[galaxy-dev] Setting up Galaxy interface to motif finding software
Dear Galaxy developers, I hope you could help me with the following issue. I wish to use galaxy tools in our AMADEUS motif finding software: http://acgt.cs.tau.ac.il/amadeus/ AMADEUS helps many users who wish to find motifs in their sequences. AMADEUS has 2 limitations: 1. It can find motifs vs all organism's genome. 2. If the user don't want to find motif vs all organism's genome then The user itself will have to supply the sequences for the motif finding according to his chipSeq peaks he got. We would like that the user won't be troubled with the second limitation by adding locally\cloud Galaxy that downloads to AMADEUS the relevant sequences (~3000 sequences) according to the peaks locations from a BED file supplied by the user. As I see it - the galaxy installation will have to follow the objectives: 1. Work on windows OS. 2. Can be installed in the user computer by a script in AMADEUS 3. downloading time of the relevant sequences (~3000) won't take above 1-2 minutes I will appreciate if someone of you will guide me with the procedure and advise me with the best way to work with Galaxy-AMADEUS interface. Thanks, Tom hait ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Failed to run display.py
Hello,
Any updates about my problem?
I tried to deactivate the proxy by typing:
unsetenv http_proxy
unsetenv ftp_proxy
./scripts/api/display.py ff76834f42d18414b4aaed577466ef**35
http://localhost:8080/api/**libraries http://localhost:8080/api/libraries
the answer that I got:
and get the following error message:
HTTP Error 403: Forbidden
Provided API key is not valid.
tried to renew the key and still got the same answer.
Could you please help?
Thanks,
Tom.
On Sun, Oct 21, 2012 at 12:11 PM, Tom Hait sth...@gmail.com wrote:
Hello,
I'm new with Galaxy api.
I'm following the ReadMe file in script/api.
I'm trying to run:
python display.py ff76834f42d18414b4aaed577466ef35
http://0.0.0.0:8080/api/libraries
and it doesn't work, it says:
HTTP Error 503: Service Unavailable
!DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01 Transitional//EN
http://www.w3.org/TR/html4/loose.dtd;
HTMLHEADMETA HTTP-EQUIV=Content-Type CONTENT=text/html;
charset=iso-8859-1
TITLEERROR: The requested URL could not be retrieved/TITLE
STYLE
type=text/css!--BODY{background-color:#ff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--/STYLE
/HEADBODY
H1ERROR/H1
H2The requested URL could not be retrieved/H2
HR noshade size=1px
P
While trying to retrieve the URL:
A HREF=
http://0.0.0.0:8080/api/libraries?key=ff76834f42d18414b4aaed577466ef35;
http://0.0.0.0:8080/api/libraries?key=ff76834f42d18414b4aaed577466ef35/A
P
The following error was encountered:
UL
LI
STRONG
Connection to 0.0.0.0 Failed
/STRONG
/UL
P
The system returned:
PREI(111) Connection refused/I/PRE
P
The remote host or network may be down. Please try the request again.
PYour cache administrator is A HREF=mailto:root;root/A.
BR clear=all
HR noshade s
so I tried to change the URL to: http://localhost:8080,
http://127.0.0.1:8080 ...
It also didn't work.
Any Ideas about could go wrong?
Thanks,
Tom.
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
[galaxy-dev] Failed to run display.py
Hello,
I'm new with Galaxy api.
I'm following the ReadMe file in script/api.
I'm trying to run:
python display.py ff76834f42d18414b4aaed577466ef35
http://0.0.0.0:8080/api/libraries
and it doesn't work, it says:
HTTP Error 503: Service Unavailable
!DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01 Transitional//EN
http://www.w3.org/TR/html4/loose.dtd;
HTMLHEADMETA HTTP-EQUIV=Content-Type CONTENT=text/html;
charset=iso-8859-1
TITLEERROR: The requested URL could not be retrieved/TITLE
STYLE
type=text/css!--BODY{background-color:#ff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--/STYLE
/HEADBODY
H1ERROR/H1
H2The requested URL could not be retrieved/H2
HR noshade size=1px
P
While trying to retrieve the URL:
A HREF=
http://0.0.0.0:8080/api/libraries?key=ff76834f42d18414b4aaed577466ef35;
http://0.0.0.0:8080/api/libraries?key=ff76834f42d18414b4aaed577466ef35/A
P
The following error was encountered:
UL
LI
STRONG
Connection to 0.0.0.0 Failed
/STRONG
/UL
P
The system returned:
PREI(111) Connection refused/I/PRE
P
The remote host or network may be down. Please try the request again.
PYour cache administrator is A HREF=mailto:root;root/A.
BR clear=all
HR noshade s
so I tried to change the URL to: http://localhost:8080,
http://127.0.0.1:8080 ...
It also didn't work.
Any Ideas about could go wrong?
Thanks,
Tom.
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
Re: [galaxy-dev] Failed to run display.py
Hi Dannon, Thanks for the reply. Galaxy is running - I just typed http://localhost:8080 on the browser and I get the galaxy with the line: *Hello world! It's running...* * * *Tom. * On Sun, Oct 21, 2012 at 3:55 PM, Dannon Baker dannonba...@me.com wrote: On Oct 21, 2012, at 6:11 AM, Tom Hait sth...@gmail.com wrote: so I tried to change the URL to: http://localhost:8080, http://127.0.0.1:8080 ... It also didn't work. Any Ideas about could go wrong? First thing I'd check would be to verify that your galaxy server is currently running, and on localhost:8080. -Dannon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
