[galaxy-dev] Error resolving Emboss tool dependencies

I have migrated Emboss tool from dist to tool-shed using the migration script and later updated it's revision. The tool was installed along with it's dependencies, but it's failing to find them during job run. It's logging following 'Failed to resolve dependency on 'emboss', ignoring' warning

Re: [galaxy-dev] Error resolving Emboss tool dependencies

Thanks for the reply Bjoern. It's installed correctly - green box. The emboss entries in tool_dependency and tool_shed_repository look fine as well. If I directly run an emboss command (e.g. antigenic) from CLI then it seems to be working. -- Shantanu On Aug 15, 2013, at 2:53 PM, Björn Grünin

Re: [galaxy-dev] Error resolving Emboss tool dependencies

There is only one EMBOSS suite in the tool panel. The EMBOSS tool repo is at revision c159a6ded912 and shows version 5.0.0 in the job panel. The tool was migrated using galaxy-dist provided migration script and later upgraded using the admin panel interface. The job fails with 'command not foun

Re: [galaxy-dev] Error resolving Emboss tool dependencies

t sure how this mismatch happened though. How do I fix this issue now? Should I update installed_changeset_revision entry in the database or migrated tool XML file or re-install emboss using tool-shed? Any help? -- Thanks, Shantanu On Aug 15, 2013, at 3:33 PM, Shantanu Pavgi (Campus) wrot

Re: [galaxy-dev] Error resolving Emboss tool dependencies

ories page to find the uninstalled repository. > - Select "activate or reinstall" from the dropdown. > - Proceed with the installation process. > > > --Dave B. > > On 8/16/13 15:45:11.000, Shantanu Pavgi (Campus) wrote: >> >> The installed depend

[galaxy-dev] ncbi_blast_plus - tool shed updates

I am trying to get repository updates for the ncbi_blast_plus tool which is making following request to the toolshed site:

[galaxy-dev] tool-shed migration - dist version still shown in UI

I have migrated few tools from dist to tool-shed and I am seeing two version select options in the UI. Both option contain same version number though. One of them is linking to dist path (underneath tools directory) and other one is using tool-shed path. The dist path isn't in place after the m

Re: [galaxy-dev] Error resolving Emboss tool dependencies

-shed migration scripts. Has anyone else seen similar problem before? -- Thanks, Shantanu On Aug 19, 2013, at 2:26 PM, Shantanu Pavgi (Campus) wrote: > > Thanks for the reply Dave.The reinstallation process worked fine, but it gave > couple of errors. > > Initially it faile

[galaxy-dev] Tool-shed: Migration scripts vs direct install

I was wondering if we can move dist installed tools to tool-shed version by installing them manually using the admin web interface. Do migration scripts provide any functionality that we would lose if we use admin web interface (dist_to_shed column in database and it's significance)? -- Thanks

[galaxy-dev] Tool-shed - bowtie and tophat dependency

We have migrated bowtie tool wrapper from dist to tool-shed using migration script # 7 with install_dependencies option. We removed our locally installed bowtie binaries so that install_dependencies option would work fine. I think an earlier release would skip dependency installation if they we

[galaxy-dev] changing datasets file_path storage location

We are planning to change datasets directory location (file_path setting in universe_wsgi.ini) in our Galaxy installation. We will be moving existing datasets to the new directory location and updating XSendfile setting in Apache as well. I was wondering if there are any side effects that we s

[galaxy-dev] counting number of dataset files on the file system

I am recovering lost dataset files from the file system and I need to verify number of recovered files with corresponding dataset records count in the database. Should number of dataset files on the file system match count obtained using following query? $ select count(*) from dataset where d

[galaxy-dev] FTP and data library uploads

I am trying to understand how FTP and data library upload options are working in Galaxy. When a non-binary file is uploaded through FTP option, it goes through three move operations: 1. First it is copied to a temporary namespace line-by-line converting newlines 2. Then the temporary file is m

Re: [galaxy-dev] FTP and data library uploads

On Jan 9, 2013, at 12:41 PM, Nate Coraor wrote: On Jan 8, 2013, at 1:27 PM, Shantanu Pavgi (Campus) wrote: I am trying to understand how FTP and data library upload options are working in Galaxy. When a non-binary file is uploaded through FTP option, it goes through three move operations: 1

[galaxy-dev] galaxy from subdirectory - new history with a page refresh

I have setup a galaxy instance from the root host (without sub-directory) and it's working fine. I have setup another galaxy instance on the same system, but it's being served from a sub-directory using the same front-end Apache. The sub-directory instance creates a new history on every visit o

[galaxy-dev] download URLs limited to twelve?

One of our users is trying to download thousands of files by pasting their URLs in 'URL/Text' box of the upload tool. It seems like Galaxy selects only first 12 URLs and ignores rest of them. The issue can be reproduced on the main public Galaxy instance as well. I

[galaxy-dev] BWA - failed to resolve dependency error

I had migrated BWA tool while at release_2013.02.08 revision. It was working fine, however, it fails to run with following warning message after updating Galaxy to release_2013.06.03. {{{ Building dependency shell command for dependency 'bwa' galaxy.tools WARNING 2013-07-11 17:16:28,429 Failed

[galaxy-dev] uninstalling migrated tool

It seems like if we uninstall a migrated tool then it's entry in the migrated_tools_conf.xml file doesn't get deleted. Does it need to be removed manually? -- Thanks, Shantanu ___ Please keep all replies on the list by using "reply all" in

Re: [galaxy-dev] BWA - failed to resolve dependency error

. It's hard to tell which revision is working as I see the same version tag for both revisions - https://www.dropbox.com/s/7ux0xafm9yb6s6h/bwa.png . Also, Galaxy updates are working fine now. -- Thanks, Shantanu On Jul 11, 2013, at 5:33 PM, Shantanu Pavgi (Campus) wrote: > > I had m