will be
available ?
Please, excuse me if this information is available on your web and if
I have not seen it.
Happy new year,
Sarah Maman
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Sarah Maman
INRA - LCG - SIGENAE
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel: +33(0)5.61.28.57.08
Tax
. This is generally due to a misconfiguration
in the upstream server.
Thank you, and best regards
Sarah Maman
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Hi Brad, Hi Christopher,
Thanks a lot.
I'm talking to Open LDAP. I have changed
RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
to
RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e
But I always have the same message /(Access to Galaxy is denied
Galaxy is configured to authenticate users
Dear all,
There is currently no link between an user ssh connection on his own
account (own space on Unix) and the Galaxy connection.
How to run Galaxy on an Unix user account? How to link the data storage
system and the Unix user account (symlink?)?
The goal is to not need to copy or move
,
*use_remote_user = True*
and
*remote_user_maildomain = toulouse.inra.fr*
Thanks in advance,
Sarah
Nate Coraor a écrit :
On Jan 19, 2012, at 10:49 AM, Sarah Maman wrote:
Hi Brad, Hi Christopher,
Thanks a lot.
I'm talking to Open LDAP. I have changed
RequestHeader set REMOTE_USER
Hello,
I managed to add a new tool coded in bash but I am having some
difficulty adding a tool coded in python.
Here are the contents of the test files:
* Content of test.xml file in galaxy/galaxy-dist/tools/test/test.xml :
tool id=test name=Test name
descriptionTest description/description
Hello,
I managed to connect to Galaxy to LDAP ;-)
Three points were blocking for me:
* Being root of my virtual machine can carry out tests
* I confused login / password of two LDAP, so I thought that my
authentication method was not good while I was using the wrong password ...
* It is better
be better for security.
Faithfully,
Sarah Maman
Nate Coraor a écrit :
On Feb 13, 2012, at 7:38 AM, Sarah Maman wrote:
Hello,
I managed to connect to Galaxy to LDAP ;-)
Three points were blocking for me:
* Being root of my virtual machine can carry out tests
* I confused login / password of two
Hello,
In a Galaxy tool, I would like to display a pre-completed path in the
xml inputbox, inside the tool.xml file.
Consequently, I would like to add a variable in an param value= /
tag , like this :
tool id=test name=test version=
command interpreter=shtest.sh $in $out/command
inputs
Thank you very much Dannon, it works.
The more I discover Galaxy, the more I appreciate its use. Again, thank
Galaxy team for this great tool.
Sarah Maman
Dannon Baker a écrit :
Hi Sarah,
You should be able to do this with the -r option of the clone command, so: `hg
clone -r b258de1e6cea
in the cloud
(https://main.g2.bx.psu.edu/). For example, Visualization menu is
absent and I think it should be related to the previous warning?
How to ensure that eggs be properly fetched?
Thank you in advance,
Sarah Maman
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Hello,
This is a great idea. I'm interested.
Thanks !
Sarah Maman
--
Message: 1
Date: Fri, 27 Apr 2012 13:45:16 -0500
From: Ann Black-Ziegelbein annbl...@eng.uiowa.edu
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev
node.
If I run `python ./scripts/fetch_eggs.py` in galaxy-dist directory, as Galaxy
user, but on my virtual machine, missing eggs are not grabed.
Do you have another solution?
Thanks,
Sarah
Nate Coraor a écrit :
On Apr 27, 2012, at 6:00 AM, Sarah Maman wrote:
Hello,
After pulling
have been updated except for Markupsafe. So I downloaded
Markupsafe from Python website.
Since then I have no warning on my runs ;-)
Thanks,
Sarah
Nate Coraor a écrit :
On Apr 27, 2012, at 6:00 AM, Sarah Maman wrote:
Hello,
After pulling latest changes (March 2012 - r 40f1816d6857
-after-DrmCommunicationException-td3651225.html
Could you please help me ?
Thanks in advance,
Sarah Maman
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Hello,
I have added a tool in my local instance to map BAM files on reference
genome fasta file thanks to BWA.
This tool runs, and the output file generated in database/files/000 is
correct (not empty and good data inside) but the output listed in the
history panel of Galaxy interface , is
script have been modified).
Faithfully,
Sarah Maman
Sarah Maman a écrit :
Hello,
I have added a tool in my local instance to map BAM files on reference
genome fasta file thanks to BWA.
This tool runs, and the output file generated in database/files/000 is
correct (not empty and good data
object could be decoded: line 1
column 0 (char 0)
Could you please help me ?
Thanks in advance,
Sarah Maman
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Hello,
The tool SAM to BAM generates a dataset from which it is possible to
download two files (instead of one) from the icon save.
As my script generates an output result and another txt output
containing information about linux command, I will wish not to generate
two datasets in history
Hello,
One of my users gets the following message when he wishes to edit the
attribute of a dataset which is generated by using a tool (same problem
as it is a tool provided by Galaxy or a tool coded by us).
Do you have any idea?
Thanks in advance,
Sarah Maman
URL:
http://sigenae
Hello,
For one of my tools that I have added to my local instance of Galaxy, I
can not add this tool in the editing workflow. When I click on the tool
name in the tools windows on the left, it does not appear in the
editing workflow.
Do you have any idea?
Thank you in advance,
Sarah Maman
Others actions are listed by not my click on this tool's name.
Is paster.log file a default file of Galaxy? Where could I find this file ?
Sarah
Dannon Baker a écrit :
Do you see any errors in Galaxy's paster.log, or in the javascript console?
-Dannon
On Dec 11, 2012, at 8:40 AM, Sarah Maman
. So, no obvious errors there. Could you check for
javascript console errors?
And, if you'd like, feel free to send the tool xml to me directly and I'll try
to see if I can reproduce the issue.
-Dannon
On Dec 11, 2012, at 10:47 AM, Sarah Maman sarah.ma...@toulouse.inra.fr wrote:
Thanks
Hello,
When updating local instance of our Galaxy, the hg aborted:
pulling from https://bitbucket.org/galaxy/galaxy-dist/
searching for changes
adding changesets
adding manifests
adding file changes
added 1482 changesets with 3989 changes to 1340 files
abort: untracked file in working directory
try and let you know.
Sarah
Daniel Blankenberg d...@bx.psu.edu a écrit :
Hi Sarah,
This looks to be due to a non-unicode character in the dataset's
info field. Are you using a Galaxy revision = 7563:fca4e12478d6?
Thanks for using Galaxy,
Dan
On Dec 11, 2012, at 8:25 AM, Sarah Maman wrote
10 09:17:12 CEST 2013 /
In this post
(http://dev.list.galaxyproject.org/tophat-for-illumina-looking-in-wrong-directory-for-bowtie2-indexes-tt4658609.html#none),
the solution isn't found.
Do you have any idea,
Sarah Maman
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INRA - LGC - SIGENAE
http
team
On 4/10/13 3:15 AM, Sarah Maman wrote:
Hello,
When I run tophat (Tophat for Illumina Find splice junctions using
RNA-seq data ), the job failed with truncated files. However, index
files are available and I get exactly the same error message using
built-in index or one of my history
.
Thank you again for your help,
Sarah
Jennifer Jackson a écrit :
Hi Sarah,
On 4/11/13 8:02 AM, Sarah Maman wrote:
Thnaks Jennifer,
Excuse me, my previous mail contains an error : In fact, the
reference genome from my history was a fasta format (the name was
GTF file but the format was fasta
:47 .
Could you please, hel me ?
Thnaks in advance,
Sarah Maman
--
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Sarah Maman
INRA - LGC - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel: +33(0)5.61.28.57.08
Fax: +33(0)5.61.28.57.53
--
Sarah Maman
INRA - LGC - SIGENAE
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel: +33(0)5.61.28.57.08
Fax: +33(0)5.61.28.57.53
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Event Horizon?
Sincerely,
Sarah Maman
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Sarah Maman
INRA - LGC - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel: +33(0)5.61.28.57.08
Fax: +33(0)5.61.28.57.53
Thanks Nate,
In fact, our ~/.sge_request set workq by default.
So, we have changed this parameter in ~/.sge_request file in order to
change the working queue.
Thanks again for your help,
Sarah
Nate Coraor a écrit :
On May 22, 2013, at 11:36 AM, Sarah Maman wrote:
Hi everyone
the eggs ' import does not
allow the use of rpy module? How to debug these tools?
Thnaks in advance,
Sarah
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Sarah Maman
INRA - LGC - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel: +33(0)5.61.28.57.08
Fax
3.0
Although we haven't started to us it, I recommend using rpy2:
http://rpy.sourceforge.net/rpy2.html
Most tools have been refactored by John Chilton
see: http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html
Regards, Hans-Rudolf
On 06/05/2013 10:19 AM, Sarah Maman wrote:
Hello
/to/my/galaxy/database/files/$1 [L]
|
|
Do you have any idea ?
Could you please help me ?
Thanks in advance,
Sarah Maman
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Sarah Maman
INRA - LGC - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel: +33(0
for others users.
Should I specify something in
galaxy-dist/tool-data/shared/ucsc/builds.txt file ?
Thanks in advance,
Sarah Maman
--
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Sarah Maman
INRA - GenPhySE - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel
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