (bash, R, php, make ...) seems to be quite error prone. Especially in regards to the existing dependancy on third party provided services on hosting R packages, no stable conditions can be expected for the setup process at all. Also, some system specific differences are not really taken into account (Ubuntu vs RHEL) and the install scripts may not work as intended. It might be better to remove install-rhel at the moment.

 

I believe deployment would be much, much easier and faster with a current version of transmart being provided as a vm-image and also better for the reproducibility of analytic results.

Best regards
Karsten

   
   
 

[karsten...@outlook.com]

Another issue:
1) The hostname for the online help is incorrect and points to the wrong location. Is is possible to set the correct path?

[karsten...@outlook.com]

2) Where can I change the mail address for the contact listed in the main page? Changes made to

cd /usr/share/tomcat7/.grails/transmartConfig/Config.groovy

// contact email address
com.recomdata.contactUs = "karsten...@outlook.com"

and

// site administrator contact email address
com.recomdata.adminEmail = "karsten...@outlook.com"

doesn't seem to have any influence here!

[Ruslan Forostianov - The Hyve]

Hi Karsten,

It's com.recomdata.administrator.

Cheers,

Ruslan

[karsten...@outlook.com]

Thank you very much, adding com.recomdata.administrator to the config and setting the mail fixed it.