Re: [galaxy-user] visualization through Trackster on local Galaxy installation

2014-01-31 Thread Yupu Liang
Using full path in the ini file fix the problem!

Thanks,
Yupu
On Jan 30, 2014, at 10:21, Jennifer Jackson j...@bx.psu.edu wrote:

 Hi Yupu,
 
 I'm sorry, I mixed up the processing for custom builds with the processing 
 for installed builds in my initial reply. A .2bit  .len file are appropriate 
 for what you are doing - and the wiki instructions are accurate.
 
 Still, I double checked with Jeremy, the scientist that developed the tool, 
 about your issue. He found that the full path to the .len file needs to be 
 specified right now in order for installed builds to function correctly.
 
 This deviates from the wiki instructions, but we consider this a bug and plan 
 to correct it in the next release.
 
 Please try using the full path and let us know how that works out,
 
 Jen
 Galaxy team
 
 On 1/29/14 11:54 AM, Yupu Liang wrote:
 Dear Jennifer:
 
 Hi, I did put 2bit file as suggested by 
 https://wiki.galaxyproject.org/Visualization%20Setup.
 
 Should I get rid of the len file?  and I assume I will also need to take off 
 the len_file_path out of the universe_wsgi.ini file.
 
 In term of using .fasta file. I have them and I am not clear where I should 
 put them for visualization purpose and also what adjustment i need to make 
 in the ini file. Any help would be appreciated and I am really excited about 
 doing all the visualization within Galaxy. I think the biologists would 
 really love these features.
 
 Thanks a lot,
 Yupu
 
 
 
 
 On Jan 29, 2014, at 14:21, Jennifer Jackson j...@bx.psu.edu wrote:
 
 Hello Yupu,
 
 Using a .len file is problematic at this time. In the upcoming release this 
 will be corrected. Using a .fasta file is the solution. In many cases, 
 using a .fasta file can be preferred as it will include the reference 
 genome sequence in the visualization, but the choice is yours, once the 
 correction is released to the distribution.
 
 More about this is in a recent post from Jeremy:
 http://lists.bx.psu.edu/pipermail/galaxy-user/2014-January/007106.html
 
 Our apologies for the confusion this caused. The advice from Hans-Rudolf is 
 under normal circumstances the best first-pass route for troubleshooting, 
 and you will want to restart after using the fasta method as well.
 
 Best,
 
 Jen
 Galaxy team
 
 On 1/28/14 11:12 AM, Yupu Liang wrote:
 Hi,
 
 I am trying to set up the visualization functionality on our local Galaxy 
 installation. I followed the instructions on  
 https://wiki.galaxyproject.org/Visualization%20Setup
 
 And here is the list of len files:
 ls -l tool-data/shared/ucsc/chrom/
 total 200
 -rw-rw-r-- 1 galaxy galaxy10 Jan 27 15:13 centromeres1.len
 -rw-rw-r-- 1 galaxy galaxy   821 Jan 27 15:13 hg15.len
 -rw-rw-r-- 1 galaxy galaxy   713 Jan 27 15:13 hg16.len
 -rw-rw-r-- 1 galaxy galaxy   792 Jan 27 15:13 hg17.len
 -rw-rw-r-- 1 galaxy galaxy   855 Jan 27 15:13 hg18.len
 -rw-rw-r-- 1 galaxy galaxy   202 Jan 27 15:13 hg19Haps.len
 -rwxr-xr-x 1 galaxy galaxy  1971 Jan 27 15:13 hg19.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hg19LggInv.len
 -rw-rw-r-- 1 galaxy galaxy  4516 Jan 27 15:13 hg19Patch10.len
 -rw-rw-r-- 1 galaxy galaxy  1983 Jan 27 15:13 hg19Patch2.len
 -rw-rw-r-- 1 galaxy galaxy  2844 Jan 27 15:13 hg19Patch5.len
 -rw-rw-r-- 1 galaxy galaxy  3879 Jan 27 15:13 hg19Patch9.len
 -rw-rw-r-- 1 galaxy galaxy 11672 Jan 27 15:13 hg38.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef1.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef2.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef3.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 repBase0.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 repBase1.len
 -rw-rw-r-- 1 galaxy galaxy 12697 Jan 27 15:13 repeats2.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 simHuman.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 simHumanMammal.len
 -rw-rw-r-- 1 galaxy galaxy   362 Jan 27 15:13 venter1.len
 
 
 When I test the visualization through Trackster. I got the following error 
 after seeing a message saying preparing the data, this can take a 
 while……:
 
 Error: The requested genome file (tool-data/shared/ucsc/chrom/hg18.len) 
 could not be opened. Exiting!
 sort: write failed: standard output: Broken pipe
 sort: write error
 Couldn't open tool-data/shared/ucsc/chrom/hg18.len , No such file or 
 directory.
 
 
 It seems something else failed in the middle of visualization as I do have 
 the hg18.len under the default path with the global reading permission……..
 
 Does anybody have similar experience? Is there is way for me to debug?
 
 Best,
 Yupu
 ___
 The Galaxy User list should be used for the discussion of
 Galaxy analysis and other features on the public server
 at usegalaxy.org.  Please keep all replies on the list by
 using reply all in your mail client.  For discussion of
 local Galaxy instances and the Galaxy source code, please
 use the Galaxy Development list:
 
   http://lists.bx.psu.edu/listinfo/galaxy-dev
 
 

Re: [galaxy-user] visualization through Trackster on local Galaxy installation

2014-01-30 Thread Jennifer Jackson

Hi Yupu,

I'm sorry, I mixed up the processing for custom builds with the 
processing for installed builds in my initial reply. A .2bit  .len file 
are appropriate for what you are doing - and the wiki instructions are 
accurate.


Still, I double checked with Jeremy, the scientist that developed the 
tool, about your issue. He found that the full path to the .len file 
needs to be specified right now in order for installed builds to 
function correctly.


This deviates from the wiki instructions, but we consider this a bug and 
plan to correct it in the next release.


Please try using the full path and let us know how that works out,

Jen
Galaxy team

On 1/29/14 11:54 AM, Yupu Liang wrote:

Dear Jennifer:

Hi, I did put 2bit file as suggested by 
https://wiki.galaxyproject.org/Visualization%20Setup.

Should I get rid of the len file?  and I assume I will also need to take off 
the len_file_path out of the universe_wsgi.ini file.

In term of using .fasta file. I have them and I am not clear where I should put 
them for visualization purpose and also what adjustment i need to make in the 
ini file. Any help would be appreciated and I am really excited about doing all 
the visualization within Galaxy. I think the biologists would really love these 
features.

Thanks a lot,
Yupu




On Jan 29, 2014, at 14:21, Jennifer Jackson j...@bx.psu.edu wrote:


Hello Yupu,

Using a .len file is problematic at this time. In the upcoming release this 
will be corrected. Using a .fasta file is the solution. In many cases, using a 
.fasta file can be preferred as it will include the reference genome sequence 
in the visualization, but the choice is yours, once the correction is released 
to the distribution.

More about this is in a recent post from Jeremy:
http://lists.bx.psu.edu/pipermail/galaxy-user/2014-January/007106.html

Our apologies for the confusion this caused. The advice from Hans-Rudolf is 
under normal circumstances the best first-pass route for troubleshooting, and 
you will want to restart after using the fasta method as well.

Best,

Jen
Galaxy team

On 1/28/14 11:12 AM, Yupu Liang wrote:

Hi,

I am trying to set up the visualization functionality on our local Galaxy 
installation. I followed the instructions on  
https://wiki.galaxyproject.org/Visualization%20Setup

And here is the list of len files:
ls -l tool-data/shared/ucsc/chrom/
total 200
-rw-rw-r-- 1 galaxy galaxy10 Jan 27 15:13 centromeres1.len
-rw-rw-r-- 1 galaxy galaxy   821 Jan 27 15:13 hg15.len
-rw-rw-r-- 1 galaxy galaxy   713 Jan 27 15:13 hg16.len
-rw-rw-r-- 1 galaxy galaxy   792 Jan 27 15:13 hg17.len
-rw-rw-r-- 1 galaxy galaxy   855 Jan 27 15:13 hg18.len
-rw-rw-r-- 1 galaxy galaxy   202 Jan 27 15:13 hg19Haps.len
-rwxr-xr-x 1 galaxy galaxy  1971 Jan 27 15:13 hg19.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hg19LggInv.len
-rw-rw-r-- 1 galaxy galaxy  4516 Jan 27 15:13 hg19Patch10.len
-rw-rw-r-- 1 galaxy galaxy  1983 Jan 27 15:13 hg19Patch2.len
-rw-rw-r-- 1 galaxy galaxy  2844 Jan 27 15:13 hg19Patch5.len
-rw-rw-r-- 1 galaxy galaxy  3879 Jan 27 15:13 hg19Patch9.len
-rw-rw-r-- 1 galaxy galaxy 11672 Jan 27 15:13 hg38.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef1.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef2.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef3.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 repBase0.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 repBase1.len
-rw-rw-r-- 1 galaxy galaxy 12697 Jan 27 15:13 repeats2.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 simHuman.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 simHumanMammal.len
-rw-rw-r-- 1 galaxy galaxy   362 Jan 27 15:13 venter1.len


When I test the visualization through Trackster. I got the following error after seeing a 
message saying preparing the data, this can take a while……:

Error: The requested genome file (tool-data/shared/ucsc/chrom/hg18.len) could 
not be opened. Exiting!
sort: write failed: standard output: Broken pipe
sort: write error
Couldn't open tool-data/shared/ucsc/chrom/hg18.len , No such file or directory.


It seems something else failed in the middle of visualization as I do have the 
hg18.len under the default path with the global reading permission……..

Does anybody have similar experience? Is there is way for me to debug?

Best,
Yupu
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

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/


--
Jennifer 

Re: [galaxy-user] visualization through Trackster on local Galaxy installation

2014-01-30 Thread Jennifer Jackson

Yupu,

Very glad! The thanks goes to Jeremy who sorted out the issue.

We had some big changes the last few release cycles, and unexpected 
issues popped out. It was very nice of you to not only take the time to 
report the problem, but to also follow up with sending feedback until 
resolved.


If this is not corrected soon for some reason (as it is expected to be), 
I will add a temporary note to the wiki instructions. But, mainling list 
Q  A, like this conversation, will show up in our Galaxy custom 
searches. So can certainly help others, just as it is, right now.


Thanks again, your patience and help confirming the work-around in a 
local build (one not run by a team member) are very much appreciated!


Best,

Jen
Galaxy team

On 1/30/14 9:17 AM, Yupu Liang wrote:

Using full path in the ini file fix the problem!

Thanks,
Yupu
On Jan 30, 2014, at 10:21, Jennifer Jackson j...@bx.psu.edu wrote:




--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

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-user] visualization through Trackster on local Galaxy installation

2014-01-29 Thread Hans-Rudolf Hotz

Hi Yupu


Just double checking: Have you restarted your Galaxy server after adding 
the len files?



Regards, Hans-Rudolf


On 01/28/2014 08:12 PM, Yupu Liang wrote:

Hi,

I am trying to set up the visualization functionality on our local Galaxy 
installation. I followed the instructions on  
https://wiki.galaxyproject.org/Visualization%20Setup

And here is the list of len files:
ls -l tool-data/shared/ucsc/chrom/
total 200
-rw-rw-r-- 1 galaxy galaxy10 Jan 27 15:13 centromeres1.len
-rw-rw-r-- 1 galaxy galaxy   821 Jan 27 15:13 hg15.len
-rw-rw-r-- 1 galaxy galaxy   713 Jan 27 15:13 hg16.len
-rw-rw-r-- 1 galaxy galaxy   792 Jan 27 15:13 hg17.len
-rw-rw-r-- 1 galaxy galaxy   855 Jan 27 15:13 hg18.len
-rw-rw-r-- 1 galaxy galaxy   202 Jan 27 15:13 hg19Haps.len
-rwxr-xr-x 1 galaxy galaxy  1971 Jan 27 15:13 hg19.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hg19LggInv.len
-rw-rw-r-- 1 galaxy galaxy  4516 Jan 27 15:13 hg19Patch10.len
-rw-rw-r-- 1 galaxy galaxy  1983 Jan 27 15:13 hg19Patch2.len
-rw-rw-r-- 1 galaxy galaxy  2844 Jan 27 15:13 hg19Patch5.len
-rw-rw-r-- 1 galaxy galaxy  3879 Jan 27 15:13 hg19Patch9.len
-rw-rw-r-- 1 galaxy galaxy 11672 Jan 27 15:13 hg38.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef1.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef2.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef3.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 repBase0.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 repBase1.len
-rw-rw-r-- 1 galaxy galaxy 12697 Jan 27 15:13 repeats2.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 simHuman.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 simHumanMammal.len
-rw-rw-r-- 1 galaxy galaxy   362 Jan 27 15:13 venter1.len


When I test the visualization through Trackster. I got the following error after seeing a 
message saying preparing the data, this can take a while……:

Error: The requested genome file (tool-data/shared/ucsc/chrom/hg18.len) could 
not be opened. Exiting!
sort: write failed: standard output: Broken pipe
sort: write error
Couldn't open tool-data/shared/ucsc/chrom/hg18.len , No such file or directory.


It seems something else failed in the middle of visualization as I do have the 
hg18.len under the default path with the global reading permission……..

Does anybody have similar experience? Is there is way for me to debug?

Best,
Yupu
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

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/


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

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-user] visualization through Trackster on local Galaxy installation

2014-01-29 Thread Yupu Liang
Yes I have restarted my Galaxy many times and I have also tried different 
genome build such as hg18 and experience the same problem.

Yupu
On Jan 29, 2014, at 3:32, Hans-Rudolf Hotz h...@fmi.ch wrote:

 Hi Yupu
 
 
 Just double checking: Have you restarted your Galaxy server after adding the 
 len files?
 
 
 Regards, Hans-Rudolf
 
 
 On 01/28/2014 08:12 PM, Yupu Liang wrote:
 Hi,
 
 I am trying to set up the visualization functionality on our local Galaxy 
 installation. I followed the instructions on  
 https://wiki.galaxyproject.org/Visualization%20Setup
 
 And here is the list of len files:
 ls -l tool-data/shared/ucsc/chrom/
 total 200
 -rw-rw-r-- 1 galaxy galaxy10 Jan 27 15:13 centromeres1.len
 -rw-rw-r-- 1 galaxy galaxy   821 Jan 27 15:13 hg15.len
 -rw-rw-r-- 1 galaxy galaxy   713 Jan 27 15:13 hg16.len
 -rw-rw-r-- 1 galaxy galaxy   792 Jan 27 15:13 hg17.len
 -rw-rw-r-- 1 galaxy galaxy   855 Jan 27 15:13 hg18.len
 -rw-rw-r-- 1 galaxy galaxy   202 Jan 27 15:13 hg19Haps.len
 -rwxr-xr-x 1 galaxy galaxy  1971 Jan 27 15:13 hg19.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hg19LggInv.len
 -rw-rw-r-- 1 galaxy galaxy  4516 Jan 27 15:13 hg19Patch10.len
 -rw-rw-r-- 1 galaxy galaxy  1983 Jan 27 15:13 hg19Patch2.len
 -rw-rw-r-- 1 galaxy galaxy  2844 Jan 27 15:13 hg19Patch5.len
 -rw-rw-r-- 1 galaxy galaxy  3879 Jan 27 15:13 hg19Patch9.len
 -rw-rw-r-- 1 galaxy galaxy 11672 Jan 27 15:13 hg38.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef1.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef2.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef3.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 repBase0.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 repBase1.len
 -rw-rw-r-- 1 galaxy galaxy 12697 Jan 27 15:13 repeats2.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 simHuman.len
 -rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 simHumanMammal.len
 -rw-rw-r-- 1 galaxy galaxy   362 Jan 27 15:13 venter1.len
 
 
 When I test the visualization through Trackster. I got the following error 
 after seeing a message saying preparing the data, this can take a while……:
 
 Error: The requested genome file (tool-data/shared/ucsc/chrom/hg18.len) 
 could not be opened. Exiting!
 sort: write failed: standard output: Broken pipe
 sort: write error
 Couldn't open tool-data/shared/ucsc/chrom/hg18.len , No such file or 
 directory.
 
 
 It seems something else failed in the middle of visualization as I do have 
 the hg18.len under the default path with the global reading permission……..
 
 Does anybody have similar experience? Is there is way for me to debug?
 
 Best,
 Yupu
 ___
 The Galaxy User list should be used for the discussion of
 Galaxy analysis and other features on the public server
 at usegalaxy.org.  Please keep all replies on the list by
 using reply all in your mail client.  For discussion of
 local Galaxy instances and the Galaxy source code, please
 use the Galaxy Development list:
 
   http://lists.bx.psu.edu/listinfo/galaxy-dev
 
 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/
 


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

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-user] visualization through Trackster on local Galaxy installation

2014-01-29 Thread Jennifer Jackson

Hello Yupu,

Using a .len file is problematic at this time. In the upcoming release 
this will be corrected. Using a .fasta file is the solution. In many 
cases, using a .fasta file can be preferred as it will include the 
reference genome sequence in the visualization, but the choice is yours, 
once the correction is released to the distribution.


More about this is in a recent post from Jeremy:
http://lists.bx.psu.edu/pipermail/galaxy-user/2014-January/007106.html

Our apologies for the confusion this caused. The advice from Hans-Rudolf 
is under normal circumstances the best first-pass route for 
troubleshooting, and you will want to restart after using the fasta 
method as well.


Best,

Jen
Galaxy team

On 1/28/14 11:12 AM, Yupu Liang wrote:

Hi,

I am trying to set up the visualization functionality on our local Galaxy 
installation. I followed the instructions on  
https://wiki.galaxyproject.org/Visualization%20Setup

And here is the list of len files:
ls -l tool-data/shared/ucsc/chrom/
total 200
-rw-rw-r-- 1 galaxy galaxy10 Jan 27 15:13 centromeres1.len
-rw-rw-r-- 1 galaxy galaxy   821 Jan 27 15:13 hg15.len
-rw-rw-r-- 1 galaxy galaxy   713 Jan 27 15:13 hg16.len
-rw-rw-r-- 1 galaxy galaxy   792 Jan 27 15:13 hg17.len
-rw-rw-r-- 1 galaxy galaxy   855 Jan 27 15:13 hg18.len
-rw-rw-r-- 1 galaxy galaxy   202 Jan 27 15:13 hg19Haps.len
-rwxr-xr-x 1 galaxy galaxy  1971 Jan 27 15:13 hg19.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hg19LggInv.len
-rw-rw-r-- 1 galaxy galaxy  4516 Jan 27 15:13 hg19Patch10.len
-rw-rw-r-- 1 galaxy galaxy  1983 Jan 27 15:13 hg19Patch2.len
-rw-rw-r-- 1 galaxy galaxy  2844 Jan 27 15:13 hg19Patch5.len
-rw-rw-r-- 1 galaxy galaxy  3879 Jan 27 15:13 hg19Patch9.len
-rw-rw-r-- 1 galaxy galaxy 11672 Jan 27 15:13 hg38.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef1.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef2.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 hlaRef3.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 repBase0.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 repBase1.len
-rw-rw-r-- 1 galaxy galaxy 12697 Jan 27 15:13 repeats2.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 simHuman.len
-rw-rw-r-- 1 galaxy galaxy67 Jan 27 15:13 simHumanMammal.len
-rw-rw-r-- 1 galaxy galaxy   362 Jan 27 15:13 venter1.len


When I test the visualization through Trackster. I got the following error after seeing a 
message saying preparing the data, this can take a while……:

Error: The requested genome file (tool-data/shared/ucsc/chrom/hg18.len) could 
not be opened. Exiting!
sort: write failed: standard output: Broken pipe
sort: write error
Couldn't open tool-data/shared/ucsc/chrom/hg18.len , No such file or directory.


It seems something else failed in the middle of visualization as I do have the 
hg18.len under the default path with the global reading permission……..

Does anybody have similar experience? Is there is way for me to debug?

Best,
Yupu
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

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/



--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

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/