subject:"Re\: \[galaxy\-dev\] read_bits64 error when loading large genomes\/data into trackster"

Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster

2014-04-16 Thread Raj Ayyampalayam


Thanks Jeremy.

-Raj

On Wednesday, April 16, 2014 9:32:23 AM, Jeremy Goecks wrote:

Hi Raj,

Thanks for sharing your datasets. This issue should be fixed as of
this commit in -central:

https://bitbucket.org/galaxy/galaxy-central/commits/3a154b52090316dee61f42993eaa5a1fa40116d3

Best,
J.

--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University



On Mar 25, 2014, at 11:15 AM, Raj Ayyampalayam mailto:ra...@uga.edu>> wrote:


Jeremy,

I uploaded my dataset to the main galaxy site and the visualization
failed.
Here is the link to the history:
https://usegalaxy.org/u/raj-a-n/h/amborella-viz-test
I used the same genome and a cufflinks gtf file instead of the bam
file (Bam is too big to load).

I am seeing the same problem on both main and my local galaxy
instances (local is tracking latest galaxy-dist).

Thanks,
-Raj


On Wednesday, March 05, 2014 11:25:26 AM, Raj Ayyampalayam wrote:

I checked the version of bx-python egg and confirmed that it is
bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg.

I will upload the dataset to the public server and try it over there
and report.

Thanks,
-Raj

On Wednesday, March 05, 2014 11:21:56 AM, Jeremy Goecks wrote:

Would it be possible that you have an old copy of the bx-python egg?
You should have bx-python 0.7.1

If you check your eggs directory and you see version 0.7.1, then there
may be something wrong with bx-python. In this case, please upload
your build and bam to our public server and try again; if it fails on
our public server, share the datasets with me and I'll take a look.

Thanks,
J.

--
Jeremy Goecks
Assistant Professor, Computational Biology Institute
George Washington University



On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam mailto:ra...@uga.edu>
> wrote:


Hello,

I am trying to visualize a large genome (Large number of scaffolds)
and a large (bam file) in trackster on our local galaxy instance
(running release_2014.02.10).
When ever I try to do the above I see the following error in the logs:

 File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query
(lib/bx/bbi/bbi_file.c:5596)
 File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query
(lib/bx/bbi/bbi_file.c:5210)
 File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize
(lib/bx/bbi/bbi_file.c:4475)
 File "bbi_file.pyx", line 248, in
bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size
(lib/bx/bbi/bbi_file.c:5656)
 File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find
(lib/bx/bbi/bpt_file.c:1388)
 File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find
(lib/bx/bbi/bpt_file.c:1154)
AttributeError: 'BinaryFileReader' object has no attribute
'read_bits64'

Trackster works OK when I load smaller data sets.

It seems that there was a fix for this in bx-python code, as per mail
from Jeremy
(http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664p4662672.html).

How do I get the fixed code into my galaxy instance?

Thanks,
-Raj


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Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster

2014-04-16 Thread Jeremy Goecks

Hi Raj,

Thanks for sharing your datasets. This issue should be fixed as of this commit 
in -central:

https://bitbucket.org/galaxy/galaxy-central/commits/3a154b52090316dee61f42993eaa5a1fa40116d3

Best,
J.

--
Jeremy Goecks
Assistant Professor of Computational Biology
George Washington University



On Mar 25, 2014, at 11:15 AM, Raj Ayyampalayam  wrote:

> Jeremy,
> 
> I uploaded my dataset to the main galaxy site and the visualization failed.
> Here is the link to the history: 
> https://usegalaxy.org/u/raj-a-n/h/amborella-viz-test
> I used the same genome and a cufflinks gtf file instead of the bam file (Bam 
> is too big to load).
> 
> I am seeing the same problem on both main and my local galaxy instances 
> (local is tracking latest galaxy-dist).
> 
> Thanks,
> -Raj
> 
> 
> On Wednesday, March 05, 2014 11:25:26 AM, Raj Ayyampalayam wrote:
>> I checked the version of bx-python egg and confirmed that it is
>> bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg.
>> 
>> I will upload the dataset to the public server and try it over there
>> and report.
>> 
>> Thanks,
>> -Raj
>> 
>> On Wednesday, March 05, 2014 11:21:56 AM, Jeremy Goecks wrote:
>>> Would it be possible that you have an old copy of the bx-python egg?
>>> You should have bx-python 0.7.1
>>> 
>>> If you check your eggs directory and you see version 0.7.1, then there
>>> may be something wrong with bx-python. In this case, please upload
>>> your build and bam to our public server and try again; if it fails on
>>> our public server, share the datasets with me and I'll take a look.
>>> 
>>> Thanks,
>>> J.
>>> 
>>> --
>>> Jeremy Goecks
>>> Assistant Professor, Computational Biology Institute
>>> George Washington University
>>> 
>>> 
>>> 
>>> On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam >> > wrote:
>>> 
 Hello,
 
 I am trying to visualize a large genome (Large number of scaffolds)
 and a large (bam file) in trackster on our local galaxy instance
 (running release_2014.02.10).
 When ever I try to do the above I see the following error in the logs:
 
  File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query
 (lib/bx/bbi/bbi_file.c:5596)
  File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query
 (lib/bx/bbi/bbi_file.c:5210)
  File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize
 (lib/bx/bbi/bbi_file.c:4475)
  File "bbi_file.pyx", line 248, in
 bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size
 (lib/bx/bbi/bbi_file.c:5656)
  File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find
 (lib/bx/bbi/bpt_file.c:1388)
  File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find
 (lib/bx/bbi/bpt_file.c:1154)
 AttributeError: 'BinaryFileReader' object has no attribute
 'read_bits64'
 
 Trackster works OK when I load smaller data sets.
 
 It seems that there was a fix for this in bx-python code, as per mail
 from Jeremy
 (http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664p4662672.html).
 
 How do I get the fixed code into my galaxy instance?
 
 Thanks,
 -Raj
 
 
 ___
 Please keep all replies on the list by using "reply all"
 in your mail client.  To manage your subscriptions to this
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 http://galaxyproject.org/search/mailinglists/
>>> 
>> 
>> 
>> ___
>> 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/
> 
> 

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Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster

2014-03-25 Thread Raj Ayyampalayam


Jeremy,

I uploaded my dataset to the main galaxy site and the visualization 
failed.
Here is the link to the history: 
https://usegalaxy.org/u/raj-a-n/h/amborella-viz-test
I used the same genome and a cufflinks gtf file instead of the bam file 
(Bam is too big to load).


I am seeing the same problem on both main and my local galaxy instances 
(local is tracking latest galaxy-dist).


Thanks,
-Raj


On Wednesday, March 05, 2014 11:25:26 AM, Raj Ayyampalayam wrote:

I checked the version of bx-python egg and confirmed that it is
bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg.

I will upload the dataset to the public server and try it over there
and report.

Thanks,
-Raj

On Wednesday, March 05, 2014 11:21:56 AM, Jeremy Goecks wrote:

Would it be possible that you have an old copy of the bx-python egg?
You should have bx-python 0.7.1

If you check your eggs directory and you see version 0.7.1, then there
may be something wrong with bx-python. In this case, please upload
your build and bam to our public server and try again; if it fails on
our public server, share the datasets with me and I'll take a look.

Thanks,
J.

--
Jeremy Goecks
Assistant Professor, Computational Biology Institute
George Washington University



On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam mailto:ra...@uga.edu>> wrote:


Hello,

I am trying to visualize a large genome (Large number of scaffolds)
and a large (bam file) in trackster on our local galaxy instance
(running release_2014.02.10).
When ever I try to do the above I see the following error in the logs:

  File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query
(lib/bx/bbi/bbi_file.c:5596)
  File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query
(lib/bx/bbi/bbi_file.c:5210)
  File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize
(lib/bx/bbi/bbi_file.c:4475)
  File "bbi_file.pyx", line 248, in
bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size
(lib/bx/bbi/bbi_file.c:5656)
  File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find
(lib/bx/bbi/bpt_file.c:1388)
  File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find
(lib/bx/bbi/bpt_file.c:1154)
AttributeError: 'BinaryFileReader' object has no attribute
'read_bits64'

Trackster works OK when I load smaller data sets.

It seems that there was a fix for this in bx-python code, as per mail
from Jeremy
(http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664p4662672.html).

How do I get the fixed code into my galaxy instance?

Thanks,
-Raj


___
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:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/





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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/



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Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster

2014-03-05 Thread Raj Ayyampalayam

I checked the version of bx-python egg and confirmed that it is 
bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs2.egg.


I will upload the dataset to the public server and try it over there 
and report.


Thanks,
-Raj

On Wednesday, March 05, 2014 11:21:56 AM, Jeremy Goecks wrote:

Would it be possible that you have an old copy of the bx-python egg?
You should have bx-python 0.7.1

If you check your eggs directory and you see version 0.7.1, then there
may be something wrong with bx-python. In this case, please upload
your build and bam to our public server and try again; if it fails on
our public server, share the datasets with me and I'll take a look.

Thanks,
J.

--
Jeremy Goecks
Assistant Professor, Computational Biology Institute
George Washington University



On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam mailto:ra...@uga.edu>> wrote:


Hello,

I am trying to visualize a large genome (Large number of scaffolds)
and a large (bam file) in trackster on our local galaxy instance
(running release_2014.02.10).
When ever I try to do the above I see the following error in the logs:

  File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query
(lib/bx/bbi/bbi_file.c:5596)
  File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query
(lib/bx/bbi/bbi_file.c:5210)
  File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize
(lib/bx/bbi/bbi_file.c:4475)
  File "bbi_file.pyx", line 248, in
bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size
(lib/bx/bbi/bbi_file.c:5656)
  File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find
(lib/bx/bbi/bpt_file.c:1388)
  File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find
(lib/bx/bbi/bpt_file.c:1154)
AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64'

Trackster works OK when I load smaller data sets.

It seems that there was a fix for this in bx-python code, as per mail
from Jeremy
(http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664p4662672.html).
How do I get the fixed code into my galaxy instance?

Thanks,
-Raj


___
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster

2014-03-05 Thread Jeremy Goecks

Would it be possible that you have an old copy of the bx-python egg? You should 
have bx-python 0.7.1  

If you check your eggs directory and you see version 0.7.1, then there may be 
something wrong with bx-python. In this case, please upload your build and bam 
to our public server and try again; if it fails on our public server, share the 
datasets with me and I'll take a look. 

Thanks,
J.

--
Jeremy Goecks
Assistant Professor, Computational Biology Institute
George Washington University



On Mar 4, 2014, at 5:14 PM, Raj Ayyampalayam  wrote:

> Hello,
> 
> I am trying to visualize a large genome (Large number of scaffolds) and a 
> large (bam file) in trackster on our local galaxy instance (running 
> release_2014.02.10).
> When ever I try to do the above I see the following error in the logs:
> 
>   File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query 
> (lib/bx/bbi/bbi_file.c:5596) 
>   File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query 
> (lib/bx/bbi/bbi_file.c:5210) 
>   File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize 
> (lib/bx/bbi/bbi_file.c:4475) 
>   File "bbi_file.pyx", line 248, in 
> bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) 
>   File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find 
> (lib/bx/bbi/bpt_file.c:1388) 
>   File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find 
> (lib/bx/bbi/bpt_file.c:1154) 
> AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' 
> 
> Trackster works OK when I load smaller data sets.
> 
> It seems that there was a fix for this in bx-python code, as per mail from 
> Jeremy 
> (http://dev.list.galaxyproject.org/trackster-error-for-viewing-rat-data-rn5-tp4662664p4662672.html).
> How do I get the fixed code into my galaxy instance?
> 
> Thanks,
> -Raj
> 
> 
> ___
> 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/

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Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster

Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster

Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster

Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster

Re: [galaxy-dev] read_bits64 error when loading large genomes/data into trackster

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