[galaxy-user] stderr on Samtools sort

Dear all, I'm trying to set up samtools sort command on local Galaxy server. But I can not success to get sorted files from its result. First time, I got error message from Galaxy as.. error at.. [bam_sort_core] merging from 13 files... To resolve this problem, I use discard_stderr_wrapper.sh fo

Re: [galaxy-user] stderr on Samtools sort

On Wed, Nov 14, 2012 at 9:00 AM, Masaki MS wrote: > Dear all, > > I'm trying to set up samtools sort command on local Galaxy server. > But I can not success to get sorted files from its result. I thought Galaxy tried to keep SAM/BAM files sorted by default... > First time, I got error message f

Re: [galaxy-user] stderr on Samtools sort

On Wed, Nov 14, 2012 at 11:07 AM, Peter Cock wrote: > On Wed, Nov 14, 2012 at 9:00 AM, Masaki MS wrote: >> Dear all, >> >> I'm trying to set up samtools sort command on local Galaxy server. >> But I can not success to get sorted files from its result. > > I thought Galaxy tried to keep SAM/BAM f

[galaxy-user] Map with Bowtie problem

Hello,   I have a problem with Bowtie : I am trying to use it and it doesn't work, I see "job is waiting to run" communicate. The others like EBI SRA or FASTQ Groomer works fine. What's wrong ? ___ The Galaxy User list should be used for th

[galaxy-user] Repeated Error with Tophat

Hello- I am trying to use Galaxy to investigate gene expression differences among datasets. The first time I used Tophat, everything worked fine and it returned a nice set of assembled transcripts. However, I have since tried to use Tophat on additional datasets (in the same format as the fir

[galaxy-user] Downgrading toolshed tools

Just today, we had a case where we wanted to rollback to a previous version of a tool that we'd installed from a toolshed. (No big reason except that our latest "fix" actually broke the tool.) Is there a way to do this? I could have sworn there was but couldn't find it in the admin interface. --

Re: [galaxy-user] Downgrading toolshed tools

Hi Paul, From your explanation, it seems that you have 2 versions of the tool installed in your Galaxy instance, the original version and the new version that is broken. If this is the case, just uninstall the newer broken version, and continue to make only the previous working version availab

[galaxy-user] Galaxy November 14, 2012 Distribution & News Brief

*Galaxy November 14, 2012 Distribution & News Brief * * Complete News Brief * *Highlights:* * *NGS: Picard (beta)* have moved from the *Galaxy distribution

Re: [galaxy-user] Map with Bowtie problem

Hello Andrew, When a job is waiting to run, that means it is in the queue waiting for available resources (server time, cluster node, etc.). Different jobs have different resource requirements, which is why some may run quicker than others. Bowtie runs on our NGS cluster and this can sometimes

Re: [galaxy-user] Repeated Error with Tophat

Hi Karen, Very sorry to learn that you are having problems. The public Main Galaxy server was under a considerable usage load the last week or so that led to some job failures. In most circumstances, the only solution to a cluster error is a re-run. I do not see any jobs associated with this

Re: [galaxy-user] Help to identify variants with clinical/phenotype associations

Hi Luis, There are a few options: The tool " Phenotype Association -> SIFT" will accept an input file of variant locations/alleles and retrieve annotations, including OMIM Disease associations. Alternatively, you could label your variants by rs identifiers (or perhaps you already have these