[galaxy-dev] workflow Editor

2013-01-28 Thread sshashi
Hi, I want to know about workflow editor and how it works internally? what type of canvas editor are you using ? doest it support only python environment ? if you have any documents related with ,can i get it . Regards shashi

[galaxy-dev] History not updating automatically

2013-01-28 Thread Sajoscha Sauer
Hi list, I have a weird problem after updating to the latest version. After doing the update as usual, the history panel is not updating automatically anymore. And when I press refresh, I get an javascript popup saying: Error getting history updates from the server. Forbidden Also, in

Re: [galaxy-dev] History not updating automatically

2013-01-28 Thread Langhorst, Brad
Hi Sajoscha: I have exactly the same problem… it started about a month ago. Also with external ldap auth. I have not yet investigated in detail, since it's not crippling - just annoying. Brad On Jan 28, 2013, at 6:38 AM, Sajoscha Sauer sa...@embl.de wrote: Hi list, I have a weird

[galaxy-dev] Uploading large files as AdminŠ Still slow!

2013-01-28 Thread Jackie Lighten
Hi, I am trying to upload 2x 2.5GB files to my data libraries (in Admin on a local instance) but it has so far been running over night and not completed. How can I speed this up? Can I upload compressed files? Can I not just copy these files directly in to $galaxy-dist/database/files/000 ?

Re: [galaxy-dev] Uploading large files as AdminŠ Still slow!

2013-01-28 Thread Dannon Baker
What probably happened here is that due to the filesize, the browser upload failed but this went undetected. The good news is that you *can* tell galaxy to copy directly, or you could even use the files exactly where they are without any copy. What you want to do is enable this section in

[galaxy-dev] Nice 'citable' URLs for Galaxy Tool Shed repositories

2013-01-28 Thread Peter Cock
Dear all, Something I am conscious of every time I have directed someone to a tool or wrapper on the Galaxy Tool Shed is the lack of nice stable URLs. The current frame based design hinders this - and as a result I usually just have to give the ToolShed URL and tell them what to search for. This

Re: [galaxy-dev] Uploading large files as AdminŠ Still slow!

2013-01-28 Thread Jackie Lighten
Thanks. I now have the option to upload via directory path. How do I create the ability to use files in their current location without a copy into Galaxy database ? Thanks, J On 2013-01-28 9:30 AM, Dannon Baker dannonba...@me.com wrote: What probably happened here is that due to the

Re: [galaxy-dev] Uploading large files as AdminŠ Still slow!

2013-01-28 Thread Jackie Lighten
Sorry. I got itŠ O the drop down menu. Thanks again. J On 2013-01-28 9:30 AM, Dannon Baker dannonba...@me.com wrote: What probably happened here is that due to the filesize, the browser upload failed but this went undetected. The good news is that you *can* tell galaxy to copy directly, or

Re: [galaxy-dev] Selecting Intermediary Files in a Workflow

2013-01-28 Thread James Taylor
You can work around this using the from_work_dir attribute when specifying the output file in your tool config. -- jt (composed on my phone) On Jan 27, 2013, at 6:13 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Sun, Jan 27, 2013 at 10:26 PM, Kolby Chien kc...@nau.edu wrote: Hello,

Re: [galaxy-dev] workflow Editor

2013-01-28 Thread James Taylor
The client side of the workflow editor is in javascript, using a mix of HTML5 Canvas and DOM elements. It communicates with the server using JSON. The server side is written in Python. The editor could be decoupled and reused, however there are some details that are fairly Galaxy specific right

[galaxy-dev] workflows stop prematurely

2013-01-28 Thread mark.rose
Hi All On my local install of galaxy I'm having problems executing workflows. I will upload data into a new history and then select to run a saved workflow. This initiates fine but, after the completion of a variable number of steps, the workflow just stops after the successful completion

[galaxy-dev] Pull request for bowtie_wrappers tool

2013-01-28 Thread Nicola Soranzo
Dear Galaxy DevTeam, I have made a few updates to the bowtie_wrappers tool from the Tool Shed, may someone please pull from: https://bitbucket.org/nsoranzo/bowtie_wrappers/ for the following changes: - Add fields for --nofw and --norc options also for single-end reads - Remove field for --cutoff

Re: [galaxy-dev] Nice 'citable' URLs for Galaxy Tool Shed repositories

2013-01-28 Thread Greg Von Kuster
Hi Peter, Thanks for your request, having citable tool shed URLs is definitely important. I've got this on my list (which is maxed out as usual). I will look into this in a timely manner and keep you posted appropriately. Greg Von Kuster On Jan 28, 2013, at 8:41 AM, Peter Cock wrote:

Re: [galaxy-dev] Nice 'citable' URLs for Galaxy Tool Shed repositories

2013-01-28 Thread Peter Cock
On Mon, Jan 28, 2013 at 6:49 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Peter, Thanks for your request, having citable tool shed URLs is definitely important. I've got this on my list (which is maxed out as usual). I will look into this in a timely manner and keep you posted

Re: [galaxy-dev] History not updating automatically

2013-01-28 Thread Nate Coraor
Hi Brad and Sajoscha, Is there any chance that your proxy configurations are not passing the username in the REMOTE_USER header when the request is to an /api path? Could you provide the relevant portions of your proxy server configs? Thanks, --nate On Jan 28, 2013, at 7:12 AM, Langhorst,

Re: [galaxy-dev] Nice 'citable' URLs for Galaxy Tool Shed repositories

2013-01-28 Thread Greg Von Kuster
I've opened a Trello card, but it's in the Galaxy development project, so not sure if you can see it or not. Here's the link to the card just in case... https://trello.com/card/nice-citable-urls-for-galaxy-tool-shed-repositories/506338ce32ae458f6d15e4b3/182 On Jan 28, 2013, at 2:28 PM, Peter

[galaxy-dev] Galaxy with EMBOSS 5 or EMBOSS 6 ?

2013-01-28 Thread Guest, Simon
Dear Galaxians, I am troubleshooting a problem with running EMBOSS infoseq on our local galaxy installation. We are running EMBOSS 6.5. There is a mismatch between the options Galaxy is passing to infoseq (-version), and what infoseq wants (-seqversion). This breaks the tool. While this

Re: [galaxy-dev] Galaxy with EMBOSS 5 or EMBOSS 6 ?

2013-01-28 Thread Guest, Simon
There is a mismatch between the options Galaxy is passing to infoseq (- version), and what infoseq wants (-seqversion). This breaks the tool. Clarification: I see the -version/-seqversion change to infoseq was made in EMBOSS 6.2.0. I'm still wondering which version I should be using with

Re: [galaxy-dev] Loading a library of bam files

2013-01-28 Thread Greg Von Kuster
Hi Kyle, I'm hoping I can help you a bit on this, although i am not very familiar with the code that is producing this behavior. Your previous reply mentions the following: During job cleanup, galaxy.jobs.__init__.py:412, because external_metadata_set_successfully returns false. An external

Re: [galaxy-dev] Galaxy with EMBOSS 5 or EMBOSS 6 ?

2013-01-28 Thread Dannon Baker
Hey Simon, You're right -- the EMBOSS version supported by the Galaxy wrappers is currently EMBOSS 5. We do have a Tool Dependency page here: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies, but unfortunately while it lists versions for many tools it doesn't cover them all.

Re: [galaxy-dev] Galaxy with EMBOSS 5 or EMBOSS 6 ?

2013-01-28 Thread Guest, Simon
You're right -- the EMBOSS version supported by the Galaxy wrappers is currently EMBOSS 5. We do have a Tool Dependency page here: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies, but unfortunately while it lists versions for many tools it doesn't cover them all. I'll update

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-01-28 Thread Carl Eberhard
I was incorrect in stating that the changes in the next galaxy-dist will help in this case, unfortunately. From the stack trace you posted, there is a deeper error with your instance that the client-side changes won't help. Can you post the size, type, and name of the file you're trying to

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-01-28 Thread Dan Tenenbaum
On Mon, Jan 28, 2013 at 1:40 PM, Carl Eberhard carlfeberh...@gmail.com wrote: I was incorrect in stating that the changes in the next galaxy-dist will help in this case, unfortunately. From the stack trace you posted, there is a deeper error with your instance that the client-side changes won't

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-01-28 Thread Carl Eberhard
If you go to your galaxy root in a terminal and then cd to eggs, what is the version listed for SQLAlchemy? Do you have SQLAlchemy installed already on that machine (apart from the one in Galaxy's eggs)? On Mon, Jan 28, 2013 at 4:50 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: On Mon, Jan 28,

Re: [galaxy-dev] error uploading file with fresh installation: this request returned None from get_history()

2013-01-28 Thread Dan Tenenbaum
On Mon, Jan 28, 2013 at 1:59 PM, Carl Eberhard carlfeberh...@gmail.com wrote: If you go to your galaxy root in a terminal and then cd to eggs, what is the version listed for SQLAlchemy? SQLAlchemy-0.5.6_dev_r6498-py2.7.egg Do you have SQLAlchemy installed already on that machine (apart from

[galaxy-dev] Tool shed and tools with dynamically generated select list parameters

2013-01-28 Thread Carlos Borroto
Hi, I'm trying to get lastz to show a locally cached reference. As I'm used to do I went ahead and copy tool-data/lastz_seqs.loc.sample(still included with galaxy-dist) to tool-data/lastz_seqs.loc and added my local references. Nothing happened. I get: galaxy.tools.parameters.dynamic_options

Re: [galaxy-dev] Tool shed and tools with dynamically generated select list parameters

2013-01-28 Thread Greg Von Kuster
Hello Carlos, On Jan 28, 2013, at 5:13 PM, Carlos Borroto wrote: Hi, I'm trying to get lastz to show a locally cached reference. As I'm used to do I went ahead and copy tool-data/lastz_seqs.loc.sample(still included with galaxy-dist) to tool-data/lastz_seqs.loc and added my local

Re: [galaxy-dev] Tool shed and tools with dynamically generated select list parameters

2013-01-28 Thread Carlos Borroto
On Mon, Jan 28, 2013 at 5:29 PM, Greg Von Kuster g...@bx.psu.edu wrote: And that did the trick. Is this the expected way of handling these cases?. Yes, however, if your install the repository from the Galaxy administrator interface, this should all happen automatically for you. If you

Re: [galaxy-dev] Loading a library of bam files

2013-01-28 Thread Kyle Ellrott
It looks like if I set 'retry_metadata_internally = False' it stops trying to index them on the queue node. The datasets get added into the library, without a BAM index file, but without error. I guess the index files can be generated on demand later on. Kyle On Mon, Jan 28, 2013 at 12:42 PM,