Re: [galaxy-dev] Difference between GitHub and Mercurial Galaxy download...

Galaxy migrated from mercurial(on Bitbucket) to git(on GitHub). If you are starting new production Galaxy going with GitHub (master branch) is a good choice. On Thu, Apr 16, 2015 at 4:03 PM Asma Riyaz wrote: > Hi, > > Is there a difference between the github and mercurial galaxy downloads? > Is

Re: [galaxy-dev] Difference between GitHub and Mercurial Galaxy download...

Hello Asma, Galaxy recently migrated from mercurial (on Bitbucket) to git (on GitHub). If you are starting new production Galaxy going with GitHub (master branch) is a good choice. If you are maintaining older version of Galaxy you can also safely continue to use https://bitbucket.org/galaxy/galax

[galaxy-dev] Difference between GitHub and Mercurial Galaxy download...

Hi, Is there a difference between the github and mercurial galaxy downloads? Is there one preferred over another? The galaxy website asks to do a Github download and many other places including the GMOD tutorial held last summer on Galaxy suggested a mercurial one? Kindly advice. Thank you, Asma

Re: [galaxy-dev] substitution of special characters in arguments of galaxy tools

Yu, You can use the sanitizer tag set for this. https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Csanitizer.3E_tag_set E.g. https://github.com/galaxyproject/tools-iuc/pull/106/files#diff-db276c72d5a0b8ccc28dba5957448192R44 I use the sanitizer block to allow [, ], ' Cheers, Eric 20

[galaxy-dev] substitution of special characters in arguments of galaxy tools

Dear galaxy developers, Galaxy seems to substitute special characters when it passes arguments to its tools (e.g. the content of input fields of type 'text'). In general, this is useful. However, '%' is substituted by 'X', i.e. the substitution is not invertible which can be a real show stoppe

Re: [galaxy-dev] $REMOTE_USER

Hi, John, it is a perfect solution for our problem. Thank you very much for the quick reply! Cheers, Yu di29her w...@lrz.de On 15 Apr 2015, at 16:49, John Chilton mailto:jmchil...@gmail.com>> wrote: Hello, I have a created an answer for this question in the planemo tool d

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

Ok, yeah, that's pretty old :) I'd second the virtualenv suggestion, then, as a next easy thing to try. It's really easy to set up, and to test it you'd basically have to do this: (sudo) pip install virtualenv cd virtualenv .venv source .venv/bin/activate sh run.sh (in this now-activated virtual

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

Hi Daniel and John, thanks a lot for your replies. I have tried creating a galaxy.json file, but I haven't had much time, so I gave up that. But I am interested to use your suggestions. For my solution, I followed the explanations in: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20

Re: [galaxy-dev] April GalaxyAdmins Meetup: April 16

Hello all, GalaxyAdmins is starting in about 25 minutes. The room is here: https://connect.johnshopkins.edu/galaxyadmins201504/ It takes a few minutes to navigate through Flash, so connecting a few minutes early is encouraged. Thanks, Dave C On Wed, Apr 15, 2015 at 9:14 AM, Dave Clements

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] Geting integer value from InputValueWrapper in plugin xml file

On Thu, Apr 16, 2015 at 9:10 AM, Peter Cock wrote: > On Thu, Apr 16, 2015 at 1:59 PM, Christian Brenninkmeijer > wrote: >> Hi, >> I am a new galaxy developer playing with writing my first plugins >> >> In my plugin xml configaration file: >> I want to be able to increase the value of one para

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

Yeah - I am not very familiar with data source tools at all - sorry. Are you creating a galaxy.json file in upload3.py? If you are creating that file but cannot distinguish between the files - I would try adding "name" or "designation" fields to the JSON lines in that file - I would think one of th

Re: [galaxy-dev] Geting integer value from InputValueWrapper in plugin xml file

On Thu, Apr 16, 2015 at 1:59 PM, Christian Brenninkmeijer wrote: > Hi, > I am a new galaxy developer playing with writing my first plugins > > In my plugin xml configaration file: > I want to be able to increase the value of one parameter based on another > using > > > #if $rows.option

Re: [galaxy-dev] pushing toolshed directories to our own repo

The answer I think depends largely on the kinds of changes you made and how quickly you need to deploy things. If the changes are bugfixes or enhancements in-line with the existing tool's structures - I think it would be best to open a pull request and try to get the tool fixed - the tophat2 tool

[galaxy-dev] Geting integer value from InputValueWrapper in plugin xml file

Hi, I am a new galaxy developer playing with writing my first plugins In my plugin xml configaration file: I want to be able to increase the value of one parameter based on another using #if $rows.option =="header_ignore" #set $data_start = $rows.ignore + 1 but I get: unsuppor

Re: [galaxy-dev] question about error output

Two things - if you really want to just hide standard output - you can use the XML CDATA idiom to eliminate the need for escaping < and >. I think this is a saner default and I would just add this block to all new tools. You may want to check out the planemo tool builder - it will bootstrap n

[galaxy-dev] question about error output

Hello, I am defining some tools for my own galaxy installation and I would like to know if there is a more elegant solution for redirecting error output than the one in the next config file: calling with gatk ln -s "${input}" input.bam ; samtools index input.bam; java -jar