Great news & info, thanks Glen for getting back to us!
On 3/1/11 2:06 PM, Glen Beane wrote:
We've upgraded python and galaxy and I don't recall seeing
this error recently. I think using our own python (2.6) rather than the Centos syst python
(2.4) took care of it.
On Mar 1, 2011, at 5:03 PM, Jennifer Jackson<jen(a)bx.psu.edu> wrote:
> Hi Glen,
> This is just a quick email to let you know that we are still working on
> your question. The development team will be getting back to you as soon
> as possible, but if you have discovered the solution yourself (perhaps
> using the most recent galaxy-dist?), both the other galaxy-dev list
> members and we would be glad to learn about how you solved the issue.
> Thank you for your patience!
> Galaxy team
> On 12/27/10 6:22 AM, Glen Beane wrote:
>> On Dec 22, 2010, at 3:26 PM, Glen Beane wrote:
>>> one of our users is experiencing this error from the SAM-to-BAM tool:
>>> Error extracting alignments from
(/hpcdata/galaxy-setup/galaxy-dist/database/files/000/dataset_85.dat), requested number of
bytes is more than a Python string can hold
>>> The SAM file has 58 million lines of mapped paired end reads.
>>> Any suggestions?
>>> The galaxy jobs running on our cluster are currently using the version of
Python installed with CentOS 5 (python 2.4.3, 64-bit). We have been considering setting
up a new python virtualenv for the galaxy user on the cluster that uses a newer version of
Python (probably 2.6 so it matches the version on the server running the galaxy web app)
>> Has anyone else experienced this? I don't think we are doing anything
unusual. Would it help to setup the galaxy user on the cluster to use a more recent
version of Python?
>> galaxy-dev mailing list
> Jennifer Jackson