ThankGod E. Ebenezer
2014-10-22 17:44:28 UTC
Dear Scott,
I have now been able to get GBrowse successfully installed. I'm doing
the volvox tutorial
(http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html), and have gotten
to C. elegans part in section 4.1 (Uploading an annotation file).
Everything was smooth, until this point where I discovered I can't
upload a track per the C. elegans tutorial.
I followed the process, and when I tried to upload the
"elegans_acceptor.gff3" file, I get this error message: UPLOADED FILE
The server returned an error during upload [Remove Message]
I have also pasted a screen shot below of the error message whilst
trying to upload file.
This is the message from apache2.log:
xxx.x.x.x - - [22/Oct/2014:18:29:07 +0100] "POST
/cgi-bin/gb2/gbrowse/eleganc_core/ HTTP/1.1" 200 433
"http://localhost/cgi-bin/gb2/gbrowse/eleganc_core/" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
xxx.x.x.x - - [22/Oct/2014:18:29:07 +0100] "POST
/cgi-bin/gb2/gbrowse/eleganc_core/ HTTP/1.1" 500 630
"http://localhost/cgi-bin/gb2/gbrowse/eleganc_core/" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
Do you have any suggestion as to what may be wrong, or how I can get
this sorted out? A quick check on the web says is normally an apache
timeout issue, but the .gff file is 156 bytes, and contains just 2 lines
or 2 IDs, and should upload in less that a sec or two.
Also, I can browse the C. elegans database, but I was wondering why the
browser points to: /cgi-bin/gb2/gbrowse/eleganC_core/ rather than
/cgi-bin/gb2/gbrowse/eleganS_core/ is the former the default for the
tutorial? I checked my database name, as well as other configurations,
and they read /eleganS_ and not /eleganC_
Regards,
ThankGod
CORE C. ELEGANS ANNOTATIONS: 40 KBP FROM C01F4:1..40,000
Browser Select Tracks Snapshots Community Tracks Custom Tracks
Preferences
CUSTOM TRACKS
_[Help with uploading custom tracks]_ [1]
There are no tracks yet.
Add custom tracks : [From text] [From a URL] [From a file]
UPLOAD A TRACK FILE
UPLOADED FILE The server returned an error during upload [Remove
Message] [Cancel]
Links:
------
[1] http://localhost/gbrowse2/annotation_help.html
I have now been able to get GBrowse successfully installed. I'm doing
the volvox tutorial
(http://cloud.gmod.org/gbrowse2/tutorial/tutorial.html), and have gotten
to C. elegans part in section 4.1 (Uploading an annotation file).
Everything was smooth, until this point where I discovered I can't
upload a track per the C. elegans tutorial.
I followed the process, and when I tried to upload the
"elegans_acceptor.gff3" file, I get this error message: UPLOADED FILE
The server returned an error during upload [Remove Message]
I have also pasted a screen shot below of the error message whilst
trying to upload file.
This is the message from apache2.log:
xxx.x.x.x - - [22/Oct/2014:18:29:07 +0100] "POST
/cgi-bin/gb2/gbrowse/eleganc_core/ HTTP/1.1" 200 433
"http://localhost/cgi-bin/gb2/gbrowse/eleganc_core/" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
xxx.x.x.x - - [22/Oct/2014:18:29:07 +0100] "POST
/cgi-bin/gb2/gbrowse/eleganc_core/ HTTP/1.1" 500 630
"http://localhost/cgi-bin/gb2/gbrowse/eleganc_core/" "Mozilla/5.0 (X11;
Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0"
Do you have any suggestion as to what may be wrong, or how I can get
this sorted out? A quick check on the web says is normally an apache
timeout issue, but the .gff file is 156 bytes, and contains just 2 lines
or 2 IDs, and should upload in less that a sec or two.
Also, I can browse the C. elegans database, but I was wondering why the
browser points to: /cgi-bin/gb2/gbrowse/eleganC_core/ rather than
/cgi-bin/gb2/gbrowse/eleganS_core/ is the former the default for the
tutorial? I checked my database name, as well as other configurations,
and they read /eleganS_ and not /eleganC_
Regards,
ThankGod
CORE C. ELEGANS ANNOTATIONS: 40 KBP FROM C01F4:1..40,000
Browser Select Tracks Snapshots Community Tracks Custom Tracks
Preferences
CUSTOM TRACKS
_[Help with uploading custom tracks]_ [1]
There are no tracks yet.
Add custom tracks : [From text] [From a URL] [From a file]
UPLOAD A TRACK FILE
UPLOADED FILE The server returned an error during upload [Remove
Message] [Cancel]
Links:
------
[1] http://localhost/gbrowse2/annotation_help.html