Re: [galaxy-dev] Macs14 - Invalid Literal for int error

Hello Greg It looks like you're running the version of the MACS14 tool from the toolshed? I think we also ran into this here and I patched the macs14_wrapper.py thusly to work around it: diff --git a/macs14/macs142_wrapper.py b/macs14/macs142_wrapper.py index ccefb10..c0cf099 100644 --- a/mac

Re: [galaxy-dev] bowtie-wrapper

Hello Alexander I've made some changes to our local copy of the bowtie tool files (bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of capturing bowtie's stderr output and adding it as an additional history item (here the statistics in this output is used as input to a local tool).

Re: [galaxy-dev] all the data files in .loc files needed to download ?

Hello Carl, Thank you very much for your help.I have some thoughts about installing my local galaxy : First,download the latest source of galaxy from https://bitbucket.org/galaxy/galaxy-dist/ ,then install it in my local computer. Second,install dependencies tools mentioned in http://wiki.galax

Re: [galaxy-dev] all the data files in .loc files needed to download ?

Hi, shenwiyn I'd also add: Fourth, replace distributed default sqlite with postgresql to your list if it's for any serious use. Sqlite is ok for testing. On Wed, Feb 27, 2013 at 9:37 PM, shenwiyn wrote: > ** > **Hello Carl, > Thank you very much for your help.I have some thoughts about installi

Re: [galaxy-dev] all the data files in .loc files needed to download ?

Hello, Ross makes an important point: if this installation is for more than one user, you should install a more complete database system. This page may help with your decisions there: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerf

[galaxy-dev] Strange issue where the dataset reported in the bug report doesn't correspond to the current dataset

Dear Galaxy mailing-list, We are currently facing a strange issue with our local Galaxy installation (distribution from Jan. 11 2013). I'm going to try to describe the problem as much as I can, and feel free to ask for more details if it can help in solving this issue. So basically, we have a

Re: [galaxy-dev] Composite datatype output for Cuffdiff

Hey Jeremy, I am trying to think about a path forward with this composite multiple file dataset implementation. It seems there is consensus among the galaxy team that it shouldn't be included because grouping actual datasets would be superior. In that light, I am revisiting this e-mail, because

Re: [galaxy-dev] bowtie-wrapper

Thanks Peter. I've added your patch to the Trello card tracking incorporation of community contributions to the Bowtie wrapper: https://trello.com/c/TdYxdbkm Best, J. On Feb 27, 2013, at 4:35 AM, Peter Briggs wrote: > Hello Alexander > > I've made some changes to our local copy of the bowtie

Re: [galaxy-dev] Macs14 - Invalid Literal for int error

Thanks Peter. I'm running it now after applying your fix. Any idea what the problem was? -Greg On Wed, Feb 27, 2013 at 4:21 AM, Peter Briggs wrote: > Hello Greg > > It looks like you're running the version of the MACS14 tool from the > toolshed? I think we also ran into this here and I patched

[galaxy-dev] Implementing dataset collections

Hi John, Thanks for your interest and willingness to take a look at this. I've changed the subject of this thread to what I see as the core issue: implementing dataset collections. The Galaxy team would prefer to see an implementation of dataset collections that can be used going forward for a

Re: [galaxy-dev] bowtie-wrapper

Thanks it is working now. Best wishes, Alex On Wed, Feb 27, 2013 at 9:35 AM, Peter Briggs wrote: > Hello Alexander > > I've made some changes to our local copy of the bowtie tool files > (bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of capturing > bowtie's stderr output and ad

[galaxy-dev] access to api when using apache ldap auth

I need to access the api using an api key… Does anybody have a working apache configuration for that? A search at galaxyproject.org/search didn't turn anything up. I tried this: but that causes the history to fail to update. Order allow,den

Re: [galaxy-dev] [External] Re: macs error for chipseq data

Hello, When I sudo galaxy user at ssh terminal, the password prompted for galaxy. What is it? Thanks, Kathryn -Original Message- From: Dannon Baker [mailto:dannonba...@me.com] Sent: Friday, January 11, 2013 12:12 PM To: Jennifer Jackson Cc: Galaxy Dev; Sun, Wenping [USA] Subject: [Extern