Unable to run in on localserver

[shashvattrip]

Hey,
I have ubuntu 14.04. I git cloned your repo it in /var/www/html
I then tried out your commands but it just outputs the file contents to stdin. Please help me out.
Thanks!

[maximilianh]

The instructions do not mention /var/www/html but your cgi-bin directory. Please google it again or look at the readme, I'm on the road it might be something like usr/lib/cgi-bin

On Mar 6, 2015, at 18:55, slearner [email protected] wrote:

Hey,
I have ubuntu 14.04. I git cloned your repo it in /var/www/html
I then tried out your commands but it just outputs the file contents to stdin. Please help me out.
Thanks!

—
Reply to this email directly or view it on GitHub.

[maximilianh]

Yes it's /usr/lib/cgi-bin on ubuntu, that's written in the readme file I
think. I'll make this clearer.

Just move everything into /usr/lib/cgi-bin and it should work.

cheers
Max

On Fri, Mar 6, 2015 at 7:06 PM, [email protected] wrote:

The instructions do not mention /var/www/html but your cgi-bin directory.
Please google it again or look at the readme, I'm on the road it might be
something like usr/lib/cgi-bin

On Mar 6, 2015, at 18:55, slearner [email protected] wrote:

Hey,
I have ubuntu 14.04. I git cloned your repo it in /var/www/html
I then tried out your commands but it just outputs the file contents to
stdin. Please help me out.
Thanks!

—
Reply to this email directly or view it on GitHub
#1.

[shashvattrip]

Hey
I did try it first in /usr/lib/cgi-bin but then got this error

Resolving localhost (localhost)... 127.0.0.1
Connecting to localhost (localhost)|127.0.0.1|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-03-07 00:27:24 ERROR 404: Not Found.

Which makes sense because all the server files are usually set up in /var/www/html for ubuntu 12.04 which is why I moved it there and then tried it out.
And thanks for helping me out. I really appreciate it! :D

[maximilianh]

what exactly did you try? Did you try localhost:/cgi-bin/ucscBeacon/query ?

/var/www/html is only for html files.
/usr/lib/cgi-bin is for scripts.

this is not an html file but a script so it really goes into
/usr/lib/cgi-bin.

I can try this on a fresh ubuntu install tomorrow.

On Fri, Mar 6, 2015 at 7:59 PM, slearner [email protected] wrote:

Hey
I did try it first in /usr/lib/cgi-bin but then got this error

Resolving localhost (localhost)... 127.0.0.1
Connecting to localhost (localhost)|127.0.0.1|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-03-07 00:27:24 ERROR 404: Not Found.

Which makes sense because all the server files are usually set up in
/var/www/html for ubuntu 12.04 which is why I moved it there and then tried
it out.

—
Reply to this email directly or view it on GitHub
#1 (comment)
.

[shashvattrip]

Yes, I did try
http://localhost/cgi-bin/ucscBeacon/query
But it just gave me this error,
The requested URL /cgi-bin/ucscBeacon/query was not found on this server.

Here's what I have done till now, in the following order,
cd /usr/lib/cgi-bin
git clone https://github.com/maximilianh/ucscBeacon.git

sudo apachctl -k restart //this gives me an error that apachctl : bad command, so I do instead
sudo apache2ctl -k restart

Next I try to test it by typing in the terminal, this is what I get :

/usr/lib/cgi-bin/ucscBeacon(branch:master) » wget 'http://localhost/cgi-bin/ucscBeacon/query' -O -

--2015-03-07 01:06:09-- http://localhost/cgi-bin/ucscBeacon/query
Resolving localhost (localhost)... 127.0.0.1
Connecting to localhost (localhost)|127.0.0.1|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-03-07 01:06:09 ERROR 404: Not Found.

[maximilianh]

OK I've figured it out, one needs to activate the cgi-bin module first in
Ubuntu, looks like I did that a long time ago on mine, I just tried on a
fresh ubuntu install, these are the commands (now in the README file too):

sudo apt-get install apache2 git
sudo a2enmod cgi
sudo service apache2 restart
cd /usr/lib/cgi-bin
git clone https://github.com/maximilianh/ucscBeacon.git

On Fri, Mar 6, 2015 at 8:38 PM, slearner [email protected] wrote:

In the following order,
cd /usr/lib/cgi-bin
git clone https://github.com/maximilianh/ucscBeacon.git

sudo apachctl -k restart //this gives me an error that apachctl : bad
command, so I do instead
sudo apache2ctl -k restart

Next I try to test it by typing in the terminal, this is what I get :

/usr/lib/cgi-bin/ucscBeacon(branch:master) » wget '
http://localhost/cgi-bin/ucscBeacon/query' -O -

--2015-03-07 01:06:09-- http://localhost/cgi-bin/ucscBeacon/query
Resolving localhost (localhost)... 127.0.0.1
Connecting to localhost (localhost)|127.0.0.1|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2015-03-07 01:06:09 ERROR 404: Not Found.

—
Reply to this email directly or view it on GitHub
#1 (comment)
.

[shashvattrip]

Ah. Perfect! It works now.
Thanks a ton!

[maximilianh]

can you tell me which data types you want to serve? and maybe a little bit
of background (institution?).

are you planning to serve allele frequencies? How "clinical" is the dataset?

On Fri, Mar 6, 2015 at 10:02 PM, slearner [email protected] wrote:

Ah. Perfect! It works now.
Thanks a ton!

—
Reply to this email directly or view it on GitHub
#1 (comment)
.

[shashvattrip]

The goal of the project is to implement a JavaScript frontend for configuring and monitoring an implementation of the beacon API. The tool should allow people without software development background to easily make a reference beacon implementation serve the data they want to share.
I want to do this for multiple beacons and am going to begin with yours.
I am doing this with Global Alliance for Genomics and Health organization.

And to be honest, I have no idea what data type I want to serve, I have no background in genetics, and have no idea how clinical the dataset it. :)
Check this out : Last Project : Beacon management console
https://docs.google.com/document/d/1PHPDTzD4Z6xVoxN0Q1F8yEPclSri-JA1vLvMTrLYUi8/edit#

[maximilianh]

oh I see. sounds cool! Who are you working with on this?

On Sat, Mar 7, 2015 at 7:22 AM, slearner [email protected] wrote:

The goal of the project is to implement a JavaScript frontend for
configuring and monitoring an implementation of the beacon API. The tool
should allow people without software development background to easily make
a reference beacon implementation serve the data they want to share.
I want to do this for multiple beacons and am going to begin with yours.
I am doing this with Global Alliance for Genomics and Health organization.

And to be honest, I have no idea what data type I want to serve, I have no
background in genetics, and have no idea how clinical the dataset it. :)

—
Reply to this email directly or view it on GitHub
#1 (comment)
.

[shashvattrip]

Working with @mcupak https://github.com/mcupak