[galaxy-dev] Galaxy September 20, 2012 Distribution & News Brief

*Galaxy September 20, 2012 Distribution & News Brief* http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_09_20 /*Highlights:* http://wiki.g2.bx.psu.edu/News / * A /*new Galaxy tool*/

Re: [galaxy-dev] Problem of running of galaxy

You changed the file universe_wsgi.ini? 2012/9/20 Chebbi Mohamed Amine > Hi Galaxy-team ! > > I have uploaded the latest version of Galaxy of 05/09. However when I run > run.sh I have the message below and I haven't found how to fix that: > > "TypeError: Invalid argument(s) 'server_side_cursors

[galaxy-dev] Problem of running of galaxy

Hi Galaxy-team ! I have uploaded the latest version of Galaxy of 05/09. However when I run run.sh I have the message below and I haven't found how to fix that: "TypeError: Invalid argument(s) 'server_side_cursors' sent to create_engine(), using configuration SQLiteDialect/SingletonThreadPool/TLEn

Re: [galaxy-dev] zombie undeletable files in toolshed, and versioning question

Hello Kevyin, As you stated, the build directory was not being tracked in your fastq_groomer_parallel repository in the tool shed - running hg status on your repository produced this: %hg status ? build/README ? build/fastq_groomer_parallel.py ? build/fastq_groomer_parallel.xml ? build/ipython/

Re: [galaxy-dev] Setting error levels in

On Thu, Sep 20, 2012 at 4:59 PM, Scott McManus wrote: > My apologies: > > > > > > Great. Something like would be shorter but I appreciate wanting to keep the syntax simple. > Again, note that the second range will not be useful as OS X and > Linux (or at least the distros I've used) wil

Re: [galaxy-dev] Setting error levels in

The wiki markup was also fixed. The "//" is not supported. -Scott - Original Message - > My apologies: > > > > > > > Again, note that the second range will not be useful as OS X and > Linux (or at least the distros I've used) will never return a value > less than 0. > > Sorry.

Re: [galaxy-dev] Setting error levels in

My apologies: Again, note that the second range will not be useful as OS X and Linux (or at least the distros I've used) will never return a value less than 0. Sorry. -Scott - Original Message - > > You should be able to use the following: > > > > > > > Square bracke

Re: [galaxy-dev] Setting error levels in

You should be able to use the following: Square brackets are not supported in the range. However, note that many shells will not return an exit code that is less than 0. Instead, the lowest 8 bits (i.e., value mod 256) will be returned. So returning -1 will give you -1 mod 256 = 255, r

[galaxy-dev] single database connection and multiple Galaxy instance

Hi Galaxy team, Can I use a single database connection to serve multiple Galaxy instance ? thanks, --Vipin ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Gala

[galaxy-dev] Setting error levels in

Hi all, Regarding https://bitbucket.org/galaxy/galaxy-central/issue/325 and the new tag is described on the wiki here: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax The wiki text is unclear - it suggests square brackets might be needed, but the example lacks them: 1 2

Re: [galaxy-dev] Do ToolShed updates cope with renaming files?

On Thu, Sep 20, 2012 at 2:52 PM, Greg Von Kuster wrote: > On Sep 20, 2012, at 9:43 AM, Peter Cock wrote: >> >> OK. What would happen if I did the rename and increased >> the version number in one step (which seems the most >> common situation)? > > Assuming you want to increase the version number

[galaxy-dev] Sanity testing of ToolShed uploads

Hi all, Having just accidental uploaded the wrong tar-ball to the ToolShed, I think it would be helpful to add some sanity testing to the ToolShed. I accidentally uploaded a tar-ball for the ncbi_blast_plus repository to the blast_datatypes repository instead. The two repositories a have no tools

Re: [galaxy-dev] Do ToolShed updates cope with renaming files?

Hi Peter, see below... On Sep 20, 2012, at 9:43 AM, Peter Cock wrote: > On Thu, Sep 20, 2012 at 2:16 PM, Greg Von Kuster wrote: >> Hi Peter, >> >> On Sep 20, 2012, at 5:53 AM, Peter Cock wrote: >> >>> Hi all, >>> >>> I'd like to check (before I try this), if is this expected to work or not? >

Re: [galaxy-dev] Error when has no value and type is float or integer

I believe you have to tag with optional="true" when omitting the value: Hi, If I have a tool wrapper with this: I get an error when I start Galaxy: galaxy.tools ERROR 2012-09-19 12:09:08,056 Error reading tool from path: RGalaxy_test_tool/foo.xml Traceback (most recent call las

Re: [galaxy-dev] Do ToolShed updates cope with renaming files?

On Thu, Sep 20, 2012 at 2:16 PM, Greg Von Kuster wrote: > Hi Peter, > > On Sep 20, 2012, at 5:53 AM, Peter Cock wrote: > >> Hi all, >> >> I'd like to check (before I try this), if is this expected to work or not? >> >> For the normal tool wrappers, is it possible to rename the XML >> file (but lea

Re: [galaxy-dev] Size of the genome indexes repos in Galaxy Main

Hi Nate, We downloaded the entire indexes repos and our guys are planning to write a script to generate loc files based on the given path to the repos. We are wondering if the galaxy team will release the loc files that are being used in the galaxy main server? So that we simply just need to repl

[galaxy-dev] Do ToolShed updates cope with renaming files?

Hi all, I'd like to check (before I try this), if is this expected to work or not? For the normal tool wrappers, is it possible to rename the XML file (but leave the tool ID inside the XML file unchanged), and have this *just work* (TM) when automatically updated via the ToolShed? Similarly, for