[galaxy-dev] How to install bowtie2 tool in galaxy

2014-03-03 Thread Ravi Alla
Hi guys, I am new to galaxy and am in the process of setting it up on a cluster with some help. I am trying to install bowtie2 to my local galaxy through the toolshed. I have a few questions. - Which bowtie2 should I install? When I search for bowtie2 a bunch of results come up? - What are repo

Re: [galaxy-dev] Unable to build pbs_python via scramble

2014-03-03 Thread Nate Coraor
Hi Pete, Your subject says you are unable to build pbs_python using scramble. Could you provide details on what's not working there? Galaxy is not going to work with a different version of pbs_python unless a bit of hacking is done to make it attempt to do so. We test Galaxy with specific version

[galaxy-dev] reference genome

2014-03-03 Thread Changyu Fan
Dear Sir or Madam, We have installed our local Galaxy server and everything looks fine. But there are some issues with reference genome index. The BWA and Mageblast is working. Here is how bwa_index.loc looks like: hg18fullhg18Human (Homo sapiens): hg18 Full /u03/galaxy/galaxy_data/hg18/

[galaxy-dev] Unable to build pbs_python via scramble

2014-03-03 Thread Pete Schmitt
Following the directions from here: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS I'm trying to get pbs_python to work as I'm using torque for scheduling galaxy jobs.   Note: This is a fresh install of galaxy from galaxy-dist on CentOS 5.1

Re: [galaxy-dev] Graph Datatypes

2014-03-03 Thread Carl Eberhard
Hey, Bjoern Not sure whether a pull request or a toolshed repo would be best, but: if you decide on a toolshed repo, graphview as it is should be able to use your datatypes if they include a 'node-edge' dataprovider. Also, graphview is on my list - but most likely I won't get to it in the near fu

Re: [galaxy-dev] Display history.id in History Panel

2014-03-03 Thread Carl Eberhard
Hi, Julie Currently, the easiest way is to add an id field in the file 'static/scripts/mvc/history/current-history-panel.js'. On (currently) line 171, after the $newRender variable has been created... 165:// handle the possibility of no model (can occur if fetching the model returns an er

Re: [galaxy-dev] Exporting & Importing Tool Shed repository is just great!

2014-03-03 Thread Greg Von Kuster
On Mar 3, 2014, at 1:13 PM, Peter Cock wrote: > Hi Guys, > > Is this stuff on the wiki? Not completely yet. > Presumably the goal is helping to > move repositories between Tool Shed instances (e.g. from > a development/private Tool Shed to a production/public > Tool Shed)? Yes. > > I can

Re: [galaxy-dev] Exporting & Importing Tool Shed repository is just great!

2014-03-03 Thread Peter Cock
Hi Guys, Is this stuff on the wiki? Presumably the goal is helping to move repositories between Tool Shed instances (e.g. from a development/private Tool Shed to a production/public Tool Shed)? I can see "Import repository capsule" as a new action at the bottom of the left hand column (under "Cre

Re: [galaxy-dev] Exporting & Importing Tool Shed repository is just great!

2014-03-03 Thread Greg Von Kuster
Many thanks, Björn for your very kind words. The Tool Shed would not be what it is without your hard work as well. We hoped the export/import capsule feature would be beneficial, so it's great to hear confirmation that it is. Also, please don't hesitate to continue to contact us with newly di

[galaxy-dev] Exporting & Importing Tool Shed repository is just great!

2014-03-03 Thread Björn Grüning
Hi Tool Shed Team! I know I'm always finding bugs and keeping you busy, but this mail is different! The Tool Shed exporting and importing feature is just great, its save so much time and is a pleasure to use. Everyone should try it! So thanks for the hard work you all put into the Tool Shed ove

Re: [galaxy-dev] LWR questions

2014-03-03 Thread John Chilton
Hey Jun, Thanks for your continued interest in the LWR. Responses inline. On Sun, Mar 2, 2014 at 7:00 PM, Jun Fan wrote: > Hi all, > > > > LWR sounds very attractive and promising. However how to program on > galaxy side to utilize LWR server is not thoroughly documented. Critique noted,

Re: [galaxy-dev] Test ToolShed misfiling missing tool tests

2014-03-03 Thread Greg Von Kuster
Hi peter, Thanks for reposrting this. I've created the follwoing Trello card for this issue, and we'll get it taken care of asap. https://trello.com/c/rArkn49z/173-incorrect-tool-test-results-for-tools-missing-tool-test-components Gfreg Von Kuster On Mar 3, 2014, at 8:38 AM, Peter Cock wrot

[galaxy-dev] Test ToolShed misfiling missing tool tests

2014-03-03 Thread Peter Cock
Hello all, Currently the Test Tool Shed seems not to be flagging all tools with missing tests. For example, the following currently lack tests yet are not listed under "Latest revision: missing tool tests" but instead under "Latest revision: all tool tests pass": http://testtoolshed.g2.bx.psu.edu

[galaxy-dev] Graph Datatypes

2014-03-03 Thread Björn Grüning
Hi, we are currently working on a few graph based tools and we would like to add some new graph-datatypes, namely: gspan, gml, gexf, graphml, pajek. I saw that xgmml and sif are already integrated into core-galaxy and I'm wondering if a PR with these new datatypes would be appropriate or a new