Re: [galaxy-dev] Data manager .loc file not installing in correct place

Hi Jeremy, I just installed and tried the data manager and it looks to be working. Have you changed any of these settings in your galaxy.ini file: # Data manager configuration options # Allow non-admin users to view available Data Manager options #enable_data_manager_user_view = False # File wher

Re: [galaxy-dev] Multiple select input error after update

Hi Alexandre, Thanks for reporting this issue. We have committed a fix here https://bitbucket.org/galaxy/galaxy-central/commits/7fd6061e43d5/ and it will be applied to additional releases soon. Please let know if you encounter additional issues. Thanks for using Galaxy, Dan On Jan 14, 2015

Re: [galaxy-dev] parallelism

Hi Roberto, It looks like you are probably still using the default sqlite database. You’ll want to update to using e.g. postgres when exploring these more database intensive functions. See e.g.: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Switching_to_a_database_ser

Re: [galaxy-dev] deleting directories from toolshed repo

Hi Nik, Are things with the repository working otherwise, beyond not being able to delete this directory? Can you let me know which repository you are having trouble with and I can take a look at it. Also, if you don’t mind can you share the tarball you are using (privately is ok)? Thanks for

Re: [galaxy-dev] Workflow bug when *.loc entries are missing

Hi Peter, I just wanted to chime in and say that I have been able to reproduce this issue locally (on a different tool), and I’d consider it a pretty significant bug for reproducibility, etc. Thanks, Dan On Mar 31, 2015, at 12:33 PM, Peter Cock wrote: > On Tue, Mar 31, 2015 at 12:04 PM, P

Re: [galaxy-dev] using DataManager to add custom genomes

Hi Nikhil, Have a look at https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_fetch_genome_dbkeys_all_fasta to add a new genome/fasta. Once you have the genome entry, then you can use additional Data Manager to make tool specific (bwa, samtools, etc) indexes. Thanks for using Galaxy, Da

Re: [galaxy-dev] a question on data manager and data table

Hi Rui, The Extract Genomic DNA Tool has not yet been updated to work with tool Data Tables. Additionally, this tool requires TwoBit formatted files when selecting from built-in data — when selecting a FASTA from your history, the fasta file is converted to TwoBit internally in the tool befor

Re: [galaxy-dev] Multiple outputs of unknown types

Hi Davids, For some a somewhat more complex example, have a look at the GenomeSpace importer tools under tools/genomespace in the distribution. They always create at least 1 dataset, but can create any number of files, of any type of datatype. In this tool, it will use the filetype declared by

Re: [galaxy-dev] a question on data manager and data table

mine if a tool is using data table is to look at the tool xml > file to see if it contains reference to a data table, right? And in > tool_data_table_conf.xml, it should contain data tables definition for all > the possible data, right? > > If you could please elaborate a bit, I'

Re: [galaxy-dev] Older galaxy I'm keeping alive by drip feed, has problem restarting when I turn debug off.

Hi Damion, Another thing to try, is to set up and use a virutalenv, as the last time this error was reported (2012), it was suggested that a local site-packages version of Paste, instead of Galaxy’s provided egg, was to blame. Thanks for using Galaxy, Dan On Apr 15, 2015, at 5:36 PM, Dannon

Re: [galaxy-dev] Using synchronous method to upload multiple files

Hi Daniele, I would suggest having a look at the tools/genomespace/genomespace_importer.py/xml tool, particularly the ‘download_from_genomespace_importer’ method, it uses a comma-separated list of URLs and downloads an adds multiple files to Galaxy, with history names of “GenomeSpace importer

Re: [galaxy-dev] Issue writing functional tool test with repeat tag in config

Hi CS, I assume you have the rest of the tags, but didn’t paste it here. One thing is that you need to close your test and tests elements properly: > > You may want to pass your config through a simple xml validator to try to shake any other issues out as well. Thanks for usi

Re: [galaxy-dev] tagset in tools

The tag won’t be going away any time soon, but in many cases there are other ways to do what this tag does, using the built-in dynamic options (in particular, currently for tab-delimited files), that are much preferred. So it is deprecated, and it should be used sparingly, but there are times w

Re: [galaxy-dev] simple example of composite data types

Hi Brian, In your example tool, you need to pass “${ test_cdt.files_path }" to your perl script, which is a not-yet-existing directory for the files you want to be part of the dataset’s extra files path. Then you create that directory and place the files you want within that directory. Than

Re: [galaxy-dev] connecting composite data elements to a display application

Hi brian, I’ve enhanced Galaxy’s external display application framework to support accessing files in the extra files path in a pull request here: https://github.com/galaxyproject/galaxy/pull/284 To enable access you need to set allow_extra_files_access="True" for the display parameter. To acc

Re: [galaxy-dev] [SPAM] RE: GalaxyAdmins Online Meetup this Thursday: Peter Briggs on Galactic Engineering at Manchester

We’re going to try this one now: https://connect.johnshopkins.edu/r283zwzv0yi On Jun 18, 2015, at 11:09 AM, Hans-Rudolf Hotz wrote: > sorry my (copy paste) mistake > > https://connect.johnshopkins.edu/galaxyadmins201506/ > > > On Jun 18, 2015, at 5:08 PM, Christian Brenninkmeijer > wrote:

Re: [galaxy-dev] galaxy.ini

It is under config/. You’ll want to copy it from /config/galaxy.ini.sample Thanks for using Galaxy, Dan On Jul 14, 2015, at 6:35 AM, Bryan Hepworth wrote: > Hi > > For the woefully inept, where in the heck is galaxy.ini stored? > > I saw the documentation that said change 127.0.0.1 to 0.0

Re: [galaxy-dev] Workflow editor stuck on loading workflow

Just a quick general suggestion: have you tried clearing your browser cache? Thanks for using Galaxy, Dan On Jul 15, 2015, at 11:18 AM, Ryan G wrote: > The error I see is "TypeError: c.effectiveMapOver is not a function" in > static/scripts/galaxy.workflow_editor.canvas.js?v=1436897004 >

Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

Oct 6, 2015, at 9:59 AM, Daniel Blankenberg wrote: > Hi Lance, > > I looked at this a bit ago and had similar concerns, particularly with the > outputs and inputs not being well-defined. In addition to the output tar ball > —> local, extract —> upload not being great, as you

Re: [galaxy-dev] Pass Working Directory from xml

Hi Todd, Can you just pass in “.”? the_tool.py -o ‘.' Thanks for using Galaxy, Dan On Dec 11, 2015, at 4:00 PM, Todd Oakley wrote: > Greetings, >I feel this must be simple, but I cannot find it. > > I'm making a wrapper for a tool that requires the output directory to be > specif

Re: [galaxy-dev] BED12 Data Format

Hi Lance, FWIW, there is an existing bedstrict and bed12 (and bed6) datatypes in Galaxy. The strict datatypes are currently usually created by implicit datatype converters and are most often used by some external display applications that need standards conforming files. bed6/12 are subclasses

Re: [galaxy-dev] BED12 Data Format

t; Lewis-Sigler Institute for Integrative Genomics >>> Princeton University >>> >>> ___ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage you

Re: [galaxy-dev] Query

Hi Chang-Hyuk, If you click on the bug icon for your error'd dataset you should be able to get the full traceback. Thanks for using Galaxy, Dan > Dear Sir, > > that is all of error message. > I attached the file to be tried. > > best regards, > Chang-Hyuk Yoo. > > 2016-02-25 오전 4:13에 V

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

pt > > 2. Put the BAM in the only order galaxy will accept. > > Christian > University of Manchester > From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of > Amelia Ireland [airel...@lbl.gov] > Sent: Wednesday, March 23, 2016 8:24 PM > To: Daniel Blank

Re: [galaxy-dev] Galaxy Blast

Hi Peter and Harry, When a tool is installed from the toolshed, the tool data table loc files are installed to the configured location and are then referenced in shed_tool_data_table_conf.xml. You should be able to modify the .loc files as referenced in this file, or, as you did, add a new entr

Re: [galaxy-dev] Galaxy Security Vulnerability - Arbitrary code execution

The server is back up. Thanks for reporting this issue. Dan > On Dec 19, 2016, at 10:02 AM, Nicola Soranzo wrote: > > Thanks David, > the issue has been already reported, see > https://github.com/galaxyproject/galaxy/issues/3332 > , hopefu

Re: [galaxy-dev] Question about Data Managers

Hi Carlos, You’ll want to set 'galaxy_data_manager_data_path' in your galaxy.ini file. Thanks for using Galaxy, Dan > On Dec 21, 2016, at 3:17 PM, Carlos Lijeron wrote: > > Everyone, > > I’m trying to setup various data managers to automatically download and index > reference indices. H

Re: [galaxy-dev] Request more details from Nikolaos Tur about pyBamTools & pyBamParser dependency packages message

he setup.py files in these two packages are no longer compatible with the > newer versions of the Python 'setuptools'), but I didn't have time to follow > it up then. > > I've now submitted pull requests with my attempted fixes on the Bitbucket > repositories

Re: [galaxy-dev] Create a new datatype svg

Just a quick note, if you want svg to be rendered as a graphics correctly via the eye preview, you’ll need to set “serve_xss_vulnerable_mimetypes = True" in galaxy.ini. Otherwise it will appear as plaintext xml. But do be aware of the security concerns if you change this setting. Downloading/sa

Re: [galaxy-dev] Create a new datatype svg

t; I would like to have it as plain text but no as a separate file in the > history but more like the solution of bam and bai files. Do you know how > to do that? > > Cheers Jochen > > On 07.02.2017 21:26, Daniel Blankenberg wrote: >> Just a quick note, if you want svg

Re: [galaxy-dev] any introduce for how Mako and JavaScript work in galaxy?

Hi Steven, For a quick first pass, have you taken a look at https://github.com/ galaxyproject/galaxy/blob/dev/client/README.md? Thanks for using Galaxy, Dan On Thu, Jul 6, 2017 at 10:11 PM, Steven Shen wrote: > Hi everyone, > > I want to make some change for my local galaxy web, actually I c

Re: [galaxy-dev] galaxy behind firewall

HI Matthias, At the firewall level, one could allow pass through to only the specific IPs/sites that you want to enable for external displays, instead of just opening up the headnode to the entire world. Additional access restrictions could be enforced at the apache/nginx proxy level as well. If

[galaxy-dev] Re: King Skrupellos hack

Hi Pat, I wanted to make sure that you were able to figure this out. As suggested previously, this is most likely just a user uploaded file, but if you are an admin of the Galaxy instance then you should be able to figure it out. If you want to learn a bit more about this specific dataset in your