Re: [galaxy-dev] Data set too large

Hello, FTP is needed for files over 2 GB by default. Try FTP upload. Please contact your campus administrator if FTP is not enabled. Your admin is the best resource for alternatives if FTP is not active and will not be (admin loads data into libraries, and the like). https://wiki.galaxyproject.or

[galaxy-dev] Data set too large

Hell I am accessing galaxy from a main computer on my university campus. I am having difficulty uploading my exome files and keep getting the following error prompt: ndex30_CACCGG_L001-L002_R1_001.bam *2.8* GB Auto-detect - Additional Species Are Below - *Failed: *File exceeds 2GB. Please

Re: [galaxy-dev] Python 2.7 vs 2.6 for galaxy after 16.01

On Wed, Mar 23, 2016 at 10:54 PM, D K wrote: > Great! thanks for the suggestions. I just tried using centos software > collections and that seems to work. I'll do some more testing but hopefully > it's as simple as that! Is there any reason that most of you who responded > have decided to compile

Re: [galaxy-dev] Python 2.7 vs 2.6 for galaxy after 16.01

Great! thanks for the suggestions. I just tried using centos software collections and that seems to work. I'll do some more testing but hopefully it's as simple as that! Is there any reason that most of you who responded have decided to compile your own pythons? D On Tue, Mar 22, 2016 at 2:26 AM,

Re: [galaxy-dev] Troubleshooting BAM file upload issues

I'm using the standard 'Upload file' tool, and choosing some local files. I can successfully upload these files to the galaxy installation on my laptop and to the usegalaxy.org server, but uploading them to the galaxy installation on the server results in their appearing to be empty and the error m

Re: [galaxy-dev] Troubleshooting BAM file upload issues

Hi Amelia, How are you uploading the files? If you are using a copy and pasted URL, can you make sure that the example file exists and is accessible to the machine where the Galaxy job is running. A 404 error, for example, can often masquerade as a “The uploaded file contains inappropriate H

Re: [galaxy-dev] Troubleshooting BAM file upload issues

On 23 March 2016 at 01:00, Björn Grüning wrote: > Hi Amelia, > > can you pleae check if you have samtools installed in your PATH? > I've got it in my tool dependencies dir and it's also available as an Environment module. The tools dependencies file looks like this: Debug me

Re: [galaxy-dev] Troubleshooting BAM file upload issues

Both, unfortunately. On 23 Mar 2016 00:41, "Hans-Rudolf Hotz" wrote: > Hi Amelia > > Does this happen with "Auto-detect" or do you pre-set the data type to > 'bam' ? > > > Regards, Hans-Rudolf > > > On 03/22/2016 07:28 PM, Amelia Ireland wrote: > >> I'm setting up a Galaxy instance on a new serve

Re: [galaxy-dev] automatic adding of a tab in a fastq header

Thank :)! Fabien Le 23/03/2016 00:01, Martin Čech a écrit : Thank you for all the help Peter! Also this is already backported and fixed in 16.01 Sorry for causing this bug in the first place. M. On Tue, Mar 22, 2016, 18:29 Peter Cock > wrote: Well done

Re: [galaxy-dev] perl version 5.18.1 repository error

Hi Nicola, Now I get this: perl 5.18.1 package Error File "lib/tool_shed/galaxy_install/install_manager.py", line 123, in in

Re: [galaxy-dev] perl version 5.18.1 repository error

Hi Philipp, can you try to reinstall the tool dependency? Go to the Admin interface, "Manage installed tools", click on the "package_perl_xml_parser_expat_2_41", then from the "Repository Actions" menu select "Manage tool dependencies", select the dependency in error and "Uninstall", then sele

Re: [galaxy-dev] Troubleshooting BAM file upload issues

The bam support is regrettably different to most of Galaxy. For some reason it can not make use of Wheels installed by Galaxy but has to use native samtools. Giving very confusing error messages such as file not found if samtools is not there. Also your bam files MUST be sorted by coordinates a

[galaxy-dev] perl version 5.18.1 repository error

Dear all, i am trying to install  tool (meme-fimo) which needs package_perl_xml_parser_expat_2_41 that has a pearl 5.18.1 dependency. however, although the tool installs just fine it shows that  package_perl_xml_parser_expat_2_41 has missing dependencies: Tool shed repository:package_per

Re: [galaxy-dev] Troubleshooting BAM file upload issues

Hi Amelia, can you pleae check if you have samtools installed in your PATH? Ciao, Bjoern Am 22.03.2016 um 19:28 schrieb Amelia Ireland: > I'm setting up a Galaxy instance on a new server and am having some > issues with BAM file uploads. I'm using the BAM files supplied with > JBrowse for testin

Re: [galaxy-dev] Troubleshooting BAM file upload issues

Hi Amelia Does this happen with "Auto-detect" or do you pre-set the data type to 'bam' ? Regards, Hans-Rudolf On 03/22/2016 07:28 PM, Amelia Ireland wrote: I'm setting up a Galaxy instance on a new server and am having some issues with BAM file uploads. I'm using the BAM files supplied wit