-Original Message-
From: Hakeem Almabrazi
Sent: Thursday, January 31, 2013 7:54 AM
To: 'Carlos Borroto'
Subject: RE: [galaxy-dev] install reference genome Bwa and Bowtie!
Thank you Carlos for your help,
I was sure that was not the case (all in tabs). Here is my bwa_indices.loc
file
Hi all,
I was hoping to make some enhancements to the ToolShed, so first
I need to be able to run my own ToolShed locally:
http://wiki.galaxyproject.org/HostingALocalToolShed
I have the latest code for bitbucket for galaxy-central:
$ hg heads default
changeset: 9117:04e221996871
user:
On Thu, Jan 31, 2013 at 2:40 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I was hoping to make some enhancements to the ToolShed, so first
I need to be able to run my own ToolShed locally:
http://wiki.galaxyproject.org/HostingALocalToolShed
I have the latest code for bitbucket
On Thu, Jan 31, 2013 at 9:09 AM, Hakeem Almabrazi halmabr...@idtdna.com wrote:
I was sure that was not the case (all in tabs). Here is my bwa_indices.loc
file look like
#
#bwaReference /usr/local/galaxy_data/hg19/bwa/
hg19_reference_genome
Thank you Carlos again.
I was just looking at that and in fact I got it to work by following the sample
file. I was misled by the tutorial
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup in regard to create
this file.
***
Setting Up loc File
Get the index files
Thanks Peter- I'll make sure to update the tool shed wiki accordingly as soon
as possible.
Greg Von Kuster
On Jan 31, 2013, at 9:48 AM, Peter Cock wrote:
On Thu, Jan 31, 2013 at 2:40 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
I was hoping to make some enhancements to the
Hi Peter,
The default sqlite database connection string has been uncommented in change
set 8707:5e60f2efceaf.
Thanks!
Greg Von Kuster
On Jan 31, 2013, at 9:48 AM, Peter Cock wrote:
On Thu, Jan 31, 2013 at 2:40 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
I noticed that the
On Tue, Jan 29, 2013 at 4:44 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Jan 29, 2013 at 4:17 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
The tool shed source is mostly in the following places.
~/lib/galaxy/webapps/community/
/lib/galaxy/tool_shed/
Hi Peter,
All of the tool-shed related required files will be automatically generated
from the samples when you start your tool shed server as of change set
8708:2a34f751c32c.
In the past, all of these same files were created if you started your Galaxy
server using run.sh. It's no excuse, but
On Thu, Jan 31, 2013 at 4:51 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
All of the tool-shed related required files will be automatically generated
from the
samples when you start your tool shed server as of change set
8708:2a34f751c32c.
In the past, all of these same files were
Hi Kathryn,
Hopefully instructions here should help you out:
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environment
I've also cc'd the galaxy-dev list as that's the best place to ask
questions like this instead of emailing team members directly. Using
Hi Peter,
Thanks for the update and your contributions. Would you like me to continue
with the work you've started, or would you like to continue yourself? I'll try
to fit this in this week if you want to hand it off to me. Please let me know.
Thanks!
Greg Von Kuster
On Jan 31, 2013, at
On Thursday, January 31, 2013, Greg Von Kuster wrote:
Hi Peter,
Thanks for the update and your contributions. Would you like me to
continue with the work you've started, or would you like to continue
yourself? I'll try to fit this in this week if you want to hand it off to
me. Please let
Hello Anthonius,
Can you elaborate on how you're invoking the API? How are you calling it?
Thanks,
Carl
On Wed, Jan 30, 2013 at 6:30 PM, Anthonius deBoer thondeb...@me.com wrote:
Hi,
I am trying to use the API with my galaxy server running behind a proxy
server.
How do I pass
Hi,
The bowtie issue was resolved. I resolved it by adding a table entry in the
xml file tool_data_table_conf.xml. Hu :)
Now, I am having the same issue with the SamTools displaying a reference
genome :)...
My reference fasta file is located at
Hi, I have installed Galaxy on our local server, which is up and running. I
have a very big file (5Gb) which I want to upload and I don't want to use the
upload option but rather sftp or use FileZilla, where should I transfer the
file to show up in my History?
thanks!
stefano
Cardinale Stefano
I don't know how to speak intelligently about this, so excuse my
imprecise language. The idea is that you need to still pass session
information (REMOTE_USER) along so JavaScript can access the API, but
for /api you need to make that optional.
I have an Apache server using TKTAuth. For that
Hey Mark,
With workflows you can do this. When you run a workflow that has at least one
Input Dataset step, you can select multiple inputs. While you can't do this
in the standard tool form yet, you can always create a simple workflow with an
Input Dataset step, and a single Tool Step.
Hi Stefano,
First you'll have to configure the instance to handle FTP uploads. Here's the
relevant documentation on our wiki:
http://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP
Good luck!
Dannon
On Jan 31, 2013, at 2:53 PM, stefano cardinale scardin...@lbl.gov wrote:
Hi, I
Hello Hakeem,
It is difficult to troubleshoot without knowing all the exact details of
your configuration, but it sounds as if you are on the right path and
the last few bits should be easy to reconcile with our documentation.
In particular, check that the builds.txt file contains the
Hi Carl,I am using the submit and get functions from the scripts/api/common.pyI actually found that I just need to add authentication to the calls, so I added thiscodedef authenticate(url, u, p): auth_handler = urllib2.HTTPBasicAuthHandler() auth_handler.add_password(realm='GALAXY@GHI.
Dear Galaxians,
We are using Galaxy with RepeatMasker 3.3.0. I don't know whether that is the
expected version, as I can't find any statement about what is required in the
Galaxy tool dependencies for RepeatMasker.
Anyway, when a job is submitted with no repeats, RepeatMasker 3.3.0 doesn't
On Jan 31, 2013, at 8:15 PM, Guest, Simon wrote:
Dear Galaxians,
We are using Galaxy with RepeatMasker 3.3.0. I don't know whether that is
the expected version, as I can't find any statement about what is required in
the Galaxy tool dependencies for RepeatMasker.
Anyway, when a job
Hi,I am trying to build some workflows for people that are part of a group and I want to share that workflow with them, so that they can run the workflow without having to make a local copy for them self.It seems I can only share a workflow in that manner with an individual, and not with a
Nope...Still only through the API can you access multiple, related files in a workflow...There is some ugly hack where you have to select the related files, and you need to hack some of the code, but if you are willing to do some editing of the source code, I believe there issomethingin this
Dear Galaxy support,
In the last 24 hours we are unable to load files to the Galaxy server.
We tried doing so as guest and by login as users but failed.
We try to load a small file (about 1M) but so far no success.
Has the Galaxy server been experienced problems recently?
Thanks a lot,
Roy
Hi Stefano
In addition to the FTP methods I recommend to use Data Libraries.
See: http://wiki.galaxyproject.org/Admin/Data%20Libraries/Libraries
also look at the configurations in universe_wsgi.ini:
library_import_dir
user_library_import_dir
allow_library_path_paste
which gives you many
Hi Christos,
Yes, I would be very interested by your modified file.
I'm forwarding to the mailing-list so this bug can be listed.
Thanks,
Pierre
Pierre Pericard
IE CDD - Projet Peptisan
Service Informatique et Bio-informatique (SIB)
Station Biologique de Roscoff
CNRS - UPMC
Place Georges
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