I'm having the same issue, has it been fixed since then?
Le 07/11/2011 21:43, Nate Coraor a écrit :
On Nov 4, 2011, at 1:11 PM, Carlos Borroto wrote:
> 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
> 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
> 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?
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.
> On Fri, Nov 4, 2011 at 11:22 AM, Carlos Borroto
> <carlos.borroto(a)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
>> do this with "Filter and Sort -> Sort". Also GATK needs the header
>> 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,
>> On Thu, Nov 3, 2011 at 6:35 PM, Jennifer Jackson<jen(a)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?
>>> Galaxy team
>>> On 11/3/11 12:43 PM, Carlos Borroto wrote:
>>>> I'm running into this error:
>>>> "Error sorting alignments from
>>>> 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
>>>> 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
>>>> nodes? I ran the same tool in a subset of the same SAM file and it ran
>>>> 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
>>>> 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,
>>>> Please keep all replies on the list by using "reply all"
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>>> Jennifer Jackson
> 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:
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: