[galaxy-dev] Galaxy environment on local resources

Hello all, Feel free to point it out if I have missed something obvious, I have done a fair bit of investigation and haven't quite found the solution yet. We have some hardware that has been around for a while for the purpose of processing Genetic data and other related tasks. To this end Galax

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

Peter, Thanks for bringing this to our attention, we're working on fixing a number of issues with the test framework, and hope to have more information for you tomorrow. --Dave B. On 2013-11-11 06:11, Peter Cock wrote: Hi Dave, I think this is a new regression from the Test Tool Shed inst

Re: [galaxy-dev] SLURM and hidden success

Hi John, Thanks so much for the reply. After investigating this more today it turns out, as you might have suspected, SLURM was a red herring. Despite our attempts to faithfully rsync everything between the two servers it looks like there was a problem with our workflows in the new database. Stran

Re: [galaxy-dev] Error editing users associated with a quota

Hey Peter, Does your universe_wsgi.ini have "enable_quotas = True" set? -John On Mon, Nov 11, 2013 at 6:08 AM, Peter Cock wrote: > Hi all, > > I'm trying to remove a user from our default quota (while they > run a large analysis), but am getting an error: > > Internal Server Error > Galaxy wa

Re: [galaxy-dev] SLURM and hidden success

This is really odd. I see no code in the job runner stuff at all that could cause this behavior outside the context of the dataset being marked hidden as part of a workflow - let alone something DRM specific that could cause this. Are you rerunning an existing job that has been marked this way in a

[galaxy-dev] DRMAA/SGE job handling regression?

Hello all, On our main Galaxy tracking galaxy-dist using DRMAA/SGE, jobs submitted to the cluster and queued and waiting (qw) are correctly shown in Galaxy as "grey" pending entries in the history. With my test instance tracking galaxy-central (along with a new visual look and new icons), such jo

Re: [galaxy-dev] Converting .gff3 to 12-column .bed

Hi, I am the author for "fml_gff3togtf" tool package, currently merged into our instance at http://galaxy.cbio.mskcc.org, The tool can be accessed with following link: https://galaxy.cbio.mskcc.org/tool_runner?tool_id=fml_gff2bed --/Vipin Sloan-Kettering Institute

Re: [galaxy-dev] Samtools and idxstats

On Thu, Nov 7, 2013 at 4:51 PM, Peter Cock wrote: > Hi Michiel, > > Did you finish wrapping samtools idxstats? I can't see it on the Tool Shed... > > If not, I may tackle this shortly. > > Peter I've implemented a 'samtools idxstats' wrapper, which seems to be working for me: https://github.com/p

Re: [galaxy-dev] Converting .gff3 to 12-column .bed

Hello, There are no tools directly on the public Galaxy site to transform a GFF3 dataset into a BED12 dataset. However, the Tool Shed has a repository called ' fml_gff3togtf' that includes a tool for this purpose, for use in a local install. The description is a bit bothersome in that it a sl

Re: [galaxy-dev] Using input dataset names in output dataset names

*I had been composing this e-mail for a while so it is a lot awkward given this mornings responses, but felt it best to just get it out there rather than continue to bake the ideas :)* If I were not employed by Penn State, I would say you guys should be using galaxy-extras - these problems are all

Re: [galaxy-dev] Using input dataset names in output dataset names

On Mon, Nov 11, 2013 at 4:09 PM, James Taylor wrote: > I have not tested the patch, just read it, but won't this result in > dataset names like: > > "Some operation on data 27 (Some operation on data 26 (Some other > operation on data 25 (...(...(..." Potentially - it depends on how the tools

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

This is not an objection, but do we need bash? Can we live with posix sh? We should ask this question about every requirement we introduce. (bash is not part of the default installation of FreeBSD or OpenBSD for example. bash is unfortunately licensed under GPLV3, so if you are trying to create an

Re: [galaxy-dev] Using input dataset names in output dataset names

I have not tested the patch, just read it, but won't this result in dataset names like: "Some operation on data 27 (Some operation on data 26 (Some other operation on data 25 (...(...(..." (avoiding this is why we came up with HIDs in the first place). -- James Taylor, Associate Professor, B

[galaxy-dev] Converting .gff3 to 12-column .bed

Hello Galaxy: I am trying overall to convert a .gff3 file to 12-column .bed file. I first tried GFF-to-BED converter, but it gave a 6-column .bed file. Then, I tried BED-to-bigBed converter by inputting the 6-column .bed file. I get an error "Unspecified genome build, click the pencil icon in th

[galaxy-dev] Trying to map fastq reads with bowtie for illumina to the reference genome sacCer3

Hello! I have SacCer uploaded to galaxy in the fasta format however to use it as a mapping genome with bowtie for illumina it says it must be in fastq format. Do you know a way that I can convert this file or what I can do to make this work? Thank you very much for your time! Sincerely, Frank ___

[galaxy-dev] Error editing users associated with a quota

Hi all, I'm trying to remove a user from our default quota (while they run a large analysis), but am getting an error: Internal Server Error Galaxy was unable to successfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, r

Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries

Hi Dave, I think this is a new regression from the Test Tool Shed installation framework, http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/f2478dc77ccb Tool test results Automated test environment Tools missing tests or test data Installation errors - no functional tests were run f

Re: [galaxy-dev] Using input dataset names in output dataset names

On Thu, Nov 7, 2013 at 3:50 PM, Peter Cock wrote: > > Getting back to my motivating example, since fasta_to_tabular.xml > does not give the output a label and depends on the default, the > small change to $on_string should result in the conversion of a > file named "My Genes" as "FASTA-to-Tabular o