Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

2012-04-30 Thread Gianmauro Cuccuru
On 04/27/2012 08:45 PM, Ann Black-Ziegelbein wrote: Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad

[galaxy-dev] How to customize Galaxy web interface?

2012-04-30 Thread Pascal Maugeri
Hi, I m running my own Galaxy instance and I would like to do some simple customization of the web interface such as adding my logos in the header frame, changing background colors, etc. I am having a look to static/ folders but I can't see clearly where the header frame is defined. Could you

Re: [galaxy-dev] Merging BLAST database support into Galaxy?

2012-04-30 Thread Peter Cock
On Thu, Apr 26, 2012 at 10:40 PM, Edward Kirton eskir...@lbl.gov wrote: your suggestion for blastdbn and blastdbp sounds fine. it's okay if a few of our users need to edit the metadata of the dbs in their history. thanks for asking and doing this. Great. Perhaps you can throw some light on

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

2012-04-30 Thread Hans-Rudolf Hotz
Hi Ann I am definitively interested in any form of collaboration - thank you very much for bringing up this idea! However, I also share some of the concerns which have been raised by others. Even in Europe, we sometimes struggle to coordinate a conference call with the Americas and very

[galaxy-dev] Error running MACS in Galaxy

2012-04-30 Thread Waldron, Michael H
We get the following error when trying to run MACS in our local installation of Galaxy: INFO @ Mon, 30 Apr 2012 09:02:14: # ARGUMENTS LIST: # name = MACS_in_Galaxy # ChIP-seq file = /proj/galaxy/000/dataset_552.dat # control file = None # effective genome size = 2.70e+09 # tag size = 36 # band

Re: [galaxy-dev] Unable to set BAM Metadata

2012-04-30 Thread Nate Coraor
On Apr 29, 2012, at 9:19 PM, Ciara Ledero wrote: This is my code for running a samtools command internally, via Galaxy: open INP, $ARGV[0] or die Cannot open file: $!; $file = $ARGV[1]; open OUT, $file or die Cannot open file: $!; @out =

Re: [galaxy-dev] What does this line of code mean

2012-04-30 Thread Nate Coraor
On Apr 29, 2012, at 9:26 PM, Ciara Ledero wrote: Hi all, Can I ask what this line of code does? job_wrapper.finish( stdout, stderr ) It's the one from the local.py. Hi Ciara, This runs the JobWrapper.finish() method in galaxy-dist/lib/galaxy/jobs/__init__.py, which performs all the

Re: [galaxy-dev] Unable to set BAM Metadata

2012-04-30 Thread Nate Coraor
On Apr 29, 2012, at 9:19 PM, Ciara Ledero wrote: This is my code for running a samtools command internally, via Galaxy: open INP, $ARGV[0] or die Cannot open file: $!; $file = $ARGV[1]; open OUT, $file or die Cannot open file: $!; @out =

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

2012-04-30 Thread Zhibin Lu
Hi, We have two galaxy instances installed within our institute, and I am very interested in communicating with other galaxy users. Please count me in. Zhibin Lu Bioinformatics Support: Databases Applications Ontario Institute for Cancer Research MaRS Centre, South Tower 101

Re: [galaxy-dev] Using REMOTE_USER with nginx

2012-04-30 Thread Nate Coraor
On Apr 29, 2012, at 1:50 AM, Peter van Heusden wrote: Hey there The instructions on using REMOTE_USER with nginx are still a bit vague in the wiki, so let me share how I got this working with nginx's http_auth_pam module and our local Kerberos setup. Really simple actually: First, I

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

2012-04-30 Thread Ryan Golhar
Agreed. User driven is good. Having developer(s) available to answer questions would be helpful...that's what I was alluding to... On Sun, Apr 29, 2012 at 10:37 PM, Dave Clements cleme...@galaxyproject.orgwrote: Hi Ryan, Ann, and everyone else I second what Nate says (I always do :-). I

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

2012-04-30 Thread Ann Black-Ziegelbein
I would like to thank everyone for their responses! I am working on a few things to hopefully get us going in the right direction: 1) a brief online web survey for everyone to fill out that will help us gauge the background of those interested in participation and help steer content for the

Re: [galaxy-dev] Stalled upload jobs under Admin, Manage jobs

2012-04-30 Thread Nate Coraor
On Apr 26, 2012, at 11:03 AM, Hans-Rudolf Hotz wrote: On 04/26/2012 04:47 PM, Peter Cock wrote: On Fri, Mar 16, 2012 at 11:00 AM, Peter Cockp.j.a.c...@googlemail.com wrote: On Mon, Feb 13, 2012 at 5:02 PM, Nate Coraorn...@bx.psu.edu wrote: On Feb 10, 2012, at 6:47 AM, Peter Cock

Re: [galaxy-dev] Interested in speaking with other

2012-04-30 Thread Dorset, Daniel C
Hi Ann, Count me in. Great idea! -Dan ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

Re: [galaxy-dev] Error running job as real user: looking et the wrong dir?

2012-04-30 Thread Nate Coraor
On Apr 25, 2012, at 9:22 AM, Louise-Amélie Schmitt wrote: Hi everyone, I'm (still) having issues with running jobs as the real user on our PBS Pro cluster. When I try running a job, it ends up in error state and displays the following error message: tou! ch: cannot touch

Re: [galaxy-dev] Running jobs as real user and extra_file_path

2012-04-30 Thread Nate Coraor
On Apr 25, 2012, at 9:39 AM, Louise-Amélie Schmitt wrote: Hi everyone, I just wanted to ask how the extra_file_path is handled in case of job running as the real user since the file_path is only writable by the galaxy user. Any clue? Hi L-A, There are actually two dataset attributes for

Re: [galaxy-dev] Error: Job output not returned from cluster

2012-04-30 Thread Nate Coraor
On Apr 25, 2012, at 8:25 AM, Louise-Amélie Schmitt wrote: Hi, Thanks a lot it actually helped. It is not exactly as straightforward in drmaa.py but somehow I could manage. However, it was not the problem. For some reason, the user needs to write files from the node to

Re: [galaxy-dev] /bin/sh: samtools: not found--WORKAROUND

2012-04-30 Thread Nate Coraor
On Apr 24, 2012, at 8:36 PM, Michael Moore wrote: There is apparently a persistent problem with samtools which normally lives at /usr/bin/samtools. I encountered a similar problem in Python when uploading BAM files. I did not resolve the problem. I hacked for a while on binary.py in a

Re: [galaxy-dev] Configuring Galaxy for FTP upload

2012-04-30 Thread Nate Coraor
On Apr 23, 2012, at 10:31 PM, Ciara Ledero wrote: Hi all, According to Galaxy, uploading files larger than 2GB will surely fail. For this reason, uploading via FTP is recommended. Unfortunately, I cannot download/install an FTP server for Galaxy since I am working on a remote server. I

Re: [galaxy-dev] /bin/sh: samtools: not found--WORKAROUND

2012-04-30 Thread Michael Moore
Yeah, I was using ['printenv| mail myaddress samtools'] inside the subprocess.Popen(['samtools'],... in upload.py. Now right before in upload.py before the subprocess was called, I had /usr/bin/ in my PATH, but inside the subprocess the story was different. I just used the symbolic link to

Re: [galaxy-dev] Galaxy parallel processing

2012-04-30 Thread Nate Coraor
Hi Kiran, This is a question best directed to the galaxy-dev list, which I have CC'd. On Apr 23, 2012, at 5:23 AM, Kiran Jaycee wrote: Dear Nate, Im deploying Galaxy in the cluster environment with 8 nodes and 96 cores. Im particularly interested in running NGS tools like BWA, BOWTIE etc

[galaxy-dev] installing tool from ToolShed - Python Error 'too many values to unpack'

2012-04-30 Thread Shantanu Pavgi
I am getting following ValueError: too many values to unpack from Python while trying to install a tool from toll_shed repository. {{{ URL:

Re: [galaxy-dev] installing tool from ToolShed - Python Error 'too many values to unpack'

2012-04-30 Thread Greg Von Kuster
Hi Shantanu, Your Galaxy instance is not current with the Galaxy central repository - are you tracking Galaxy dist? In order to use the features that provide communication between Galaxy and a tool shed, you'll have use the latest code from Galaxy central - see

[galaxy-dev] Cutadapt

2012-04-30 Thread Jennifer Jackson
Hi Tilahun, This tool is in the Galaxy Tool Shed (http://wiki.g2.bx.psu.edu/Tool%20Shed) so to use for now, use with a local/cloud instance (http://getgalaxy.org) would be the best route: http://galaxy.psu.edu/search/getgalaxy/ search for cutadapt I will also forward this to the galaxy-dev

Re: [galaxy-dev] installing tool from ToolShed - Python Error 'too many values to unpack'

2012-04-30 Thread Shantanu Pavgi
That's right Greg, I was using the latest revision from the galaxy-dist and not the galaxy-central. It worked fine after using the latest code on from the galaxy-central. Thanks for the help. -- Shantanu On Apr 30, 2012, at 1:54 PM, Greg Von Kuster wrote: Hi Shantanu, Your Galaxy

Re: [galaxy-dev] Remove libraries using Galaxy code or API

2012-04-30 Thread Nate Coraor
On Apr 23, 2012, at 4:55 AM, liram_va...@agilent.com liram_va...@agilent.com wrote: Hello, I am using Galaxy API for some actions and I must say that this is indeed a really great feature with a great power. Anyway, I am trying to write a python script that one of its goals is to

[galaxy-dev] Is there a bowtie2 wrapper

2012-04-30 Thread Oleksandr Moskalenko
I wonder if someone has a functional bowtie2 wrapper that they can share. Thanks, Alex ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use