Re: [galaxy-dev] PATH set in tool env.sh leaking through to set_metadata.py

On 01/20/2015 06:20 PM, Wolfgang Maier wrote: I have not seen this error before (I believe not with latest_2014.10.06) update: confirmed this now. It's enough to hg update to latest_2014.10.06 and things are working again. The difference is that when building the dependency shell command

Re: [galaxy-dev] PATH set in tool env.sh leaking through to set_metadata.py

jmchil...@gmail.com wrote: Are you using the local job runner (this will be the case if you haven't explicitly configured something like pbs or DRMAA in your job_conf.xml file)? -John On Tue, Jan 20, 2015 at 12:34 PM, Wolfgang Maier wolfgang.ma...@biologie.uni-freiburg.de wrote: On 01/20/2015 06:20

Re: [galaxy-dev] LD_LIBRARY_PATH not exporting to galaxy

Since there are so many surprising new details in your last mail, maybe it would help if you could tell where you got your Python from. Is it a regular system installation or a toolshed installed version inside Galaxy (which may use its own env.sh to manipulate paths) ? Best, Wolfgang On

Re: [galaxy-dev] samtools dependency changes ?

hmm, no replies yet, so is anybody able to reproduce this behavior and would you not consider it a bug? Best, Wolfgang On 06/16/2015 03:11 PM, Wolfgang Maier wrote: Dear all, with older Galaxies (prior to latest_15.03 I think), you could satisfy Galaxy's samtools dependence for indexing bam

[galaxy-dev] default value for param type color

Hi, I've started to explore the relatively new color parameter type, which is not explained in the ToolConfigSyntax section of the Wiki yet. It's a pretty neat new feature, but I haven't found a way to specify a default color yet (the color selection is always set to a very light orange

[galaxy-dev] updated eggs needed for OS X El Capitan compatibility

Hi, today, there was a complaint on the Galaxy Biostar forum that Galaxy fails to start under the new OS X El Capitan (https://biostar.usegalaxy.org/p/14492/). I had noticed this last week already, and that post prompted me to investigate the problem in more detail. The result (now checked

Re: [galaxy-dev] CloudMap_Hawaiian_Variant & missing tools on new Galaxy instance

Ah, the link should have been to www.celegans.de/mimodd directly. Sorry for the inconvenience, Wolfgang On 26.06.2016 14:53, Nikolaos Tur wrote: Hi, imported from usegalaxy.org workflow CloudMap_Hawaiian_Variant_Mapping_with_WGS to local Galaxy instance (16.04) shows

Re: [galaxy-dev] CloudMap_Hawaiian_Variant & missing tools on new Galaxy instance

Hi Nikolaos, you may want to take a look at MiModD (www.celegans.de), our new tool suite for mapping-by-sequencing analyses, as a simple and modern replacement for CloudMap. It offers all the functionality of CloudMap, but is more flexible in the types of analyses it can perform and has much

[galaxy-dev] conda management of tools dependent on python3

Dear all, I'm still pretty new to conda tool dependencies management and there is one thing I cannot find documented anywhere: How can I let conda manage tool dependencies that involve python3? If I let Galaxy install conda for me, it creates an environment with python2, then if there is a

Re: [galaxy-dev] conda management of tools dependent on python3

Hi Björn, Hmm, I guess I should have phrased my question more clearly. What I'm trying to do is to get Galaxy to satisfy a missing tool dependency at *tool runtime* using a bioconda package that is only available for Python3. I am able to satisfy the dependency *manually* by running: conda

[galaxy-dev] controlling dataset formats in output collections

Dear all, as the title says I'm wondering whether there is any way to control the format of the elements of a collection generated by a tool. I know how to specify the type of the collection itself (list, paired or nested), but this is about the elements themselves. For example, I would like

[galaxy-dev] html with styles

Dear all, until recently extra html files linked from html datasets got displayed with style information applied, but this seems to have changed. I did not investigate the change in detail, but is this a consequence of the backported

Re: [galaxy-dev] html with styles

as HTML.  Local galaxy administrators can use the display whitelist (left side of the admin window) to configure 'safe' applications, which will then no longer be sanitized on display.  Let me know if this doesn't solve the problem for you! -Dannon On Fri, Nov 3, 2017 at 12:37 PM, Wolfgang

Re: [galaxy-dev] html with styles

(left side of the admin window) to configure 'safe' applications, which will then no longer be sanitized on display.  Let me know if this doesn't solve the problem for you! -Dannon On Fri, Nov 3, 2017 at 12:37 PM, Wolfgang Maier <wolfgang.ma...@biologie.uni-freiburg.de <mailto:wolfg

Re: [galaxy-dev] html with styles

, Nov 3, 2017 at 12:58 PM, Wolfgang Maier <wolfgang.ma...@biologie.uni-freiburg.de <mailto:wolfgang.ma...@biologie.uni-freiburg.de>> wrote: Maybe a dumb follow-up question, but I just don't know much about web server security: Why does sanitization have to care about in-do