ATAQS installation on a windows 7 64bit machine
Fabian Bindel
just to introduce myself a bit. I recently started my PhD in the field
of Targeted Proteomics using SRM. While I was searching for post-data
analysis I found your cool paper (I like the concept having a complete
project management available) introducing ATAQS.
I immediately downloaded it to my machine (Windows 7 64 bit). The
installation guide is quite challeging for me. I installed each of the
required software, also with the recommended version.
each software runs smoothly seperately (apache on localhost, mysql
server, firegoose, java jdk has to be installed instead of jre).
But after this I was kind of lost. Because I did not know where to put
the ATAQS "installation" files (just unpacked it). At first I put it
into the localhost accessible folder (tomcat.root/webapps/root/ATAQS).
After this I just continued with B and D.
So as far as I understood the point E you do not need to configure any
file because the only file to modify to your needs will be the
"build.properties" in the conf directory. But there I had problems
when then compiling at the end.
My build.properties look like this:
webapp.name=ATAQS
tomcat.root=C:/Program Files/Apache Software Foundation/Tomcat 6.0/
deployment.root=${tomcat.root}/webapps/ROOT/
webapp.root=${deployment.root}/${webapp.name}
# zip root directory
zip.dir=${webapp.root}/analysis/zip
# configuration file root directory
conf.xml.dir=${webapp.root}/conf
# output file root directory
output.dir=${webapp.root}/ATAQS_output
# data file root directory e.g. LCMS data
data.webserver.dir=${webapp.root}/mzxml
# Location of the executables and scripts.
# IMPORTANT: The property (bin.webserver.dir) should be specified ONLY
if the
# directory is accessible on the machine hosting the
webserver.
# In addition, the value should be the same as that given
# in the bin_location element of conf/locations.xml file.
# If the directory is not accessible on the webserver,
# comment out this property.
bin.webserver.dir=${tomcat.root}/webapps/ROOT/ATAQS/
# DataBase connection properties
database.connection.url=jdbc:mysql://loclahost:3306/ataqs
database.connection.username=****
database.connection.password=****
##############################################################################
# Job scheduler Properties
# If jobs should be submitted as a special user, the following
properties
# have to be set.
# Password-less ssh to scheduler.ssh.host needs to be set up for
# the scheduler.ssh.user.
##############################################################################
srm.scheduler.ssh.host=localhost:8080
srm.scheduler.ssh.user=ataqs
srm.scheduler.ssh.idfile=~/.ssh/id_dsa
# -------------------------------------------------------------------
# GWT properties
# -------------------------------------------------------------------
# Target OS can be one of "mac", "linux" or "windows"
# This is used for selecting the appropriate gwt jar file for running
# the GWT compiler.
targetos=windows
For point G I just created with the code inside the createDB.sql file
the mysql database (in this file there are already 6 users) and the
admin password is for sure encrypted. Thus I created a new admin with
my info. But I had a problem to add the information of the mysql url.
In your example you have jdbc:mysql://YOUR-DATABASE-URL/ATAQS with the
User and Password, but the user and password are not in the database
itself, thus I think this is just random and you have to use the info
as an admin I created ( jdbc:mysql://localhost:3033/ATAQS).
After all the steps I went to the ATAQS installation directory in the
command line of Windows and made the different steps: ant build, ant
war_build, ant war_deploy. Subsequently I wanted to try it on my
localhost:8080/ATAQS but there was no page available because there was
no *.html or *.php.
So I tried to access the localhost:8080/ATAQS/warATAQS/warATAQS.html.
There I got the page that I can login, but I do not know which user.
I know a lot of info. To put in into a nutshell:
1) I do not get the directory structure for the installation and in
the build.properties
2) After the ant build steps I do not know where to acces ATAQS then.
But this could be related to the first point. Because I compiled it
wrong.
3) Have you actually ever tried ATAQS on Windows?
4) Would it be possible to just download a virtual machine with linux?
Besides my problems thank you for the effort you put into this! I
looking forward for more stuff of you.
Any further suggestions/comments/help is totally welcome. Maybe
somebody already installed it into a virtual machine with linux and it
is running.
Thank you very much and yours faithfully,
Fabian
Mi-Youn Brusniak
Dear Fabian,
Thank you for the detailed information on what you are trying to do. SRM is an exciting technology for investigating proteomics study (in my opinion : -).
First, I would like to mention that similar to any academic software, we have developed the pipeline and software for our institutional needs for studying biology. More specifically, from the day one, we put our efforts to run software in server sides with multi user access in minds. Therefore, all the heavy duty works and files are in servers and clients (chemists/ biologists/ bioinformaticians) simply need firefox browser in their desktop or laptop.
Therefore, in spite of the comments block in build.properties regarding target OS, we really did not test out for mac or windows other than linux. We thought about expansion to other OS but not any time soon in near future given funding :-( However, we might put some effort to put them in Clouds computing in near future. I hope that if there are needs, capable window software engineer from this community contributes porting of the open source ATAQS codes for window and mac someday.
Meanwhile, I can answer some of your questions (inserted to your questions in red) and some of them I can't since I do not have experience on deploying ATAQS in window and I am J2EE linux software engineer and computational biologist, not good window OS software engineer :-)
Warm Regards,
Mi-Youn
Mi-Youn Brusniak, PhD
Computational Biologist/Sr. Software Engineer
Institute for Systems Biology | Seattle Proteome Center | 401 Terry Ave N. Seattle WA 98109
Revolutionizing science. Enhancing life.
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> Please take a look at section H for configure MYSQL.
You can use org.systemsbiology.apps.gui.server.provider.user.PasswordEncrypter. More specifically, you can invoke the following command line and you can get your encrypted password. In this example, "yourpasswd" was encrypted.
java -cp /serum/analysis/SRM/bin/ATAQS.jar:/serum/analysis/SRM/bin/aebersoldlab_apache995.jar org.systemsbiology.apps.gui.server.provider.user.PasswordEncrypter yourpasswd
ae782bd3b4ff14129c585c5b64bca56ed941319
> Put the encrypted pass word to sql/createDB.sql with your email, user name etc. Please make sure that last field “admin BOOLEAN” to be true.
> use the following command to add your group or your password (admin) to ATAQSDatabase
Mysql –u root –p < createDB.sql
Ø Now, when you login using the username and password that you created, you will get “admin” page that you can add other users. – please see ATAQS tutorial in http://tools.proteomecenter.org/ATAQS/ATAQS.html
Ø
I know a lot of info. To put in into a nutshell:
1) I do not get the directory structure for the installation and in
the build.properties
2) After the ant build steps I do not know where to acces ATAQS then.
But this could be related to the first point. Because I compiled it
wrong.
3) Have you actually ever tried ATAQS on Windows?
> All three questions, I do not know the answer since it’s window specific L sorry. Could anybody else can help on this?
The build.properties and configuration file is an example of LINUX system we are using (not window).
4) Would it be possible to just download a virtual machine with linux?
In theory, it should work in virtual machine with linux. I highly recommend to go this route rather than window.
Besides my problems thank you for the effort you put into this! I
looking forward for more stuff of you.
Any further suggestions/comments/help is totally welcome. Maybe
somebody already installed it into a virtual machine with linux and it
is running.
Thank you very much and yours faithfully,
Fabian
Warm Regards,
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Fabian Bindel
thank you very much for your fast answer. I hoped for another one,
more user and windows friendly :).
Because I am only an End-User of Windows with beginner experience on
(Web)Server installation
and configuration.
Therefore I am also hoping for the help of other ATAQS users, too.
Maybe somebody of you has
already some advice.
By the way, would it be also not easier for your distribution of ATAQS
to
share it via a working virtual machine? I found http://www.thoughtpolice.co.uk/vmware/
where you can download already linux images for free. I just
downloaded
the fedora version 14. So I just wanted to proceed with that.
Do you have maybe by any chance a more detailed installation
instruction
for linux beginners?
Thank you very much for your effort.
Kind Regards,
Fabian
On 1 Jul., 19:35, "Mi-Youn Brusniak" <mbrusn...@systemsbiology.org>
wrote:
> * Now, when you login using the username and password that you
> created, you will get "admin" page that you can add other users. - please
> see ATAQS tutorial inhttp://tools.proteomecenter.org/ATAQS/ATAQS.html
> *
> 1) I do not get the directory structure for the installation and in
> the build.properties
> 2) After the ant build steps I do not know where to acces ATAQS then.
> But this could be related to the first point. Because I compiled it
> wrong.
> 3) Have you actually ever tried ATAQS on Windows?
> > All three questions, I do not know the answer since it's window specific