[galaxy-dev] GATK problems with data-manager files

Hi all, One of my co-administrators is having some issues with data indexed/processed with data managers in GATK. His email to me: Currently there is no way to load a genome into versions of GATK above version 1.4. No version seems to be able to load a reference from history and only version 1

Re: [galaxy-dev] Difficulty uploading BAM files

Hi Peter, Thanks to you and all the other responders who were so helpful! This did solve my problem right away. Best regards, Scott On Fri, Feb 26, 2016 at 3:13 PM, Peter Cock wrote: > Hi Scott, > > Galaxy itself requires samtools (to deal with BAM files), separately > from any Tool Dependenc

Re: [galaxy-dev] Difficulty uploading BAM files

Hi Scott, Galaxy itself requires samtools (to deal with BAM files), separately from any Tool Dependency within the tool calling framework. Right now there is no mechanism for datatype definitions to declare a dependency (e.g. on a binary like samtools, or a Python library). Probably samtools sho

Re: [galaxy-dev] Downgrade tool upload tool

Hello, The Upload tool is a direct component of Galaxy. To use an earlier version of the tool, I believe that you would have to run an earlier version of Galaxy. Others here can amend this, if they know of an alternative. Thanks, Jen -- Jennifer Hillman-Jackson Galaxy Application Support http:

Re: [galaxy-dev] Issue with Using Bar

Hello, I recalculated usage and it is correct at around 180 GB. To check for data that may be deleted, but not *permanently deleted (required to free space)*, this wiki has instructions (including a help video): https://wiki.galaxyproject.org/Learn/ManagingDatasets#Delete_vs_Delete_Permanently T

Re: [galaxy-dev] Difficulty uploading BAM files

It is a shame and a but surprising that unlike most other dependencies samtools can not come from an egg now wheel. Christian From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of Marius van den Beek [m.vandenb...@gmail.com] Sent: Friday, Feb

Re: [galaxy-dev] correctly installing to toolshed

Thanks! Sent from Nine From: Gildas Le Corguillé Sent: Feb 25, 2016 3:17 PM To: Karen Reddy Cc: Xianrong; Björn Grüning; Xianrong Wong; galaxy-...@lists.bx.psu.edu Subject: Re: [galaxy-dev] correctly installing to toolshed Hi all, You will found in attachment the modi

[galaxy-dev] Issue with Using Bar

Hello, I am using Galaxy for a school project, but I’m running into an issue with my “Using Bar” in the top right corner. I started off running programs at roughly 30% using. I then downloaded a number of sequences to analyze and went above 100% on my Using Bar. I then purged the entirety of my

Re: [galaxy-dev] Difficulty uploading BAM files

I too had trouble with BAM files as https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py Line 201 class Bam( Binary ): ... def _get_samtools_version( self ): ... samtools_exec = which('samtools') Assumes samtools is installed on the server and was not finin

Re: [galaxy-dev] Difficulty uploading BAM files

Hello Scott, you do need a samtools binary on GALAXY's PATH. This is not samtools installed from the toolshed. Best, Marius On 26 February 2016 at 18:49, Scott Szakonyi wrote: > Hi, > > I'm having trouble uploading BAM files in our development environment. > Other files types are uploading wit

[galaxy-dev] Difficulty uploading BAM files

Hi, I'm having trouble uploading BAM files in our development environment. Other files types are uploading without issue. I'm testing with a small BAM file I downloaded, and I'm able to successfully upload it on our production server and usegalaxy.org. When I try to upload in the development envir

Re: [galaxy-dev] samtools view tools

Hi Christian, all this functionality is available either in the picard tools or in the samtools collection. bam_filter is also available and based on bam_utils. There is also a suite of bam-tools. So many tools to choose from :) Hope this helps, Bjoern Am 26.02.2016 um 17:35 schrieb Christian Br

[galaxy-dev] samtools view tools

Hi All, Has anyone written galaxy tools for the samtools view functions such as samtools view -f 0x0002 -F 0x0100 -uo and/or samtools view -uSo Thanks Christian University of Manchester ___ Please keep all replies on the list by using "re

Re: [galaxy-dev] Seeking Job Metrics Clarity

Hi Nate Thanks for the response. It was indeed part of the problem. I needed collectl installed on the individual cluster instances.(job runners) Seems to be working properly now. I plan to work on using the metrics to dynamical & intelligently choose job destination of mapping jobs for example.

Re: [galaxy-dev] Seeking Job Metrics Clarity

On Wed, Feb 24, 2016 at 5:37 AM, Ziphozakhe Mashologu wrote: > Hi All > > I have enabled job metrics on a local galaxy install, with latest code > from dev branch. I have " " uncommented in job_metrics_conf.xml > file: > > Following are the errors in the logs: > > galaxy.jobs.metrics ERROR 2016-0

[galaxy-dev] Downgrade tool upload tool

Hello everyone, I was wondering whether it's possible to downgrade the upload tool to the previous version(1.1.4). I copied the upload.py and upload.xml scripts from a previous galaxy version to the tools/data_source/ directory and reloaded the tool as admin but it hasn't changed even when I r

Re: [galaxy-dev] Broken package_perl_5_18, was Re: JBrowse on dev branch: progress

Thanks Peter - this specific package has now been fixed in the toolsheds and should work without patching the Galaxy code. I understand that more generally Nicola is working on applying the same fix (removing whitespace around the target URL when using the "download_file" action) in other packa

Re: [galaxy-dev] Lost prostgresql database

Hi Amos, As Hans-Rudolf said, if you really have lost the database and its backups, there is not much you can do. If you have just a few very valuable datasets that have to be recovered, I would look at the file dates (guided by the automatically incremented dataset numbers), sizes, and look at t

Re: [galaxy-dev] Lost prostgresql database

Hi Amos Since the PostgreSQL database stores much more than the links to and previews of the individual datasets, you need to restore it from your PostgreSQL backup file. Hans-Rudolf On 02/25/2016 08:53 PM, Raphenya, Amogelang wrote: Hi All, Our server hard drive failed and we lost the d

Re: [galaxy-dev] packaging R scripts

Hi, For me, three solutions : - You can find existing packages which will install your library (https://testtoolshed.g2.bx.psu.edu/view/jeltje/package_dnacopy_1_40_0/118417199f06 ). So you will just need to li

[galaxy-dev] packaging R scripts

Hi, I am trying to package an R script (that requires certain R packages) into a galaxy tool. Any advice would be deeply appreciated! I have tested it on planemo and it works. When I tried the version I uploaded onto the toolshed, I got an error saying that the R packages do not exist. I ne