Does anyone have any tips about this, please :)?
Regards
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Hakeem Almabrazi
Sent: Monday, April 21, 2014 3:49 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] DRMAA configuring issue
Hi
Hi,
I am trying to get DRMAA runner working for my local galaxy cluster. However,
I am having hard time configuring it my system.
So far,
I have installed Torque 2.5.12 and it seems to work as expected.
I installed drmaa_1.0.17 and here is DRMAA_LIBRARY_PATH
galaxy_env)galaxy@GalaxyTest01[/h
...@lists.bx.psu.edu] On Behalf Of Hakeem Almabrazi
Sent: Tuesday, March 11, 2014 11:44 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Internal server error when importing workflows!
Hi,
I have upgraded my local galaxy to the latest stable version and it works fine
but I get an error when I
Hi,
I have upgraded my local galaxy to the latest stable version and it works fine
but I get an error when I try to import workflows that were created older
version of Galaxy. Here is the error I keep getting.
Internal Server Error
Galaxy was unable to successfully complete your request
URL:
Hi,
Has anyone use the API workflow_execute.py to run workflows with a lot of
steps? The reason why I am asking is that I keep getting some errors when I
ran workflows that are long (i.e ~ 50 steps). The same workflow could be
executed successfully from the GUI. The first Few steps (16 steps
Hi,
I have been trying to use workflow_execute.pl to execute a workflow that has
~50 steps. I keep getting this error after running for few seconds knowing I
could run the same workflow from the GUI without any issue.
HTTP Error 500: Internal Server Error
500 Internal Server Er
I do not know what happened but I keep getting the following issue when I try
to start my Local Galaxy. Can someone tell me how to fix this issue please?
Starting galaxy...
Traceback (most recent call last):
File "./scripts/check_eggs.py", line 32, in
from galaxy.eggs import Crate
ImportE
Hi,
I started getting the following error whenever I try to load a file into Galaxy
local.
Traceback (most recent call last):
File "/usr/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 8, in
from galaxy import eggs
ImportError: cannot import name eggs
I will appreciate if so
In case someone has the same issue,
This is resolved by extending the sleep time found here
http://gmod.827538.n3.nabble.com/Trouble-Shooting-example-watch-folder-py-td4030355.html
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Hakeem
Hi guys,
I am sure I will be looking into this shortly but now I want to get the one
file case working first :). Do you guys have any idea why the
example_watch_folder.pl will copy the file but not its contents? The file it
copies into the library folder is empty. How can I go about resolvin
Sorry for bringing this back but I am having an issue with the
example_watch_folder.pl script. After running in and put a fasta file, it gets
copied over but it is empty. Any idea how to fix this issue.
Uploaded by: galaxy@
Date uploaded: 2013-05-30
File size: 0 bytes
Data type: txt
Build: ?
M
can create a new history every time
they get executed unless I am totally off.
Regards
From: Dannon Baker [mailto:dannon.ba...@gmail.com]
Sent: Tuesday, April 30, 2013 2:48 PM
To: Hakeem Almabrazi
Cc: galaxy-dev@lists.bx.psu.edu List
Subject: Re: [galaxy-dev] print out workflow execution
that info?
From: Dannon Baker [mailto:dannon.ba...@gmail.com]
Sent: Tuesday, April 30, 2013 2:11 PM
To: Hakeem Almabrazi
Cc: galaxy-dev@lists.bx.psu.edu List
Subject: Re: [galaxy-dev] print out workflow execution commands!
Hi Hak,
Yes, you can get all of the information saved for a particular
Hi everyone,
Is there an easy way to view/save/print out the executed commands and their
parameters for a workflow? I want to see what is going on for certain steps
in my workflow.
Regards,
Hak
___
Please keep all replies on the list
Hi,
Is there a heatmap tool for Galaxy? If so can someone send me a link to how to
integrate it to a local galaxy?
I appreciate your help.
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage yo
Hi,
I am sure these questions had been asked before but could not find the right
answer or did not look enough :) . I just want to add new aligner tool wrapper
into local galaxy. I used the existing wrappers (i.e bwa) as template and then
modified it accordingly.
Here are what I did:
Create
I have followed the instructions on how to setup a local cluster closely
(http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster). Frankly, the
(Galaxy Configuration) section was not clear for me. I am not sure if those
outlined steps should be applied to the server's universe_wsgi.in
Hi,
I am interested in this too. So how do you do this please? Should I first
create an html file outside galaxy and then load that file into Galaxy/history
second? Or there is better way to do this? I understood the images need to be
somewhere where Galaxy can access and display.
Regards,
Thank Alfonso,
Where is the Options menu though? I do not see anything called Options.
Thank you
-Original Message-
From: Alfonso Garrido-Lecca [mailto:alfonso.garrido-le...@colorado.edu]
Sent: Tuesday, February 19, 2013 2:54 PM
To: Hakeem Almabrazi; Galaxy Dev
Subject: Re: [galaxy
Hi,
I have my own local galaxy installed and things are great. However, I am
running of space, is there a better way to free space from the GUI? I have
been deleting sets/files from my history but it looks like the Usage still
going up. I manually run the following scripts but still nothing
Thank you Greg,
I will contact the owner of that software and see if we can get it installed.
Regards
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Friday, February 15, 2013 10:13 AM
To: Hakeem Almabrazi
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] Install NGSRich in local galaxy
Hello
ol other than what I did above? Or if what I
did is missing something?
I appreciate your help...
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Thursday, February 14, 2013 5:29 PM
To: Hakeem Almabrazi
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] Install NGSRich in local galaxy
Hello Hakee
HI,
Does anyone know who to install NGSRich software on a local instance of Galaxy?
I tried to install it from the shed_tool but it does not show up in the
repository, so I manually downloaded it from
http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&operation=view_or_manage_rep
mean? Is there something wrong with this script?
Thank you...
-Original Message-
From: Dannon Baker [mailto:dannonba...@me.com]
Sent: Tuesday, February 05, 2013 11:37 AM
To: Hakeem Almabrazi
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] Error! Sam-to-bam samtools command not found
Hakeem,
Hi,
I installed a local galaxy on Centos 6 and I followed the instructions on how
to install samtools/bwa/bowtie found here
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup.
I setup the correct env. for these programs correctly. Since I have no issues
with the bwa and bowtie so I assum
FO 2013-02-04 14:04:07,068 Parsing the tool configuration
./migrated_tools_conf.xml
-Original Message-
From: Nicola Soranzo [mailto:sora...@crs4.it]
Sent: Monday, February 04, 2013 11:52 AM
To: Hakeem Almabrazi
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] File Upload doesn't generate
Thank you Nicola,
Should I replace my current galaxy-dist with this version or is there different
way to upgrade?
Thank you...
-Original Message-
From: Nicola Soranzo [mailto:sora...@crs4.it]
Sent: Monday, February 04, 2013 10:50 AM
To: Hakeem Almabrazi
Cc: Dannon Baker; Galaxy Dev
o:dannonba...@me.com]
Sent: Monday, February 04, 2013 9:40 AM
To: Hakeem Almabrazi
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] File Upload doesn't generate any activity
On Feb 4, 2013, at 10:36 AM, Hakeem Almabrazi wrote:
> No there was nothing special about this installation. I installed i
nything else that might help debugging
this issue.
Regards,
-Original Message-
From: Dannon Baker [mailto:dannonba...@me.com]
Sent: Sunday, February 03, 2013 7:14 PM
To: Hakeem Almabrazi
Cc: Stephen Groenewold; Galaxy Dev; galaxy-b...@bx.psu.edu Bugs
Subject: Re: [galaxy-dev] File Upload doesn't g
Stephen,,,
Here is your solution:
In the Tools panel select "Get Data", "Upload File". You can either upload a
file, or enter one or more URLs in the "URL/Text" box. Enter
"http://galaxy.psu.edu/CPMB/TAF1_ChIP.txt"; in the box and click "Execute"
I am not sure what happened there but it seems
"
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Hakeem Almabrazi
Sent: Friday, February 01, 2013 10:50 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] loading file into local galaxy for first time
I just looked at the paster.log fil
---
I am not really sure if I followed this. I could not see the pencil icon to
change it. Can you please rephrase the above so I can follow it?
Thank you...
-Original Message-
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Friday, February 01, 2013 9:32 AM
To: Hakee
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Hakeem Almabrazi
Sent: Friday, February 01, 2013 10:02 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] loading file into local galaxy for first time
Hi,
I just finished installed a local galaxy.
Hi,
I just finished installed a local galaxy. I tried to load a simple small fasta
file using Load Data and it is still showing as Queued (Blue). It should not
take it that much to load. SO I assumed I have some issues in my installation.
Can someone tell me what could ne the issue? Or how
ifer Jackson [mailto:j...@bx.psu.edu]
Sent: Thursday, January 31, 2013 6:45 PM
To: Hakeem Almabrazi
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] install reference genome Bwa and Bowtie!
Hello Hakeem,
It is difficult to troubleshoot without knowing all the exact details of
your config
Hi Stefano,
I am still configuring my local Galaxy and stuck at displaying reference genome
for SAM Tools but I came across this tutorial which explains how to setup ftp
site to load to data. It may not be what you want but I thought of sharing it
anyway.
Here is the http://wiki.galaxyproject
ose the source for the reference
list:
I do not see anything so far.
Is there something I am missing or is there anything else I need to change at
this point.
Regards,
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of
[mailto:carlos.borr...@gmail.com]
Sent: Thursday, January 31, 2013 8:50 AM
To: Hakeem Almabrazi
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: FW: [galaxy-dev] install reference genome Bwa and Bowtie!
On Thu, Jan 31, 2013 at 9:09 AM, Hakeem Almabrazi wrote:
>
> I was sure that was not the case (
January 31, 2013 8:50 AM
To: Hakeem Almabrazi
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: FW: [galaxy-dev] install reference genome Bwa and Bowtie!
On Thu, Jan 31, 2013 at 9:09 AM, Hakeem Almabrazi wrote:
>
> I was sure that was not the case (all in tabs). Here is my bwa_indices.loc
-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
Hi,
I just installed Galaxy in local Centos Vm. I did my best to get everything
working ( I think). I followed the instructions in this Wiki
(http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup) to install reference
genomes for the tools Bwa and Bowtie. Here is what I did in details:
1.
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