Re: [galaxy-dev] Special considerations for installing localinstance of Galaxy on Mac OS X (10.6.7)?

2011-04-27 Thread Gordon, Assaf
Regarding the fastx-splitter: This one is a perl+shell script, not a binary, so try installing GNU sed (no need to override Mac's sed, the GNU sed will probably be installed as "gsed"), and modify the shell script (from "sed" to "gsed"). On Apr 27, 2011, at 19:15, "Pieter Neerincx" wrote: >

Re: [galaxy-dev] Display BAM with IGV

2011-04-27 Thread Dave Walton
I’m getting this same error and I’m running nginx as a proxy server. Is there a specfic parameter we should be aware of to allow partial gets? I don’t see anything in the wiki page for setting up the ProductionServer. Thanks, Dave On 4/27/11 12:33 PM, "Daniel Blankenberg" wrote: Hi Alex,

Re: [galaxy-dev] Special considerations for installing local instance of Galaxy on Mac OS X (10.6.7)?

2011-04-27 Thread Pieter Neerincx
Hi Jeff, On Apr 28, 2011, at 12:42 AM, Whyte, Jeffrey wrote: > Hi Pieter, > > Thanks to both you and Florent for the suggestion of MacPorts. GnuPlot is > now working well in Galaxy after I installed the port. :) > I also appreciate the information on specifying the custom environment. > T

Re: [galaxy-dev] Special considerations for installing local instance of Galaxy on Mac OS X (10.6.7)?

2011-04-27 Thread Whyte, Jeffrey
One more note on the FASTX barcode splitter error: After a little searching, I believe the problem is with the options used for sed utility, specifically the -r option An error occurred running this job:sed: illegal option -- r If I log in to my Linux server, and type "man sed", one of

Re: [galaxy-dev] Special considerations for installing local instance of Galaxy on Mac OS X (10.6.7)?

2011-04-27 Thread Whyte, Jeffrey
Hi Pieter, Thanks to both you and Florent for the suggestion of MacPorts. GnuPlot is now working well in Galaxy after I installed the port. I also appreciate the information on specifying the custom environment. That could be related to the only other problem I am having: the FASTX toolkit b

Re: [galaxy-dev] bwa failure preparing job

2011-04-27 Thread Vipin TS
Hi Branden, Vipin, thanks for the tip. I was not aware of data tables at all. > > I checked bwa_wrapper.xml and it is still using the from_file attribute for > the reference genome parameter, not from_data_table. It would appear then > that BWA is not using data tables? Additionally, I have no

Re: [galaxy-dev] Display BAM with IGV

2011-04-27 Thread Daniel Blankenberg
Hi Alex, Displaying BAM files at external applications usually requires an http server that supports partial gets. Unfortunately, the current lightweight http server that is built into Galaxy does not support these advanced http options. However, this limitation can be overcome by using a prox

Re: [galaxy-dev] User Name "not set" with external LDAP authentication

2011-04-27 Thread Leandro Hermida
Hi Pieter, On Wed, Apr 27, 2011 at 4:14 PM, Pieter Neerincx wrote: > Hi Leandro, > > On Apr 27, 2011, at 3:50 PM, Leandro Hermida wrote: > > > Hi, > > > > Just wondering if I got my setup right, I have Galaxy front-ended by > Apache doing the static caching, proxying and LDAP auth. What's nice i

Re: [galaxy-dev] User Name "not set" with external LDAP authentication

2011-04-27 Thread Pieter Neerincx
Hi Leandro, On Apr 27, 2011, at 3:50 PM, Leandro Hermida wrote: > Hi, > > Just wondering if I got my setup right, I have Galaxy front-ended by Apache > doing the static caching, proxying and LDAP auth. What's nice is that user's > don't have to be created by an admin if the user authenticates

[galaxy-dev] Display BAM with IGV

2011-04-27 Thread Alexander Graf
Hello all, I just updated our local copy of Galaxy and just wanted to try the new IGV display application. When I try to display a BAM file with the local IGV or the web IGV I encounter following error complaining about the Null content-length. Has any of you encountered the same problem? Do I miss

[galaxy-dev] User Name "not set" with external LDAP authentication

2011-04-27 Thread Leandro Hermida
Hi, Just wondering if I got my setup right, I have Galaxy front-ended by Apache doing the static caching, proxying and LDAP auth. What's nice is that user's don't have to be created by an admin if the user authenticates and authorizes properly against the LDAP config then Galaxy will automaticall

Re: [galaxy-dev] Does REMOTE_USER have to be an email address?

2011-04-27 Thread Leandro Hermida
Hi everyone, To answer my own question after testing various front-end auth setups it looks like REMOTE_USER must be the email address, and what's nice about LDAP is that you can have users authenticate with a username or other ID that is not the email address and still return the email address to

Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

2011-04-27 Thread Dannon Baker
Not currently, though the API is being continually extended with new features as the need arises. -Dannon On Apr 27, 2011, at 9:40 AM, Leandro Hermida wrote: > Hi Dannon, > > Thanks for your replies and advice, this leads me to a quesion... is it > possible to execute a tool job via the Galaxy

Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

2011-04-27 Thread Leandro Hermida
On Thu, Apr 21, 2011 at 2:40 PM, Dannon Baker wrote: > Leandro, > > I see what you mean, I misunderstood your original goal. There currently > isn't a way to execute single tools in this fashion. > > It isn't exactly straightforward, but you could construct a workflow that > consisted of two ste

Re: [galaxy-dev] Special considerations for installing local instance of Galaxy on Mac OS X (10.6.7)?

2011-04-27 Thread Pieter Neerincx
Hi Jeff, 1. As Florent wrote, probably the easiest solution is to install the dependencies with MacPorts. Only if stuff is not available via MacPorts or the version available is too old / incompatible with other dependencies I install things manually. MacPorts will add a line like this: ---