On Nov 4, 2011, at 1:11 PM, Carlos Borroto wrote:

> Hi,
> 
> Reading a little more about this problem, I see Galaxy uses python
> tempfile library (http://docs.python.org/library/tempfile.html),
> specifically at line 70 in tools/samtools/sam_to_bam.py:
> tmp_dir = tempfile.mkdtemp()
> 
> mkdtemp should honor TMPDIR, TEMP or TMP environment variables, I
> setup all tree of them in "~/.bashrc" with no results. I'm using:
> "default_cluster_job_runner = drmaa://-q all.q -V/"
> 
> With "-V" I was hoping to be able to export all my environment
> variables, which seems to work for everything else, but not for the
> TMP.
> 
> I ended hardcoding the "dir" argument, which is not good workaround,
> as I'm guessing this is not the only tool that will run into this
> problem:
> tmp_dir = tempfile.mkdtemp( dir='/home/cborroto/galaxy_dist/database/tmp')
> 
> Any advice? In a more SGE related question, is there a way for me to
> debug what environment I'm getting when running Galaxy jobs?

Hi Carlos,

Try submitting an SGE job from the command line and having a look at the 
environment variables set on the execution host.  Most likely, SGE is setting 
its own TMPDIR variable which would be overriding the value set with -V.

--nate

> 
> Thanks,
> Carlos
> 
> On Fri, Nov 4, 2011 at 11:22 AM, Carlos Borroto
> <carlos.borr...@gmail.com> wrote:
>> Hi Jen,
>> 
>> Thanks for the quick response. The workaround you describe could work,
>> but I might run into trouble later on.
>> 
>> My interest is to develop a workflow for GATK, which have very strict
>> requirements on the input BAM file. One of which is that the sorting
>> have to be exactly the same as the reference. My reference is not
>> sorted lexicographically "chr1, chr10, chr11, ....", but instead is
>> sorted karyotypically "chr1, chr2, ...". I don't think I'll be able to
>> do this with "Filter and Sort -> Sort". Also GATK needs the header for
>> the @RG tags, which I could resolve by just reintroducing the header
>> later on, but still it will be cumbersome.
>> 
>> I'll work on my galaxy/cluster configuration and see if I can find why
>> the SAM-to-BAM tool is failing.
>> 
>> Thanks again,
>> Carlos
>> 
>> On Thu, Nov 3, 2011 at 6:35 PM, Jennifer Jackson <j...@bx.psu.edu> wrote:
>>> 
>>> Hello Carlos,
>>> 
>>> If what you want is a sorted SAM file, then the tool "Filter and Sort ->
>>> Sort" may be a better choice. A SAM file is a tabular file.
>>> 
>>> If there is header data at the beginning of the SAM file, it can be removed
>>> before running Sort with the tool "Filter and Sort -> Select" (with a "not"
>>> matching regex). Although, you can choose to not include header output as a
>>> BWA option.
>>> 
>>> Perhaps this will solve the immediate problem?
>>> 
>>> Best,
>>> 
>>> Jen
>>> Galaxy team
>>> 
>>> On 11/3/11 12:43 PM, Carlos Borroto wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> I'm running into this error:
>>>> "Error sorting alignments from
>>>> (/tmp/5800600.1.all.q/tmpXOc5mD/tmpAZCzt_),"
>>>> 
>>>> When using SAM-to-BAM tool on a locally install Galaxy using a SGE
>>>> cluster. I'm using the last version of galaxy-dist. I'm guessing I
>>>> have a problem with the configuration for the tmp folder. I have this
>>>> on "universe_wsgi.ini":
>>>> # Temporary files are stored in this directory.
>>>> new_file_path = /home/cborroto/galaxy_dist/database/tmp
>>>> 
>>>> But I don't see this directory being used and from the error looks
>>>> like /tmp in the node is used. I wonder if this is the problem, as I
>>>> don't know if there is enough space in the local /tmp directory at the
>>>> nodes? I ran the same tool in a subset of the same SAM file and it ran
>>>> fine.
>>>> 
>>>> Also, I see this in the description of the tool:
>>>> "This tool uses the SAMTools toolkit to produce an indexed BAM file
>>>> based on a sorted input SAM file."
>>>> 
>>>> But what I actually need is to sort a SAM file output from bwa, I
>>>> haven't found any other way than to converting it to BAM. Looking at
>>>> "sam_to_bam.py" I see the BAM file will also be sorted. Would it be
>>>> wrong to feed an unsorted SAM file into this tool?
>>>> 
>>>> Finally, just to be sure there is nothing wrong with the initial SAM
>>>> file, I ran "samtools view ..." and "samtools sort ..." on this file
>>>> manually outside of Galaxy and it ran fine.
>>>> 
>>>> Thanks in advance,
>>>> Carlos
>>>> ___________________________________________________________
>>>> Please keep all replies on the list by using "reply all"
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>>>>   http://lists.bx.psu.edu/
>>> 
>>> --
>>> Jennifer Jackson
>>> http://usegalaxy.org
>>> http://galaxyproject.org/wiki/Support
>>> 
>> 
> 
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